Contacts of the helix formed by residues 67 - 77 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56G ILE* 4.0 19.3 - - + -
60G VAL* 4.2 13.9 - - + -
65G LEU* 3.3 7.4 - - + +
66G PHE* 1.4 80.9 - - + +
68G ALA* 1.3 64.8 + - - +
70G GLN* 3.2 22.3 - - + +
71G VAL* 3.0 24.5 + - + +
109G CYS* 5.4 0.2 - - - -
112G THR* 3.5 24.0 - - - +
115G ILE* 3.7 27.6 - - + -
235G GLY 3.8 4.5 - - - +
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Residues in contact with ALA 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G PHE* 3.0 35.6 + - + +
67G PRO* 1.3 68.5 - - - +
69G ALA* 1.3 65.3 + - - +
70G GLN* 4.0 0.2 + - - -
71G VAL* 3.4 2.5 + - - +
72G LYS* 3.1 24.1 + - - +
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Residues in contact with ALA 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G PRO 3.5 0.6 - - - -
68G ALA* 1.3 78.0 - - - +
70G GLN* 1.3 71.1 + - + +
72G LYS* 3.4 7.8 + - - +
73G LYS* 3.0 37.5 + - - +
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Residues in contact with GLN 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G PHE* 3.8 3.7 - - + -
52G GLU* 3.7 27.3 + - + +
53G LEU* 4.1 17.5 - - + -
56G ILE* 3.4 42.1 - - + +
67G PRO* 3.2 28.9 - - + +
69G ALA* 1.3 84.8 + - - +
71G VAL* 1.3 59.1 + - - +
73G LYS* 3.2 9.1 + - + +
74G MET* 2.8 34.2 + - - +
112G THR* 5.1 1.6 - - - +
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Residues in contact with VAL 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G PHE* 4.1 16.4 - - + -
67G PRO* 3.0 27.6 + - + +
68G ALA* 3.8 9.0 - - - +
70G GLN* 1.3 75.7 - - - +
72G LYS* 1.3 59.1 + - - +
74G MET* 3.7 9.3 - - + +
75G GLY 2.8 23.6 + - - -
80G LEU* 3.4 27.2 - - + +
112G THR* 5.1 8.1 - - + -
115G ILE* 3.9 25.1 - - + -
146G GLY 4.5 6.3 - - - +
149G ILE* 4.2 16.8 - - + -
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Residues in contact with LYS 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G ALA 3.1 13.4 + - - +
69G ALA* 3.6 10.8 - - - +
71G VAL* 1.3 75.5 - - - +
73G LYS* 1.3 64.2 + - + +
75G GLY* 3.1 2.1 + - - -
76G GLY* 2.9 19.8 + - - -
145G SER 3.8 4.3 - - - +
146G GLY* 4.0 22.6 + - - +
147G ASP* 4.3 14.6 - - - +
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Residues in contact with LYS 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G PHE* 3.9 16.8 - - + -
52G GLU* 3.7 35.4 - - + +
69G ALA* 3.0 23.4 + - - +
70G GLN* 3.5 9.6 - - - +
72G LYS* 1.3 75.9 - - + +
74G MET* 1.3 58.1 + - - +
76G GLY* 3.0 17.8 + - - -
77G LEU* 3.1 15.8 + - - +
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Residues in contact with MET 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G PHE* 3.3 31.4 - - + -
53G LEU* 4.8 1.1 - - - -
70G GLN 2.8 21.2 + - - +
71G VAL* 3.7 11.2 - - + +
73G LYS* 1.3 72.3 - - - +
75G GLY* 1.3 63.2 + - - +
77G LEU* 3.1 8.6 + - - +
79G LEU* 3.0 44.8 + - + +
80G LEU* 3.8 23.3 - - + -
105G ILE* 4.2 7.4 - - + -
112G THR* 3.0 36.8 - - + -
116G MET* 3.8 28.3 - - + +
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Residues in contact with GLY 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G VAL 2.8 11.6 + - - -
72G LYS 3.1 4.7 + - - -
74G MET* 1.3 76.6 - - - +
76G GLY* 1.3 60.1 + - - +
78G GLY* 3.2 11.3 + - - -
80G LEU* 3.5 27.5 - - - +
144G THR 3.5 14.9 - - - +
145G SER* 3.5 19.9 - - - -
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Residues in contact with GLY 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G LYS 2.9 13.0 + - - -
73G LYS* 3.0 6.9 + - - -
75G GLY* 1.3 77.9 - - - +
77G LEU* 1.3 59.9 + - - +
78G GLY 3.3 1.3 + - - -
145G SER* 3.7 6.2 + - - -
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Residues in contact with LEU 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G THR* 4.8 20.9 - - + -
48G PHE* 3.5 42.2 - - + -
73G LYS* 3.1 12.7 + - + +
74G MET* 3.1 7.9 + - - +
76G GLY* 1.3 79.0 - - - +
78G GLY* 1.3 58.8 + - - +
79G LEU* 3.3 21.3 + - + +
82G MET* 5.9 0.3 - - - +
91G ALA* 5.3 2.1 - - - +
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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