Contacts of the helix formed by residues 57 - 69 (chain B) in PDB entry 2VSH
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 TRP 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 3.6 38.4 - + + -
53B VAL* 3.6 6.5 - - + -
54B HIS* 2.8 38.7 + + + +
56B ASP* 1.3 84.3 - - + +
58B VAL* 1.3 58.7 + - - +
59B SER 3.4 2.2 - - - -
60B HIS* 3.3 50.2 + + + +
61B ALA* 2.9 30.5 + - - +
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Residues in contact with VAL 58 (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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53B VAL* 3.6 21.3 - - + -
54B HIS 3.9 2.7 - - - +
55B GLY* 3.6 16.8 - - - +
56B ASP 3.5 2.2 - - - -
57B TRP* 1.3 77.7 - - - +
59B SER* 1.3 59.4 + - - +
61B ALA* 3.2 4.9 + - - +
62B GLU* 2.9 44.3 + - - +
78B ILE* 3.7 17.8 - - + +
79B THR* 4.1 2.2 - - - -
80B LYS* 4.1 27.4 - - + +
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASP 5.0 4.1 + - - -
57B TRP 3.4 0.4 - - - -
58B VAL* 1.3 78.9 - - - +
60B HIS* 1.3 59.8 + - - +
62B GLU* 3.3 17.0 + - - +
63B ASP* 2.9 43.1 + - - +
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Residues in contact with HIS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.7 29.7 + + - +
56B ASP 5.2 1.7 + - - +
57B TRP* 3.3 50.2 + + + +
58B VAL 3.2 0.4 - - - -
59B SER* 1.3 82.1 + - - +
61B ALA* 1.3 56.9 + - - +
63B ASP* 3.3 10.6 + - - +
64B LEU* 3.0 49.7 + - + +
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Residues in contact with ALA 61 (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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24B PHE* 4.4 8.7 - - + -
33B LEU* 4.4 6.3 - - + +
53B VAL* 4.0 17.7 - - + -
57B TRP 2.9 16.2 + - - +
58B VAL 3.6 4.5 - - - +
60B HIS* 1.3 76.0 - - - +
62B GLU* 1.3 58.7 + - - +
64B LEU* 3.3 14.2 - - - +
65B VAL* 3.0 31.9 + - - +
78B ILE* 3.9 23.8 - - + -
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 2.9 31.3 + - - +
59B SER* 3.5 18.7 - - - +
61B ALA* 1.3 74.7 - - - +
63B ASP* 1.3 63.0 + - - +
65B VAL* 3.4 6.3 + - - +
66B ASP* 3.0 33.8 + - - +
78B ILE* 3.8 27.7 + - + +
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Residues in contact with ASP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER* 2.9 29.4 + - - +
60B HIS* 3.3 8.6 + - - +
62B GLU* 1.3 75.7 - - - +
64B LEU* 1.3 57.6 + - + +
66B ASP* 3.2 12.7 + - - +
67B LYS* 2.8 37.2 + - - +
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Residues in contact with LEU 64 (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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24B PHE* 3.6 36.3 - - + +
31B PRO* 3.8 32.3 - - + -
33B LEU* 4.3 10.1 - - + -
34B ILE* 3.9 10.3 - - + -
60B HIS* 3.0 35.6 + - + +
61B ALA* 3.3 11.9 - - - +
63B ASP* 1.3 76.3 - - + +
65B VAL* 1.3 57.8 + - - +
67B LYS* 3.3 3.9 + - + -
68B TYR* 2.9 46.6 + - + +
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Residues in contact with VAL 65 (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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33B LEU* 6.2 0.7 - - + -
34B ILE* 4.2 7.9 - - + -
37B ILE* 4.3 13.7 - - + -
61B ALA 3.0 17.6 + - - +
62B GLU* 3.6 9.6 - - - +
63B ASP 3.4 0.2 - - - -
64B LEU* 1.3 74.1 - - - +
66B ASP* 1.3 60.3 + - - +
69B LEU* 2.8 38.3 + - + +
73B LYS* 3.8 28.0 - - + +
76B ILE* 3.9 45.8 - - + +
78B ILE* 4.2 10.5 - - + -
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Residues in contact with ASP 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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62B GLU* 3.0 20.2 + - - +
63B ASP* 3.2 15.7 + - - +
65B VAL* 1.3 75.8 - - - +
67B LYS* 1.3 62.0 + - - +
70B PRO* 3.3 28.4 - - - +
73B LYS* 3.6 29.2 + - - +
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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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63B ASP 2.8 21.1 + - - +
64B LEU* 3.8 6.3 - - + +
66B ASP* 1.3 76.3 - - - +
68B TYR* 1.3 98.4 + - + +
70B PRO* 4.0 5.5 - - - +
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Residues in contact with TYR 68 (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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26B GLU* 5.2 2.1 + - - -
29B ASP 3.6 25.2 + - - -
30B ARG* 3.6 22.7 - - + -
31B PRO* 3.5 27.3 - - + +
34B ILE* 3.8 24.5 - - + -
38B GLU* 4.9 1.9 - - - +
64B LEU* 2.9 30.8 + - + +
67B LYS* 1.3 115.2 + - + +
69B LEU* 1.3 70.0 + - - +
70B PRO* 3.4 8.0 - - - +
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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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34B ILE* 4.0 26.2 - - + -
37B ILE* 3.6 33.2 - - + -
38B GLU* 3.6 33.2 - - + +
41B VAL* 4.9 4.7 - - + -
65B VAL* 2.8 20.7 + - + +
68B TYR* 1.3 82.9 - - - +
70B PRO* 1.4 65.0 - - - +
71B LEU 3.1 2.7 - - - -
72B TYR* 2.9 40.2 + - + -
73B LYS* 3.2 9.5 + - - -
76B ILE* 4.0 12.6 - - + -
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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