Contacts of the helix formed by residues 79 - 89 (chain B) in PDB entry 5VXA
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 GLY 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B VAL 4.3 0.2 - - - +
75B GLU* 2.8 24.5 + - - -
76B LEU 4.7 0.4 + - - -
77B HIS 3.8 0.6 - - - -
78B PHE* 1.3 81.2 - - - +
80B ALA* 1.3 60.8 + - - -
81B GLN 3.4 2.6 + - - -
82B VAL* 3.6 0.5 + - - +
83B ARG* 3.1 26.2 + - - +
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Residues in contact with ALA 80 (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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75B GLU* 3.9 25.8 - - - +
79B GLY* 1.3 70.7 - - - -
81B GLN* 1.3 60.6 + - - +
83B ARG* 3.3 4.5 + - - +
84B ARG* 2.9 57.2 + - + +
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Residues in contact with GLN 81 (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* 3.7 30.9 - - + +
79B GLY 3.4 0.6 - - - -
80B ALA* 1.3 74.0 - - + +
82B VAL* 1.3 67.0 + - + +
84B ARG* 3.1 27.6 + - - +
85B LEU* 3.1 24.9 + - - +
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Residues in contact with VAL 82 (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* 3.9 30.5 - - + +
56B GLN* 3.5 26.2 - - + +
57B ALA 4.4 8.1 - - - +
60B LEU* 3.7 21.8 - - + -
74B VAL* 4.0 5.6 - - + -
78B PHE* 3.6 37.0 + - + +
79B GLY 3.6 1.2 + - - -
80B ALA 3.4 0.2 - - - -
81B GLN* 1.3 76.6 - - + +
83B ARG* 1.3 64.9 + - - +
85B LEU* 3.2 5.9 + - - +
86B VAL* 3.0 27.2 + - + +
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Residues in contact with ARG 83 (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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71B LEU* 3.5 50.6 + - + +
72B ASP* 2.8 26.5 + - - +
74B VAL* 4.0 10.1 - - - +
75B GLU* 2.6 47.4 + - + +
79B GLY 3.1 18.1 + - - +
80B ALA* 3.6 6.5 - - - +
82B VAL* 1.3 78.6 - - - +
84B ARG* 1.3 64.6 + - - +
86B VAL* 3.4 2.2 + - - +
87B GLU* 2.9 46.7 + - - +
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Residues in contact with ARG 84 (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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80B ALA* 2.9 40.3 + - - +
81B GLN* 3.1 37.5 + - - +
83B ARG* 1.3 82.4 - - - +
85B LEU* 1.3 65.2 + - + +
87B GLU* 3.4 10.2 + - - +
88B GLU* 3.0 31.2 + - + +
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Residues in contact with LEU 85 (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* 3.8 25.8 - - + +
54B VAL* 3.9 19.5 - - + -
57B ALA* 3.6 28.5 - - + -
81B GLN 3.1 13.7 + - - +
82B VAL 3.7 3.8 - - - +
84B ARG* 1.3 74.6 - - + +
86B VAL* 1.3 65.0 - - - +
88B GLU* 3.1 19.5 + - - +
89B VAL* 3.2 18.3 + - - +
112B SER* 3.5 13.9 - - - +
114B GLY* 3.7 8.1 - - - +
115B ALA* 3.4 29.6 - - - +
118B VAL* 5.3 1.8 - - + -
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Residues in contact with VAL 86 (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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57B ALA* 4.0 19.5 - - - +
60B LEU* 4.0 36.1 - - + +
61B HIS* 4.5 5.4 - - - +
63B THR* 4.9 0.9 - - - +
64B VAL* 4.2 13.5 - - + -
71B LEU* 4.2 12.6 - - + -
74B VAL* 4.5 7.4 - - + -
82B VAL* 3.0 25.1 + - + +
83B ARG* 3.8 5.8 - - - +
85B LEU* 1.3 74.3 - - - +
87B GLU* 1.3 59.4 + - - +
89B VAL* 3.0 11.4 + - - +
90B THR* 2.7 40.1 + - - +
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Residues in contact with GLU 87 (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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71B LEU* 3.6 29.4 - - + +
83B ARG* 2.9 41.7 + - - +
84B ARG* 3.6 9.8 - - - +
86B VAL* 1.3 77.0 - - - +
88B GLU* 1.3 62.5 + - + +
90B THR* 3.2 20.7 + - - +
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Residues in contact with GLU 88 (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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84B ARG* 3.0 19.3 + - + +
85B LEU* 3.1 16.4 + - - +
87B GLU* 1.3 76.4 - - - +
89B VAL* 1.3 60.5 + - - +
90B THR 3.7 1.4 + - - +
107B GLN* 4.9 7.1 - - - +
110B HIS 4.8 0.2 - - - +
111B SER* 3.4 11.3 - - - -
112B SER* 2.6 51.4 + - - -
115B ALA* 3.5 15.5 - - + +
119B LYS* 3.7 16.5 + - - +
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Residues in contact with VAL 89 (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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57B ALA* 5.4 1.3 - - + +
61B HIS* 3.7 39.2 - - + +
65B GLU* 3.6 9.0 - - - +
85B LEU* 3.2 14.6 + - + +
86B VAL* 3.2 19.1 - - - +
88B GLU* 1.3 77.5 - - - +
90B THR* 1.3 59.7 + - - +
91B ASP* 3.6 2.5 + - - +
115B ALA* 4.1 13.5 - - + +
118B VAL* 4.1 18.4 - - + -
119B LYS* 3.9 30.7 - - + +
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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