Contacts of the strand formed by residues 161 - 171 (chain E) in PDB entry 3HPN
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 CYS 161 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E SER* 6.1 0.2 - - - -
42E VAL 3.3 2.9 - - - -
43E CYS* 2.1 46.4 - - - -
45E VAL* 3.8 3.4 - - + +
75E VAL* 3.3 5.0 - - - +
76E ARG* 2.8 45.1 + - + +
81E PHE* 3.9 13.7 - - + -
88E CYS* 5.1 0.2 - - - -
89E LYS 4.1 3.2 + - - -
160E ALA* 1.3 73.0 - - - +
162E VAL* 1.3 59.3 + - - +
33F ASN* 3.1 34.5 - - - +
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Residues in contact with VAL 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E TRP* 4.3 16.9 - - + -
40E TYR 3.9 0.7 - - - +
41E SER* 3.3 6.4 + - - -
42E VAL* 3.0 30.3 + - + +
73E PHE* 4.2 4.7 - - + -
74E THR 3.2 11.0 - - - +
75E VAL* 4.4 6.7 - - + -
91E THR 4.9 0.2 - - - +
92E PHE* 3.8 44.4 - - + -
157E ASP* 4.7 4.9 - - - +
160E ALA* 3.5 29.4 - - + +
161E CYS* 1.3 73.5 - - - +
163E ALA* 1.3 70.7 + - - +
164E LEU* 4.4 2.7 - - + +
33F ASN* 3.8 2.5 - - - -
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Residues in contact with ALA 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E MET* 4.2 13.5 - - - -
40E TYR 3.7 3.1 - - - -
41E SER* 4.1 7.6 - - - +
73E PHE* 3.0 6.2 - - - +
74E THR* 2.9 46.5 + - - +
162E VAL* 1.3 75.0 - - - +
164E LEU* 1.3 60.0 + - - +
165E LEU* 3.0 14.4 - - + +
32F MET* 3.8 15.7 - - - -
33F ASN* 3.5 7.7 + - - +
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Residues in contact with LEU 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 4.1 4.0 - - + -
16E TRP* 5.1 0.7 - - + -
25E TRP* 4.3 14.1 - - + -
39E MET* 3.4 4.1 - - - -
40E TYR* 2.7 39.9 + - + +
54E LEU* 4.2 17.0 - - + -
71E LEU* 4.2 16.4 - - + -
72E LYS 3.5 15.3 - - - +
73E PHE* 4.1 11.7 - - + -
92E PHE* 4.4 10.5 - - + -
155E PHE* 4.0 28.0 - - + -
162E VAL* 4.0 2.6 - - + -
163E ALA* 1.3 69.2 - - - +
165E LEU* 1.3 60.7 + - - +
166E SER 4.0 10.5 - - - +
167E VAL* 3.8 24.2 - - + -
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Residues in contact with LEU 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 3.6 10.0 - - - -
8E ALA* 4.2 0.2 - - - +
37E ILE* 4.5 13.2 - - + -
38E TYR 4.3 4.3 - - - +
39E MET* 3.2 41.5 - - + -
72E LYS 2.7 15.4 + - - +
73E PHE* 4.1 8.3 - - - -
74E THR* 4.1 14.1 - - + +
136E LEU* 4.2 10.3 - - + -
163E ALA* 3.0 39.7 - - + +
164E LEU* 1.3 73.6 - - - +
166E SER* 1.3 57.8 + - - +
32F MET* 4.3 9.4 - - + -
132F ARG* 2.6 46.1 + - + +
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Residues in contact with SER 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ASP* 5.0 2.1 + - - -
7E PHE* 4.1 6.7 - - - -
8E ALA* 4.2 12.8 + - - +
70E GLU* 4.1 7.0 + - - -
71E LEU* 3.4 4.9 - - - -
72E LYS* 2.9 57.6 + - - +
164E LEU* 3.5 3.4 - - - +
165E LEU* 1.3 83.1 - - - +
167E VAL* 1.3 72.5 + - - +
168E ARG* 4.6 4.9 + - - +
130F GLU 4.9 3.2 + - - -
132F ARG* 4.2 9.0 - - - -
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Residues in contact with VAL 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LEU* 3.7 7.7 - - + +
6E ASP* 3.5 3.9 + - - -
7E PHE* 2.9 46.3 + - + +
16E TRP* 3.9 21.5 - - + -
56E THR* 5.2 0.2 - - + -
69E ILE* 4.9 0.4 - - + -
70E GLU 3.4 2.9 - - - -
71E LEU* 3.9 18.2 - - + -
153E LEU* 4.6 6.1 - - + -
155E PHE* 4.0 13.2 - - + -
164E LEU* 3.8 29.2 - - + -
166E SER* 1.3 81.7 + - - +
168E ARG* 1.3 62.4 + - - +
169E VAL* 4.4 16.2 - - + -
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Residues in contact with ARG 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E GLU* 3.1 32.7 + - - +
3E VAL* 3.7 29.2 - - + +
5E LEU 3.5 5.8 - - - +
6E ASP* 4.0 23.8 + - - +
68E PHE 3.6 1.0 - - - +
69E ILE* 3.5 1.7 - - - -
70E GLU* 2.7 71.2 + - + +
166E SER* 4.8 5.4 - - - +
167E VAL* 1.3 75.3 - - - +
169E VAL* 1.3 62.2 + - - +
170E TYR* 3.6 24.2 - - + -
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Residues in contact with VAL 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E VAL* 3.6 2.7 - - - +
4E LEU* 2.7 37.1 + - + -
5E LEU* 2.8 37.8 + - + +
67E ILE* 3.9 30.5 - - + -
68E PHE 3.2 9.6 - - - +
69E ILE* 4.5 5.4 - - + -
151E PHE* 4.0 15.7 - - + -
153E LEU* 3.6 27.1 - - + -
167E VAL* 4.4 6.3 - - + -
168E ARG* 1.3 77.8 - - - +
170E TYR* 1.3 60.2 + - - +
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Residues in contact with TYR 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E GLU* 3.3 41.6 + - + -
2E VAL 3.1 21.5 - - - +
3E VAL* 4.1 7.6 - - + -
4E LEU* 4.3 2.5 - - - +
67E ILE* 3.4 5.2 - - - -
68E PHE* 2.6 68.3 + + + +
70E GLU* 4.7 4.0 - - + -
140E GLU* 2.7 37.7 + - - -
168E ARG* 3.6 32.1 - - - +
169E VAL* 1.3 77.5 - - - +
171E TYR* 1.3 67.3 + - - +
172E LYS* 3.8 20.5 + - - -
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Residues in contact with TYR 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E GLU* 3.7 3.3 - - - -
2E VAL* 3.0 58.4 + - + +
4E LEU* 4.0 20.2 - - + -
61E ARG 4.7 2.0 - - - -
62E GLY* 5.7 0.6 - - - -
63E GLU* 3.5 19.2 + - + +
64E ALA* 3.5 39.5 - - + -
65E GLU 5.1 0.7 - - - -
66E ARG 3.2 24.2 - - - +
67E ILE* 4.3 2.5 - - + -
68E PHE* 4.3 2.2 - - - -
170E TYR* 1.3 75.6 - - - +
172E LYS* 1.3 73.4 + - - +
173E LYS* 3.1 44.2 + - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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