Contacts of the helix formed by residues 82 - 111 (chain D) in PDB entry 3E1J
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 82 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D TRP* 4.3 4.9 - - - -
81D GLU* 1.3 77.8 - - - +
83D VAL* 1.3 65.8 + - - +
84D GLU* 3.6 8.9 + - - +
85D GLU* 3.0 39.1 + - - +
86D MET* 2.8 27.2 + - - +
146D LEU* 6.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D PHE* 4.0 16.6 - - + -
35D TRP* 4.4 7.7 - - + -
37D LEU* 3.9 17.7 - - + -
40D LEU* 4.2 4.3 - - + -
82D ASP* 1.3 72.1 - - - +
84D GLU* 1.3 54.5 + - - +
86D MET* 3.0 11.5 + - - +
87D LEU* 2.7 55.1 + - + +
141D ILE* 4.3 3.8 - - + -
146D LEU* 5.0 7.6 - - + -
149D TYR* 4.0 20.4 - - + -
150D LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ASP* 3.4 7.2 + - - +
83D VAL* 1.3 77.8 - - - +
85D GLU* 1.3 57.8 + - - +
87D LEU* 3.1 2.4 + - - +
88D ARG* 2.6 70.3 + - - +
138D LEU* 3.9 22.1 - - + +
141D ILE* 4.2 20.4 - - + +
142D GLN* 3.9 19.6 + - - +
146D LEU* 5.7 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D GLY* 4.0 12.8 - - - -
81D GLU* 3.7 31.5 + - - +
82D ASP* 3.0 37.5 + - - +
84D GLU* 1.3 75.7 - - - +
86D MET* 1.3 58.3 + - - +
88D ARG* 3.4 8.2 + - - +
89D SER* 3.0 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D HIS* 3.2 58.1 - - + +
31D MET* 3.7 44.0 - - + -
32D PHE* 3.4 31.2 - - + -
35D TRP* 3.7 17.0 - - + -
79D ILE 3.3 10.3 - - - +
80D GLY* 4.5 2.0 - - - +
82D ASP 2.8 26.8 + - - +
83D VAL* 3.3 11.9 - - - +
85D GLU* 1.3 75.7 - - - +
87D LEU* 1.3 63.5 + - - +
89D SER* 3.2 1.7 + - - -
90D ASP* 3.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D PHE* 3.9 24.5 - - + -
40D LEU* 5.1 2.9 - - + -
44D GLU* 3.8 22.4 - - - +
83D VAL* 2.7 36.5 + - + +
86D MET* 1.3 73.9 - - - +
88D ARG* 1.3 62.4 + - - +
90D ASP* 3.2 7.5 + - - +
91D LEU* 3.0 22.2 + - - +
133D TRP* 4.7 6.5 - - + -
134D LEU* 4.1 17.8 - - + +
137D GLU* 4.1 15.5 - - + -
138D LEU* 3.7 18.6 - - + -
141D ILE* 4.2 10.3 - - + -
149D TYR* 3.9 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D GLU* 2.6 51.9 + - - +
85D GLU* 3.7 8.1 - - - +
87D LEU* 1.3 77.7 - - - +
89D SER* 1.3 58.2 + - - +
91D LEU* 3.3 8.9 + - + +
92D ALA* 2.9 28.2 + - - +
138D LEU* 4.0 36.5 + - + +
142D GLN* 5.1 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLN* 3.1 11.0 + - - -
28D HIS* 4.6 0.2 - - - -
78D ASN* 2.6 52.9 + - - +
79D ILE 4.7 1.1 - - - -
80D GLY* 5.9 0.4 - - - -
85D GLU 3.0 18.0 + - - -
86D MET* 3.6 7.2 - - - -
87D LEU 3.1 0.2 - - - -
88D ARG* 1.3 78.4 - - - +
90D ASP* 1.3 61.6 + - - +
92D ALA* 3.4 7.1 + - - +
93D LEU* 3.1 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLN* 2.9 32.1 + - - +
25D TYR* 3.5 31.4 + - + +
28D HIS* 2.7 29.3 + - - -
44D GLU* 2.9 21.0 - - - +
86D MET 3.1 7.6 + - - +
87D LEU* 3.5 9.2 - - - +
89D SER* 1.3 74.8 - - - +
91D LEU* 1.3 61.3 + - - +
93D LEU* 3.2 7.0 + - - +
94D GLU* 3.0 26.5 + - - +
134D LEU* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LEU 3.0 13.1 + - - +
