Contacts of the helix formed by residues 67 - 78 (chain B) in PDB entry 2VIG
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 PRO 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ILE* 4.0 14.6 - - + -
60B VAL* 4.1 10.8 - - + -
65B LEU 3.3 5.4 - - - +
66B PHE* 1.3 81.7 - - + +
68B ALA* 1.3 58.2 + - - +
70B GLN* 3.1 17.2 - - + +
71B VAL* 3.0 30.1 + - + +
109B CYS* 5.2 0.2 - - - -
111B SER 5.3 0.2 - - - -
112B THR* 3.4 28.0 - - - +
115B ILE* 3.6 28.3 - - + -
235B GLY* 3.8 5.2 - - - +
503B EDO 3.3 12.8 - - - +
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Residues in contact with ALA 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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66B PHE* 3.0 36.4 + - + +
67B PRO* 1.3 70.9 - - - +
69B ALA* 1.3 63.3 + - - +
71B VAL* 3.4 2.8 + - - +
72B LYS* 3.0 23.0 + - - +
146B GLY 5.6 0.2 - - - +
503B EDO 3.9 2.2 + - - -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO 3.5 0.8 - - - -
68B ALA* 1.3 77.8 - - - +
70B GLN* 1.3 75.0 + - - +
72B LYS* 3.3 8.1 + - - +
73B LYS* 3.1 40.5 + - - +
503B EDO 4.5 2.4 + - - +
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Residues in contact with GLN 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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48B PHE* 3.8 4.5 - - + -
52B GLU* 3.7 32.4 + - + +
53B LEU* 4.1 18.6 - - + -
56B ILE* 3.6 28.7 - - + +
67B PRO* 3.1 15.7 - - + +
69B ALA* 1.3 80.6 + - - +
71B VAL* 1.3 62.0 + - - +
73B LYS* 3.3 12.1 + - - +
74B MET* 2.9 33.3 + - - +
112B THR* 5.1 0.9 - - - +
503B EDO 2.6 34.1 + - - -
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE* 4.3 12.3 - - + -
67B PRO* 3.0 36.3 + - + +
68B ALA* 3.8 6.7 - - - +
69B ALA 3.4 0.2 - - - -
70B GLN* 1.3 73.6 - - - +
72B LYS* 1.3 61.8 + - - +
74B MET* 3.5 8.5 + - + +
75B GLY 3.0 21.5 + - - -
80B LEU* 3.3 25.4 - - + +
112B THR* 4.8 10.1 - - + +
115B ILE* 4.3 25.6 - - + -
146B GLY 4.7 5.8 - - - +
149B ILE* 4.4 15.3 - - + -
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Residues in contact with LYS 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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68B ALA 3.0 13.7 + - - +
69B ALA* 3.5 11.0 - - - +
70B GLN 3.3 0.4 - - - -
71B VAL* 1.3 74.0 - - - +
73B LYS* 1.3 66.9 + - + +
75B GLY* 3.1 2.6 + - - -
76B GLY* 3.0 28.9 + - - +
145B SER* 2.7 30.5 + - - +
146B GLY* 3.8 24.0 + - - +
147B ASP* 4.2 9.0 - - - +
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Residues in contact with LYS 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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48B PHE* 3.8 15.7 - - + -
51B LYS* 5.6 0.7 - - - +
52B GLU* 3.8 38.4 + - + +
69B ALA* 3.1 31.8 + - - +
70B GLN* 3.3 10.8 + - - +
72B LYS* 1.3 76.5 - - + +
74B MET* 1.3 64.2 + - - +
76B GLY* 3.1 5.1 + - - +
77B LEU* 3.0 24.5 + - + +
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Residues in contact with MET 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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48B PHE* 3.5 25.6 - - + -
53B LEU* 4.8 0.4 - - - -
70B GLN 2.9 23.0 + - - +
71B VAL* 3.5 12.8 - - + +
73B LYS* 1.3 74.1 - - - +
75B GLY* 1.3 62.0 + - - +
77B LEU* 3.1 4.8 + - - +
78B GLY 3.1 17.5 + - - -
79B LEU* 3.1 30.3 + - + -
80B LEU* 4.2 12.1 - - + -
105B ILE* 4.0 8.1 - - + -
112B THR* 3.0 37.5 - - + +
116B MET* 3.7 40.6 - - + -
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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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71B VAL 3.0 10.9 + - - -
72B LYS 3.1 2.9 + - - -
74B MET* 1.3 77.2 - - - +
76B GLY* 1.3 59.5 + - - +
78B GLY* 3.2 10.2 + - - -
80B LEU* 3.7 15.2 - - - +
144B THR 3.8 5.0 - - - +
145B SER* 3.4 40.3 - - - -
146B GLY 3.7 3.8 - - - -
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Residues in contact with GLY 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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72B LYS* 3.0 21.7 + - - -
73B LYS* 3.1 6.0 + - - -
75B GLY* 1.3 76.8 - - - +
77B LEU* 1.3 61.4 + - - +
78B GLY 3.6 0.2 + - - -
145B SER* 3.7 1.9 + - - -
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Residues in contact with LEU 77 (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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44B THR* 4.8 19.5 - - + -
48B PHE* 3.5 42.8 - - + -
73B LYS 3.0 13.4 + - - +
74B MET 3.1 8.2 + - - +
76B GLY* 1.3 79.0 - - - +
78B GLY* 1.3 57.7 + - - +
79B LEU* 3.5 21.8 + - + +
91B ALA* 5.4 1.9 - - - +
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Residues in contact with GLY 78 (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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74B MET 3.1 3.2 + - - -
75B GLY 3.2 12.2 + - - -
76B GLY 3.4 0.8 + - - -
77B LEU* 1.3 78.8 - - - +
79B LEU* 1.3 64.0 + - - +
80B LEU 3.2 3.4 - - - -
81B ALA* 3.2 25.3 + - - +
82B MET* 3.5 9.1 + - - +
90B GLY 5.9 0.2 - - - -
91B ALA* 3.9 16.1 - - - +
144B THR 5.0 4.3 - - - -
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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