Contacts of the helix formed by residues 101 - 122 (chain D) in PDB entry 2YYN
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 SER 101 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ASN* 3.6 12.1 - - - +
98D GLU* 2.9 24.2 + - - -
100D ASP* 1.3 85.0 + - - +
102D GLU* 1.3 65.9 + - - +
103D VAL* 4.0 4.5 + - - +
104D ALA* 3.2 16.5 + - - +
105D ASN* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D MET* 4.6 15.8 - - - +
101D SER* 1.3 73.1 - - - +
103D VAL* 1.3 56.8 + - + +
105D ASN* 2.9 10.8 + - - +
106D ALA* 2.7 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ALA* 4.3 17.7 - - + +
41D PHE* 3.8 25.4 - - + -
93D CYS* 3.7 2.7 - - - -
97D ASN* 3.7 29.4 - - - +
101D SER* 3.4 4.4 + - - +
102D GLU* 1.3 77.0 - - + +
104D ALA* 1.3 63.9 + - - +
106D ALA* 2.9 7.7 + - - +
107D GLY 2.8 20.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
93D CYS* 3.9 15.5 - - - +
94D ALA* 5.9 2.0 - - - +
97D ASN* 4.0 10.2 - - + +
98D GLU 3.0 32.3 - - - +
99D PRO* 4.1 12.3 - - + +
101D SER* 3.2 11.9 + - - +
103D VAL* 1.3 79.0 - - - +
105D ASN* 1.3 58.2 + - - +
107D GLY* 3.4 1.0 + - - -
108D ILE* 3.2 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D PRO 3.2 22.1 + - - +
100D ASP* 3.7 8.4 - - - -
101D SER 3.1 17.3 + - - +
102D GLU* 2.9 15.5 + - - +
104D ALA* 1.3 77.9 - - - +
106D ALA* 1.3 64.0 + - - +
107D GLY 3.2 0.2 - - - -
108D ILE* 3.6 7.9 + - - +
109D LYS* 3.3 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D MET* 3.6 42.8 - - + +
40D ALA* 5.9 2.2 - - + -
41D PHE* 4.0 7.6 - - + -
102D GLU* 2.7 23.3 + - - +
103D VAL* 2.9 12.5 + - + +
105D ASN* 1.3 70.7 - - - +
107D GLY* 1.3 61.3 + - - +
109D LYS* 3.3 3.6 + - - +
110D LEU* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PHE* 3.5 23.7 - - - -
90D PHE* 3.7 11.7 - - - -
93D CYS* 4.0 9.0 - - - -
103D VAL 2.8 11.9 + - - -
104D ALA 3.8 2.0 - - - -
106D ALA* 1.3 75.6 - - - +
108D ILE* 1.3 64.1 + - - +
110D LEU* 3.3 4.5 + - - +
111D GLU* 3.0 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D PHE* 5.9 1.8 - - + +
94D ALA* 5.3 13.7 - - + -
99D PRO 6.2 0.2 - - - +
104D ALA* 3.2 19.2 + - + +
105D ASN* 4.0 8.7 - - - +
106D ALA 3.4 0.2 - - - -
107D GLY* 1.3 75.7 - - - +
109D LYS* 1.3 65.4 + - + +
111D GLU* 3.5 19.4 + - - +
112D ASN* 3.2 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D HIS* 4.9 7.1 + - + +
36D GLU* 5.0 7.1 + - - -
37D MET* 3.8 32.6 - - + +
105D ASN* 3.3 17.3 + - - +
106D ALA 3.6 8.1 - - - +
107D GLY 3.2 0.6 - - - -
108D ILE* 1.3 80.4 - - + +
110D LEU* 1.3 62.9 + - - +
112D ASN* 3.2 9.1 + - - +
113D TYR* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.6 34.3 - - + +
35D HIS* 4.3 25.4 - - + -
37D MET* 3.6 18.5 - - - +
38D SER* 4.2 8.7 - - - -
41D PHE* 3.9 25.8 - - + -
62D LEU* 5.1 5.8 - - + -
89D ILE* 5.4 0.2 - - + -
90D PHE* 3.5 23.6 - - + -
106D ALA 3.0 16.5 + - - +
107D GLY* 3.3 6.3 + - - +
109D LYS* 1.3 74.8 - - - +
111D GLU* 1.3 52.0 + - - +
113D TYR* 3.3 6.2 + - + +
114D PHE* 2.7 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ARG* 5.3 4.2 - - - +
90D PHE* 3.7 43.8 - - + +
107D GLY 3.0 16.3 + - - +
108D ILE* 3.6 24.3 - - - +
110D LEU* 1.3 74.7 - - - +
112D ASN* 1.3 68.7 + - - +
114D PHE* 3.4 0.7 - - - +
