Contacts of the helix formed by residues 81 - 104 (chain D) in PDB entry 3UNE
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 LEU 81 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PHE* 4.1 19.7 - - + -
16C LEU* 4.2 14.1 - - + -
150C SER* 5.7 9.2 - - - -
30D ALA* 4.7 9.9 - - + +
79D SER 3.9 1.7 + - - -
80D GLY* 1.3 70.3 - - - -
82D ILE* 1.3 64.9 + - - +
83D ALA* 3.3 3.5 + - + +
84D ASP* 3.4 27.3 + - - +
85D ALA* 3.4 5.9 + - - +
135D ARG* 4.1 10.1 - - - +
138D GLY* 3.4 19.7 + - - +
139D VAL* 3.3 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C THR* 4.4 20.6 + - + +
154C HIS* 6.3 2.9 - - + -
35D SER* 5.6 2.2 - - - +
65D GLU 5.1 2.2 - - - +
66D LYS* 4.4 31.9 - - + +
78D MET* 4.0 18.2 - - + +
79D SER* 6.1 1.3 - - - -
80D GLY 3.5 17.0 - - - +
81D LEU* 1.3 69.8 - - - +
83D ALA* 1.3 64.8 + - - +
85D ALA* 3.2 16.6 + - - +
86D LYS* 3.3 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLN* 3.4 19.0 - - + +
150C SER* 3.5 24.5 - - - +
151C GLY 3.5 29.2 - - - +
152C THR* 3.9 10.6 + - - +
81D LEU* 3.3 3.7 - - + -
82D ILE* 1.3 80.2 - - - +
84D ASP* 1.3 61.8 + - - +
86D LYS* 3.7 13.6 + - - +
87D THR* 3.6 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 4.9 1.4 - - - +
116C GLN* 2.7 32.1 + - - +
119C THR* 4.8 1.6 + - - -
120C GLN* 3.8 1.4 - - - +
81D LEU* 3.4 24.1 + - - +
82D ILE 3.3 0.6 - - - -
83D ALA* 1.3 75.7 - - - +
85D ALA* 1.3 64.8 + - - +
87D THR* 3.5 11.8 + - - -
88D LEU* 3.7 3.3 + - - +
135D ARG* 2.7 41.1 + - - -
137D PHE* 3.5 29.9 - - + -
138D GLY 4.6 0.7 + - - +
139D VAL* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D MET* 3.6 27.6 - - + -
81D LEU 3.4 7.6 + - - +
82D ILE* 3.2 12.0 + - - +
84D ASP* 1.3 75.1 - - - +
86D LYS* 1.3 56.4 + - - +
87D THR 3.1 4.9 - - - -
88D LEU* 2.9 21.3 + - - +
89D ILE* 2.9 22.5 + - + +
139D VAL* 3.6 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ARG* 6.0 1.8 - - + -
151C GLY 5.7 2.7 + - - +
152C THR* 5.3 3.0 - - - +
153C TYR* 3.3 52.9 + - + +
63D SER 5.9 1.0 + - - -
65D GLU* 4.9 14.3 + - - +
78D MET* 4.4 15.7 - - + -
82D ILE* 3.3 35.2 + - + +
83D ALA* 3.7 9.4 + - - +
84D ASP 3.4 0.8 - - - -
85D ALA* 1.3 75.1 - - - +
87D THR* 1.3 59.8 + - - +
89D ILE* 4.1 10.0 - - + +
90D ASP* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLN* 2.8 33.7 + - - +
117C ARG* 5.9 4.7 - - + -
120C GLN* 5.4 0.7 - - - +
83D ALA 3.6 4.2 + - - -
84D ASP 3.5 7.6 + - - -
85D ALA 3.1 0.8 - - - -
86D LYS* 1.3 78.4 - - - +
88D LEU* 1.3 61.5 + - - +
89D ILE 3.5 0.2 - - - -
90D ASP* 3.7 5.3 + - - +
91D LYS* 3.3 22.3 + - - +
133D MET* 6.2 2.2 - - + -
137D PHE* 4.2 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ASP 3.7 10.7 + - - +
85D ALA* 2.9 8.3 + - - +
87D THR* 1.3 75.8 - - - +
89D ILE* 1.3 59.3 + - + +
91D LYS* 3.4 6.3 + - - +
92D ALA* 3.0 27.8 + - - +
116D VAL* 3.9 32.7 - - + +
119D LEU* 4.6 17.0 - - + +
137D PHE* 3.8 49.8 - - + -
139D VAL* 4.2 19.1 - - + +
141D LEU* 4.2 19.5 - - + -
156D MET* 5.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D VAL* 3.8 27.6 - - + -
70D ILE* 5.0 7.7 - - + +
76D CYS* 4.3 16.4 - - + -
78D MET* 3.9 19.1 - - - -
85D ALA 2.9 27.1 + - - +
86D LYS* 4.4 8.3 - - + +
88D LEU* 1.3 74.5 - - + +
90D ASP* 1.3 62.2 + - - +
92D ALA* 3.2 7.4 + - - +
93D ARG* 2.9 55.4 + - + +
141D LEU* 3.8 29.2 - - + -
143D PHE* 6.1 1.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
86D LYS 3.3 19.1 + - - +
87D THR* 3.9 5.8 - - - +
88D LEU 3.3 0.2 - - - -
89D ILE* 1.3 80.0 - - + +
91D LYS* 1.3 61.5 - - - +
93D ARG* 3.4 16.2 + - - +
94D VAL* 3.3 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D THR 3.3 16.3 + - - +