88D ARG* 3.5 13.5 - - + +
90D ASP* 1.3 72.8 - - - +
92D ALA* 1.3 66.5 + - - +
94D GLU* 3.2 2.1 + - - +
95D LEU* 3.0 41.4 + - + +
131D ILE* 4.0 28.3 - - + -
134D LEU* 4.0 20.5 - - + +
135D GLU* 4.1 22.2 - - + +
138D LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ARG 2.9 15.9 + - - +
89D SER* 3.4 7.4 + - - +
91D LEU* 1.3 75.8 - - - +
93D LEU* 1.3 58.0 + - - +
95D LEU* 3.3 11.9 + - - +
96D ASP* 3.0 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ASN* 5.2 6.5 - - + +
20D VAL* 3.7 36.8 - - + -
21D ALA* 3.8 26.9 - - + +
24D GLN* 4.0 21.1 - - + +
25D TYR* 6.1 2.0 - - + -
76D LYS 5.0 5.4 - - - +
89D SER 3.1 12.5 + - - +
90D ASP* 3.4 11.4 - - - +
91D LEU 3.1 0.2 - - - -
92D ALA* 1.3 78.9 - - - +
94D GLU* 1.3 58.3 + - + +
96D ASP* 3.3 8.9 + - + +
97D GLY* 3.0 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ALA* 6.0 1.6 - - - -
25D TYR* 2.4 37.1 + - + +
51D GLU* 3.6 2.9 - - - +
90D ASP 3.0 19.4 + - - +
91D LEU* 3.2 5.8 + - - +
93D LEU* 1.3 72.2 - - + +
95D LEU* 1.3 60.8 + - - +
97D GLY* 3.2 2.5 + - - +
98D ALA* 2.8 31.7 + - - +
127D GLU* 2.5 38.6 - - - +
130D HIS* 3.0 25.8 + - - +
131D ILE* 3.6 22.9 - - + +
134D LEU* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LEU* 3.0 37.3 + - + +
92D ALA* 3.5 8.7 - - - +
94D GLU* 1.3 77.6 - - - +
96D ASP* 1.3 63.9 + - - +
98D ALA* 3.4 5.3 + - + +
99D LYS* 3.2 30.6 + - - +
131D ILE* 3.6 35.2 - - + -
135D GLU* 5.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ASN* 5.5 1.1 - - - +
92D ALA* 3.0 22.8 + - - +
93D LEU* 3.3 10.6 + - + +
95D LEU* 1.3 77.1 - - - +
97D GLY* 1.3 61.3 + - - +
99D LYS* 3.4 26.8 + - - +
100D ASN* 3.2 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ASN* 3.6 27.3 + - - -
93D LEU 3.0 13.6 + - - -
94D GLU* 3.2 3.3 + - - -
96D ASP* 1.3 76.9 - - - +
98D ALA* 1.3 59.9 + - - +
100D ASN* 3.3 2.6 + - - +
101D LEU* 2.9 37.2 + - - +
127D GLU* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLU 2.8 17.9 + - - +
95D LEU* 3.8 7.2 - - + +
96D ASP 3.3 0.2 - - - -
97D GLY* 1.3 75.6 - - - +
99D LYS* 1.3 57.0 + - - +
101D LEU* 3.2 5.1 + - - +
102D ARG* 2.9 56.9 + - - +
124D LEU* 3.9 17.7 - - + +
127D GLU* 5.4 3.1 - - + +
128D GLU* 5.2 0.4 - - - +
131D ILE* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D LEU* 3.2 19.7 + - - +
96D ASP* 3.4 32.7 + - - +
97D GLY 3.2 0.2 - - - -
98D ALA* 1.3 75.1 - - - +
100D ASN* 1.3 65.8 + - - +
102D ARG* 3.2 10.7 + - - +
103D GLU* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D TYR* 4.8 3.5 - - + -
13D LYS* 3.5 34.1 + - - +
14D LEU* 3.6 19.8 - - + +
17D ASN* 2.9 26.1 + - - +
96D ASP* 3.2 15.0 + - - +
97D GLY 3.3 4.9 + - - +
99D LYS* 1.3 80.2 - - - +
101D LEU* 1.3 56.9 + - - +
103D GLU* 3.3 15.8 + - - +
104D ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LEU* 3.8 20.6 - - + -
18D GLU* 5.2 1.6 - - - +
58D TYR* 3.5 21.8 - - - +
97D GLY 2.9 22.1 + - - +
98D ALA 3.5 4.9 - - - +
100D ASN* 1.3 73.1 - - - +