115D GLU* 2.8 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ILE* 3.2 27.0 + - - +
109D LYS* 3.2 10.1 + - - +
111D GLU* 1.3 84.6 + - - +
113D TYR* 1.3 64.1 + - - +
115D GLU* 3.4 6.3 + - - +
116D GLU* 3.1 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PHE* 3.6 45.9 + - - +
32D LEU* 3.9 13.9 - - + -
35D HIS* 3.2 39.3 - + + +
109D LYS 3.1 12.4 + - - +
110D LEU* 3.5 8.3 - - + +
112D ASN* 1.3 77.7 - - - +
114D PHE* 1.3 62.3 + - - +
116D GLU* 3.1 17.4 + - + +
117D LEU* 3.1 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 4.0 21.8 - - + -
32D LEU* 3.7 32.1 - - + -
83D VAL* 4.6 7.6 - - + -
86D PHE* 3.3 47.8 - + + -
87D ARG* 4.4 11.4 - - + -
90D PHE* 3.9 21.5 - + + -
110D LEU 2.7 20.6 + - - +
111D GLU 3.2 5.4 + - - +
113D TYR* 1.3 73.3 - - - +
115D GLU* 1.3 85.4 + - - +
117D LEU* 3.2 6.4 + - - +
118D LEU* 2.9 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ARG* 2.7 54.1 + - - +
111D GLU* 2.8 37.9 + - + +
112D ASN* 3.9 7.6 - - - +
114D PHE* 1.3 83.3 - - + +
116D GLU* 1.3 57.3 + - - +
118D LEU* 3.3 10.1 + - - +
119D LYS* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLU* 3.5 30.3 - - - +
112D ASN* 3.1 16.8 + - - +
113D TYR* 3.1 19.5 + - + +
115D GLU* 1.3 73.3 - - - +
117D LEU* 1.3 67.8 + - + +
119D LYS* 3.1 7.7 + - - +
120D ASN* 3.1 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ARG* 6.1 1.1 - - - +
28D LEU* 3.9 18.4 - - + -
31D PHE* 3.5 45.8 - - + -
32D LEU* 4.3 11.9 - - + -
113D TYR* 3.1 43.2 + - + +
114D PHE 3.7 6.1 - - - +
116D GLU* 1.3 77.4 - - + +
118D LEU* 1.3 58.5 + - - +
120D ASN* 3.4 9.9 + - + +
121D LEU* 3.0 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 4.2 16.5 - - + +
83D VAL* 4.0 15.0 - - + -
87D ARG* 4.1 19.3 - - - +
114D PHE* 2.9 34.1 + - + +
115D GLU* 3.5 11.2 - - - +
117D LEU* 1.3 77.3 - - - +
119D LYS* 1.3 61.2 + - - +
121D LEU* 4.7 1.1 - - + -
122D TYR* 3.2 45.1 + - + +
125D LYS 5.9 0.2 - - - +
127D PHE* 3.4 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D GLU 2.9 16.0 + - - +
116D GLU* 3.1 9.2 + - - +
118D LEU* 1.3 79.1 - - - +
120D ASN* 1.3 67.5 + - - +
122D TYR 3.4 5.6 - - - +
123D PRO* 3.3 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU* 3.7 37.1 - - + +
37C MET* 4.3 4.2 - - - +
109C LYS* 4.5 8.7 + - - +
116D GLU* 3.1 27.8 + - - +
117D LEU* 4.0 11.2 - - + +
119D LYS* 1.3 82.5 + - - +
121D LEU* 1.3 60.4 + - - +
123D PRO* 3.3 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU* 3.7 36.1 - - + +
37C MET* 4.9 4.0 - - - +
39C LEU* 4.3 11.4 - - + -
24D LYS* 2.8 62.1 + - + +
27D ARG* 3.7 25.6 - - + +
28D LEU* 4.0 24.5 - - + -
31D PHE* 6.4 0.2 - - + -
117D LEU* 3.0 18.2 + - + +
118D LEU* 4.3 0.9 - - - +
120D ASN* 1.3 77.0 - - - +
122D TYR* 1.3 72.6 + - + +
123D PRO* 3.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLU* 3.7 21.1 - - - -
21D ASP* 2.5 34.7 + - - -
24D LYS* 3.3 35.2 - - + +
28D LEU* 5.3 2.0 - - + -
79D PRO* 4.0 14.1 - - + +
82D PHE* 3.8 18.1 - + - -
118D LEU* 3.2 40.4 + - + +
119D LYS* 3.4 9.6 - - - +
121D LEU* 1.3 90.0 - - + +
123D PRO* 1.3 64.8 - - - +
124D GLU 3.3 2.9 - - - -
125D LYS* 3.2 27.4 - - + +
127D PHE* 4.1 22.4 - + + -
----------------------------------------------------------
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