Contacts of the strand formed by residues 161 - 171 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ASN* 3.1 38.1 - - - +
42B VAL 3.3 3.4 - - - -
43B CYS* 2.1 46.2 - - - -
45B VAL* 3.8 4.2 - - + +
75B VAL* 3.3 4.6 - - - +
76B ARG* 2.9 42.9 + - + +
81B PHE* 3.9 10.3 - - + -
88B CYS* 5.1 0.6 - - - -
89B LYS 4.2 2.2 + - - -
160B ALA* 1.3 71.2 - - - +
162B VAL* 1.3 60.5 + - - +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASN* 3.7 2.2 - - - -
25B TRP* 4.3 18.3 - - + -
40B TYR 4.0 0.5 - - - +
41B SER* 3.2 6.9 + - - -
42B VAL* 3.0 31.7 + - + +
73B PHE* 4.2 4.7 - - + -
74B THR 3.3 10.8 - - - +
75B VAL* 4.4 7.4 - - + -
92B PHE* 3.8 43.7 - - + -
157B ASP* 4.7 4.0 - - - +
160B ALA* 3.6 28.3 - - + +
161B CYS* 1.3 75.0 - - - +
163B ALA* 1.3 72.1 + - - +
164B LEU* 4.0 3.1 - - + +
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET* 3.7 22.2 - - - -
33A ASN* 3.5 5.9 + - - +
39B MET* 4.3 9.4 - - - -
40B TYR 3.7 4.0 - - - -
41B SER* 4.0 11.2 - - - +
73B PHE* 3.0 6.2 - - - -
74B THR* 2.9 46.8 + - - +
162B VAL* 1.3 76.3 - - - +
164B LEU* 1.3 59.4 + - - +
165B LEU* 3.1 8.4 - - + +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PHE* 4.0 4.6 - - + -
16B TRP* 5.2 0.4 - - + -
25B TRP* 4.3 13.0 - - + -
39B MET* 3.3 4.5 - - - -
40B TYR* 2.7 45.3 + - + +
54B LEU* 4.3 12.1 - - + -
71B LEU* 4.4 11.9 - - + -
72B LYS 3.7 14.4 - - - +
73B PHE* 3.9 12.6 - - + -
92B PHE* 4.3 15.7 - - + -
155B PHE* 3.8 33.0 - - + -
162B VAL* 4.0 1.9 - - + -
163B ALA* 1.3 71.6 - - - +
165B LEU* 1.3 58.7 + - - +
166B SER 3.9 8.5 + - - +
167B VAL* 3.8 24.2 - - + -
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET* 4.1 10.3 - - + -
132A ARG* 2.8 49.3 + - + -
7B PHE* 3.7 6.5 - - - -
37B ILE* 4.4 12.1 - - + -
38B TYR 3.8 4.2 - - - +
39B MET* 3.3 42.2 - - + -
72B LYS 2.7 15.2 + - - +
73B PHE* 4.1 8.3 - - - -
74B THR* 4.1 9.9 - - + +
136B LEU* 4.2 15.7 - - + -
163B ALA* 3.1 39.3 - - + +
164B LEU* 1.3 72.0 - - - +
166B SER* 1.3 56.3 + - - +
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLU 4.8 3.2 + - - -
132A ARG* 4.2 8.5 - - - -
6B ASP* 5.0 1.7 + - - -
7B PHE* 4.0 6.5 - - - -
8B ALA* 4.2 11.4 + - - +
70B GLU* 4.3 6.6 + - - -
71B LEU* 3.5 3.8 - - - -
72B LYS* 3.0 57.7 + - - +
164B LEU* 3.5 3.3 - - - +
165B LEU* 1.3 82.1 - - - +
167B VAL* 1.3 74.3 + - - +
168B ARG* 4.6 4.3 + - - +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.8 6.7 - - + +
6B ASP* 3.4 3.3 + - - -
7B PHE* 2.9 43.3 + - + +
16B TRP* 3.9 22.0 - - + -
69B ILE* 4.8 0.4 - - + -
70B GLU 3.4 3.8 - - - -
71B LEU* 3.9 17.7 - - + -
153B LEU* 4.7 5.8 - - + -
155B PHE* 3.9 12.1 - - + -
164B LEU* 3.8 28.3 - - + -
166B SER* 1.3 82.9 + - - +
168B ARG* 1.3 62.8 + - - +
169B VAL* 4.3 17.3 - - + -
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Residues in contact with ARG 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B GLU* 3.1 32.9 + - - +
3B VAL* 3.7 30.1 - - + +
5B LEU 3.4 6.3 - - - +
6B ASP* 4.0 24.6 + - - +
68B PHE 3.7 0.7 - - - +
69B ILE* 3.4 2.6 - - - +
70B GLU* 2.7 67.8 + - + +
166B SER* 4.9 4.7 - - - +
167B VAL* 1.3 76.4 - - - +
169B VAL* 1.3 62.9 + - - +
170B TYR* 3.6 24.2 - - + -
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 3.6 2.3 - - - +
4B LEU* 2.7 31.1 + - + -
5B LEU* 2.8 37.2 + - + +
67B ILE* 3.9 30.1 - - + -
68B PHE 3.2 8.5 - - - +
69B ILE* 4.4 4.5 - - + -
151B PHE* 4.0 16.2 - - + -
153B LEU* 3.5 28.5 - - + -
167B VAL* 4.3 6.1 - - + -
168B ARG* 1.3 77.7 - - - +
170B TYR* 1.3 64.9 + - - +
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Residues in contact with TYR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B GLU* 3.1 41.8 + - + -
2B VAL 3.0 21.8 - - - +
3B VAL* 4.1 6.7 - - + -
4B LEU* 4.3 2.2 - - - +
67B ILE* 3.4 6.1 - - - -
68B PHE* 2.6 65.4 + + + +
70B GLU* 4.7 7.0 - - + -
140B GLU* 2.6 35.9 + - - -
168B ARG* 3.6 25.4 - - - +
169B VAL* 1.3 81.1 - - - +
171B TYR* 1.3 67.4 + - - +
172B LYS* 3.7 21.1 + - + -
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Residues in contact with TYR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B GLU* 3.7 3.5 - - - -
2B VAL* 3.0 60.5 + - + +
4B LEU* 3.9 20.2 - - + -
61B ARG 4.6 1.8 - - - -
62B GLY* 5.7 0.6 - - - -
63B GLU* 3.5 20.1 + - + +
64B ALA* 3.4 40.4 - - + -
65B GLU 5.3 0.4 - - - -
66B ARG 3.2 23.3 - - - +
67B ILE* 4.2 2.0 - - + -
68B PHE* 4.3 2.9 - - - -
170B TYR* 1.3 77.4 - - - +
172B LYS* 1.3 72.1 + - - +
173B LYS* 3.1 43.1 + - + -
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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