102D ARG* 1.3 60.7 + - - +
104D ALA* 3.3 2.5 + - - +
105D ILE* 2.9 40.3 + - + +
120D MET* 3.7 31.4 - - + +
123D ILE* 4.1 7.4 - - + -
124D LEU* 3.9 32.8 - - + -
127D GLU* 4.0 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ALA* 2.9 46.0 + - - +
99D LYS* 3.2 9.8 + - - +
101D LEU* 1.3 77.0 - - - +
103D GLU* 1.3 63.4 + - - +
105D ILE* 3.5 8.3 + - - +
106D GLY* 3.3 16.8 + - - -
124D LEU* 4.1 19.8 - - + +
128D GLU* 2.7 36.1 + - - -
131D ILE* 5.9 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LYS* 5.1 1.6 + - - -
10D TYR* 2.6 39.9 + - + +
13D LYS* 5.7 3.1 - - - -
99D LYS 3.1 11.3 + - - +
100D ASN* 3.7 19.0 + - - +
101D LEU 3.3 0.2 - - - -
102D ARG* 1.3 75.3 - - - +
104D ALA* 1.3 63.0 + - - +
106D GLY* 3.2 4.2 + - - -
107D TYR* 3.1 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D TYR* 3.7 35.8 - - + +
14D LEU* 3.9 11.0 - - + -
100D ASN 2.9 19.8 + - - +
101D LEU 3.3 2.2 + - - +
103D GLU* 1.3 72.4 - - - +
105D ILE* 1.3 57.2 + - - +
107D TYR* 3.2 3.3 + - - +
108D ALA* 2.9 31.0 + - - +
120D MET* 3.6 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 2.9 24.0 + - + +
102D ARG* 3.8 6.1 - - - +
104D ALA* 1.3 73.6 - - - +
106D GLY* 1.3 65.4 + - - +
108D ALA* 3.5 0.9 + - - +
109D ASP 3.2 17.3 + - - -
117D ARG* 3.3 40.1 + - + +
120D MET* 3.6 39.5 - - + +
121D ILE* 4.0 21.5 - - + -
124D LEU* 3.9 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ARG 3.3 7.4 + - - -
103D GLU 3.2 6.7 + - - -
105D ILE* 1.3 78.2 - - - +
107D TYR* 1.3 61.8 + - - +
109D ASP* 3.5 6.0 + - - +
110D SER* 3.2 20.4 + - - -
117D ARG* 4.3 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ASP* 2.9 37.2 + - - -
6D LYS* 3.4 31.3 - - + +
7D VAL* 3.7 15.3 - - + -
10D TYR* 3.8 36.6 - + + +
103D GLU 3.1 9.6 + - - +
104D ALA 3.8 3.6 - - - +
105D ILE 3.2 0.2 - - - -
106D GLY* 1.3 75.0 - - - +
108D ALA* 1.3 66.2 + - - +
110D SER* 2.9 27.5 + - - -
111D VAL* 3.1 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 4.4 7.9 - - + -
104D ALA 2.9 17.2 + - - +
105D ILE 3.8 3.6 - - - +
106D GLY 3.5 0.2 - - - -
107D TYR* 1.3 78.3 - - - +
109D ASP* 1.3 60.9 + - - +
111D VAL* 3.4 9.3 + - - +
112D HIS 3.0 3.5 + - - -
113D ASP* 2.8 50.8 + - + +
116D SER* 4.7 1.3 - - - -
117D ARG* 4.1 5.2 - - + +
120D MET* 3.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ILE 3.2 5.1 + - - -
106D GLY 3.5 8.7 - - - +
107D TYR 3.2 0.4 - - - -
108D ALA* 1.3 76.5 - - - +
110D SER* 1.3 65.4 + - - +
112D HIS* 3.2 11.6 + - - -
114D TYR* 3.3 35.6 + - - -
117D ARG* 3.2 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D GLY 3.2 7.0 + - - -
107D TYR* 2.9 32.5 + - - -
109D ASP* 1.3 83.1 - - - +
111D VAL* 1.3 60.7 + - - +
112D HIS* 3.4 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ASP* 3.8 17.5 - - + +
7D VAL* 3.7 28.0 - - + -
107D TYR* 3.1 44.7 + - + +
108D ALA 3.6 7.4 - - - +
110D SER* 1.3 78.6 - - - +
112D HIS* 1.3 70.0 + - - +
113D ASP* 3.3 5.3 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il