88D LEU* 3.7 6.1 - - - +
89D ILE 3.3 0.6 - - - -
90D ASP* 1.3 77.1 - - - +
92D ALA* 1.3 62.1 + - - +
94D VAL* 3.5 13.5 + - - +
95D GLU* 3.2 43.3 + - + +
115D ALA 5.5 3.8 - - - +
116D VAL* 6.3 0.7 - - + -
119D LEU* 3.7 40.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
70D ILE* 3.4 24.4 - - + +
88D LEU 3.0 17.3 + - - +
89D ILE* 3.2 8.9 + - - +
91D LYS* 1.3 76.8 - - - +
93D ARG* 1.3 63.0 + - - +
95D GLU* 3.5 7.2 + - - +
96D THR* 3.3 23.7 + - - +
112D VAL* 4.4 9.4 - - + +
115D ALA* 6.1 0.7 - - - -
116D VAL* 3.8 23.3 - - + +
143D PHE* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D VAL* 3.5 28.5 - - - +
69D GLU* 2.9 28.4 + - - +
70D ILE* 3.7 24.9 - - - +
89D ILE* 2.9 34.3 + - + +
90D ASP* 3.7 16.9 + - - +
91D LYS 3.3 0.4 - - - -
92D ALA* 1.3 75.6 - - - +
94D VAL* 1.3 62.7 + - + +
96D THR* 2.7 20.1 + - - -
97D GLN* 3.3 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ASP* 3.3 23.9 + - - +
91D LYS* 3.8 14.6 - - + +
92D ALA 3.3 0.4 - - - -
93D ARG* 1.3 76.0 - - + +
95D GLU* 1.3 55.4 + - + +
97D GLN* 3.1 6.7 + - + +
98D ASN* 2.8 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LYS* 3.2 43.5 + - + +
92D ALA* 3.9 7.6 - - - +
93D ARG 3.4 0.4 - - - -
94D VAL* 1.3 79.1 - - + +
96D THR* 1.3 55.8 + - - +
98D ASN* 3.5 19.1 + - - +
99D HIS* 3.1 22.7 + - - +
107D MET* 3.5 20.9 - - + +
112D VAL* 6.2 0.2 - - + -
115D ALA* 4.3 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ILE* 3.8 19.7 + - + -
71D ASP* 4.1 24.0 - - + +
73D HIS* 5.7 1.1 - - + -
74D ILE* 5.6 1.3 - - + -
92D ALA 3.3 14.0 + - - +
93D ARG* 2.7 26.3 + - - -
95D GLU* 1.3 77.5 - - - +
97D GLN* 1.3 62.1 + - - +
99D HIS* 3.7 3.4 + - - +
100D TRP* 3.1 24.8 + - - +
105D GLU 5.0 1.6 - - - +
106D THR* 5.9 0.9 - - - -
107D MET* 3.7 26.7 + - + +
112D VAL* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ILE 5.0 3.8 + - - -
71D ASP* 3.9 23.6 + - - -
93D ARG 3.3 13.7 + - - +
94D VAL* 3.1 9.9 + - - +
96D THR* 1.3 83.2 + - - +
98D ASN* 1.3 63.8 + - - +
99D HIS 3.3 0.7 - - - -
100D TRP* 3.7 27.3 - - + +
101D PHE* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D VAL* 2.8 41.7 + - - +
95D GLU* 3.8 21.3 + - - +
97D GLN* 1.3 79.5 - - - +
99D HIS* 1.3 57.7 + - - +
101D PHE* 3.6 6.2 + - - +
102D THR* 2.8 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLU 3.1 18.2 + - - +
96D THR 3.9 2.9 - - - +
98D ASN* 1.3 75.0 - - - +
100D TRP* 1.3 62.1 + - - +
103D TYR* 2.9 67.2 + + + +
105D GLU* 3.7 35.4 + - + +
107D MET* 3.4 40.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ASP* 6.1 0.4 - - - +
96D THR 3.1 18.4 + - - +
97D GLN* 3.7 28.5 - - + +
98D ASN 3.3 0.4 - - - -
99D HIS* 1.3 77.7 - - - +
101D PHE* 1.3 77.4 + + + +
104D ASN* 3.1 38.4 + - - +
105D GLU* 3.8 27.5 + - - +
106D THR* 5.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D GLN 3.0 17.7 + - - +
98D ASN* 3.8 7.6 - - - +
99D HIS 3.3 0.2 - - - -
100D TRP* 1.3 97.0 - + + +
102D THR* 1.3 67.5 + - + +
104D ASN* 4.8 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ASN 2.8 19.0 + - - -
101D PHE* 1.3 87.0 - - - +
103D TYR* 1.3 89.1 + - + +
104D ASN 3.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D HIS* 2.9 51.3 + + + +
102D THR* 1.3 102.0 - - + +
104D ASN* 1.3 70.4 + - - +
105D GLU* 3.3 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D TRP* 3.1 37.2 + - - +
101D PHE 4.7 1.0 - - - +
102D THR 3.7 1.0 - - - -
103D TYR* 1.3 79.2 - - - +
105D GLU* 1.3 58.5 + - - +
----------------------------------------------------------
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