Contacts of the helix formed by residues 107 - 118 (chain B) in PDB entry 2VES
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 ALA 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B HIS 3.5 24.2 - - - +
82B ALA* 4.4 4.0 - - + -
106B SER* 1.3 71.7 - - - +
108B GLY* 1.3 63.9 + - - +
109B PRO* 3.4 2.7 - - - -
110B PHE* 3.1 9.3 + - - +
111B VAL* 2.9 23.7 + - - +
181B PHE* 4.4 11.0 - - + -
186B SER* 2.9 23.4 + - - +
240B LEU* 3.7 20.3 - - + +
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Residues in contact with GLY 108 (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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104B ASP* 5.3 0.7 - - - -
106B SER* 3.0 8.6 + - - -
107B ALA* 1.3 76.9 - - - +
109B PRO* 1.3 69.0 - - - +
111B VAL* 3.3 8.6 + - - +
112B PHE* 3.0 23.2 + - - +
186B SER* 3.1 15.3 + - - -
187B ARG* 4.5 9.9 - - - -
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Residues in contact with PRO 109 (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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103B MET* 3.7 38.1 - - + -
104B ASP* 3.2 36.8 - - + +
106B SER* 3.7 4.7 - - - +
107B ALA 3.6 3.6 - - - -
108B GLY* 1.3 90.5 - - - +
110B PHE* 1.3 56.7 + - + +
112B PHE* 3.3 6.6 + - + +
113B LEU* 2.9 36.0 + - + +
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Residues in contact with PHE 110 (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 LEU* 4.5 10.8 - - + -
28B LEU* 6.2 1.6 - - + -
78B HIS* 4.0 11.0 - - + -
79B LEU* 3.7 47.6 - - + -
82B ALA* 3.7 16.2 - - + -
100B VAL* 3.8 21.3 - - + -
101B PRO* 3.5 24.7 - - + -
102B ILE 5.0 2.5 - - - -
103B MET* 3.7 25.8 - - + -
106B SER 4.0 20.4 - - - -
107B ALA* 3.1 6.4 + - - +
109B PRO* 1.3 74.1 - - + +
111B VAL* 1.3 67.4 + - - +
113B LEU* 3.8 13.1 - - + +
114B ILE* 2.9 30.1 + - - +
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Residues in contact with VAL 111 (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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82B ALA* 3.8 15.0 - - + +
86B LEU* 3.8 17.4 - - + +
107B ALA 2.9 17.3 + - - +
108B GLY* 3.5 9.4 - - - +
110B PHE* 1.3 76.4 - - - +
112B PHE* 1.3 57.1 + - - +
114B ILE* 3.8 1.2 - - - +
115B GLN* 2.9 57.6 + - - +
181B PHE* 4.0 12.1 - - + -
182B VAL* 4.3 16.4 - - + -
186B SER* 3.8 24.7 - - - +
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Residues in contact with PHE 112 (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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108B GLY 3.0 13.2 + - - +
109B PRO* 3.6 9.9 - - + +
111B VAL* 1.3 77.8 - - - +
113B LEU* 1.3 65.2 + - + +
115B GLN* 3.4 19.1 + - + +
116B SER* 2.9 34.0 + - - -
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Residues in contact with LEU 113 (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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11B ILE* 3.9 22.0 - - + +
12B ARG 4.1 10.8 - - - +
13B ALA* 3.7 22.9 - - + -
26B LEU* 4.8 9.2 - - + -
28B LEU* 4.2 14.4 - - + -
103B MET* 4.2 16.4 - - + -
109B PRO* 2.9 23.1 + - + +
110B PHE* 3.8 15.3 - - + +
112B PHE* 1.3 80.7 - - + +
114B ILE* 1.3 64.3 - - - +
116B SER* 2.4 23.9 + - - +
117B ALA* 3.0 10.0 + - - +
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Residues in contact with ILE 114 (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 LEU* 3.9 7.6 - - + -
28B LEU* 4.2 9.9 - - + -
79B LEU* 4.5 3.1 - - + -
82B ALA* 3.7 28.5 - - + +
83B MET* 3.7 41.7 - - + +
86B LEU* 3.4 21.8 - - + -
88B ILE* 3.7 27.1 - - + -
110B PHE 2.9 21.4 + - - +
113B LEU* 1.3 74.1 - - - +
115B GLN* 1.3 63.2 + - - +
117B ALA* 3.0 18.4 + - - +
118B GLY* 3.3 11.6 + - - +
119B LEU* 4.8 3.5 - - + +
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Residues in contact with GLN 115 (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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86B LEU* 4.2 18.0 - - + +
111B VAL* 2.9 38.3 + - - +
112B PHE* 3.6 23.7 - - + +
114B ILE* 1.3 77.1 - - - +
116B SER* 1.3 62.0 + - - +
118B GLY* 3.2 14.1 + - - +
119B LEU* 5.6 4.9 - - + -
182B VAL* 4.7 8.3 - - - +
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Residues in contact with SER 116 (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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9B ASN* 5.1 3.5 + - - +
11B ILE* 3.6 25.2 - - - +
112B PHE* 2.9 25.3 + - - -
113B LEU* 2.4 31.4 + - - +
115B GLN* 1.3 76.1 - - - +
117B ALA* 1.3 61.6 + - - +
118B GLY* 3.3 0.9 + - - -
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Residues in contact with ALA 117 (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 LEU* 4.0 24.5 - - + -
8B LYS* 3.4 3.5 + - - +
9B ASN* 2.9 46.5 + - - +
11B ILE* 3.4 26.2 - - + -
28B LEU* 5.5 0.7 - - + -
113B LEU 3.0 9.8 + - - +
114B ILE* 3.0 11.4 + - - +
116B SER* 1.3 77.3 + - - +
118B GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 118 (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 LEU* 3.4 13.7 - - - +
8B LYS* 3.0 25.2 + - - -
9B ASN* 5.3 0.9 - - - -
114B ILE 3.3 3.4 + - - +
115B GLN 3.2 12.7 + - - -
116B SER 3.2 5.3 - - - -
117B ALA* 1.3 79.1 - - - +
119B LEU* 1.3 68.8 + - - +
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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