Contacts of the helix formed by residues 65 - 76 (chain B) in PDB entry 2WVL
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 ARG 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B ASN 4.4 0.4 + - - -
64B GLU* 1.3 75.5 - - - +
66B LEU* 1.3 66.2 + - - +
67B LYS* 4.3 11.0 - - + +
68B LEU* 3.2 31.3 + - + +
69B LEU* 3.3 10.0 + - - +
92B ARG* 4.4 9.3 - - - +
171B TYR* 4.9 6.9 + - - -
312B GLU* 3.3 28.7 + - - +
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Residues in contact with LEU 66 (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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64B GLU 4.4 2.0 - - - +
65B ARG* 1.3 72.3 - - - +
67B LYS* 1.3 64.6 + - + +
69B LEU* 2.8 11.5 + - + +
70B GLU* 2.8 31.9 + - - +
92B ARG* 4.2 20.0 - - - +
95B MET* 3.6 36.3 - - + +
96B GLU* 3.9 33.2 - - + +
99B LEU* 3.6 30.2 - - + +
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Residues in contact with LYS 67 (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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306A ARG* 5.3 0.9 + - - -
65B ARG* 5.0 12.1 - - + +
66B LEU* 1.3 93.0 - - + +
68B LEU* 1.3 61.5 + - - +
70B GLU* 3.6 26.5 + - - +
71B GLY* 3.1 17.5 + - - -
99B LEU* 4.9 7.7 - - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU* 4.0 12.6 - - + -
65B ARG* 3.2 29.3 + - + +
67B LYS* 1.3 79.2 - - - +
69B LEU* 1.3 56.3 + - - +
71B GLY* 3.3 3.7 + - - -
72B VAL* 3.0 29.8 + - - +
168B ALA* 3.6 12.6 - - + +
169B ASP* 4.2 5.4 - - - -
170B ASN 3.7 36.4 - - - +
171B TYR* 4.2 25.8 - - + -
312B GLU* 3.3 37.2 - - + +
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Residues in contact with LEU 69 (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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59B VAL* 3.8 29.4 - - + -
61B THR* 4.4 17.5 - - + +
64B GLU* 5.4 4.9 - - + +
65B ARG 3.3 7.1 + - - +
66B LEU* 2.8 15.5 + - + +
68B LEU* 1.3 75.8 - - - +
70B GLU* 1.3 68.5 + - - +
72B VAL* 3.3 4.8 + - + +
73B LEU* 2.9 42.6 + - + +
84B VAL* 4.8 11.0 - - + -
96B GLU* 3.9 33.7 - - + +
99B LEU* 4.5 11.7 - - + -
168B ALA* 4.3 12.1 - - + -
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Residues in contact with GLU 70 (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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22A ARG* 3.6 25.7 + - - -
306A ARG* 3.2 31.0 + - - +
66B LEU 2.8 14.8 + - - +
67B LYS* 3.8 29.5 - - - +
69B LEU* 1.3 76.3 - - - +
71B GLY* 1.3 65.4 + - - +
73B LEU* 3.1 4.4 + - - +
74B SER* 2.9 21.0 + - - -
99B LEU* 3.9 24.7 - - + +
103B PHE* 5.2 9.1 - - + -
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Residues in contact with GLY 71 (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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306A ARG* 3.7 14.4 - - - +
67B LYS 3.1 12.4 + - - -
68B LEU 3.5 4.7 - - - -
69B LEU 3.2 0.4 - - - -
70B GLU* 1.3 77.3 - - - +
72B VAL* 1.3 61.1 + - - +
74B SER* 2.9 21.0 + - - -
75B GLY 3.2 5.0 + - - -
170B ASN 5.5 1.6 - - - -
173B PRO* 3.4 22.7 - - - +
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Residues in contact with VAL 72 (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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59B VAL* 4.0 27.8 - - + -
68B LEU 3.0 15.6 + - - +
69B LEU* 3.3 8.3 + - - +
71B GLY* 1.3 73.7 - - - +
73B LEU* 1.3 66.2 + - - +
75B GLY* 3.0 12.5 + - - -
76B ILE* 3.4 12.2 + - + +
166B ILE* 3.8 25.8 - - + -
167B ASP 4.1 0.4 - - - +
168B ALA* 3.8 24.9 - - + +
170B ASN* 3.9 25.3 + - + +
176B VAL* 3.7 14.5 - - + +
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Residues in contact with LEU 73 (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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59B VAL* 4.6 5.2 - - + -
69B LEU* 2.9 33.1 + - + +
70B GLU 3.4 6.1 - - - +
72B VAL* 1.3 76.7 - - - +
74B SER* 1.3 57.3 + - - +
75B GLY 3.0 5.9 + - - -
76B ILE* 3.0 29.6 + - + +
82B ILE* 3.8 29.2 - - + -
84B VAL* 4.5 4.9 - - + -
99B LEU* 3.9 27.6 - - + -
100B LEU* 3.7 24.9 - - + -
103B PHE* 3.4 38.3 - - + -
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Residues in contact with SER 74 (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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24A LEU 3.4 21.3 - - - -
25A GLU* 3.9 3.9 - - - +
26A LEU* 3.0 29.9 + - - +
27A ASP 4.8 0.3 + - - -
306A ARG* 3.5 40.2 + - - +
70B GLU 2.9 12.3 + - - -
71B GLY 2.9 13.2 + - - -
73B LEU* 1.3 74.1 - - - +
75B GLY* 1.3 57.8 + - - +
76B ILE 3.5 1.5 + - - +
103B PHE* 3.9 12.1 - - - -
173B PRO* 3.8 4.2 - - - +
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Residues in contact with GLY 75 (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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26A LEU* 3.9 11.4 - - - -
27A ASP 6.1 0.2 - - - -
71B GLY 3.2 4.4 + - - -
72B VAL 3.0 9.6 + - - -
74B SER* 1.3 77.6 - - - +
76B ILE* 1.3 65.2 + - - +
77B PRO* 3.1 10.7 - - - +
173B PRO* 3.7 22.4 - - - -
176B VAL* 4.1 5.2 - - - -
177B TRP* 3.3 21.2 - - - +
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Residues in contact with ILE 76 (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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25A GLU* 5.0 1.4 - - - +
27A ASP* 4.4 4.1 + - - +
57B ILE* 3.8 33.9 - - + -
59B VAL* 4.0 18.4 - - + -
72B VAL* 3.4 18.4 - - + +
73B LEU* 3.0 18.8 + - + +
74B SER 4.7 2.4 - - - +
75B GLY* 1.3 78.3 - - - +
77B PRO* 1.3 86.8 - - + +
78B HIS 3.2 0.9 + - - -
80B ALA* 3.9 15.0 - - + -
82B ILE* 4.2 15.0 - - + -
109B ARG* 3.0 30.4 + - - +
176B VAL* 4.1 10.8 - - + -
180B VAL* 4.8 2.2 - - + -
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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