Contacts of the helix formed by residues 67 - 78 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ILE* 4.1 8.5 - - + -
60A VAL* 4.0 24.0 - - + -
65A LEU* 3.6 7.2 - - + +
66A PHE* 1.4 80.9 - - + +
68A ALA* 1.3 64.3 + - - +
70A GLN* 3.3 21.8 - - + +
71A VAL* 3.1 22.2 + - + +
111A SER* 5.3 0.2 - - - -
112A THR* 3.5 24.0 - - - +
115A ILE* 3.7 27.4 - - + -
235A GLY* 3.8 5.4 - - - +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 3.0 35.6 + - + +
67A PRO* 1.3 69.6 - - - +
69A ALA* 1.3 67.2 + - - +
71A VAL* 3.4 3.4 + - - +
72A LYS* 3.0 24.3 + - - +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PRO 3.5 0.6 - - - -
68A ALA* 1.3 77.8 - - - +
70A GLN* 1.3 72.0 + - - +
72A LYS* 3.4 7.1 + - - +
73A LYS* 3.1 44.0 + - - +
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.9 4.3 - - + -
52A GLU* 3.7 25.1 + - + +
53A LEU* 4.0 17.7 - - + -
56A ILE* 3.3 41.1 - - + +
67A PRO* 3.3 27.4 - - + +
69A ALA* 1.3 88.1 + - - +
71A VAL* 1.3 59.8 + - - +
73A LYS* 3.2 11.1 + - + +
74A MET* 2.9 34.7 + - - +
112A THR* 5.1 1.3 - - - +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 4.2 14.8 - - + -
67A PRO* 3.1 25.3 + - + +
68A ALA* 3.4 8.7 + - - +
70A GLN* 1.3 75.6 - - - +
72A LYS* 1.3 59.1 + - - +
74A MET* 3.4 16.3 + - + +
75A GLY 2.9 23.7 + - - -
80A LEU* 3.3 28.8 - - + +
112A THR* 5.1 4.0 - - + -
115A ILE* 4.1 25.6 - - + -
146A GLY 4.7 4.5 - - - +
149A ILE* 4.3 16.4 - - + -
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Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA 3.0 13.8 + - - +
69A ALA* 3.6 11.7 - - - +
71A VAL* 1.3 76.3 - - - +
73A LYS* 1.3 64.5 + - + +
75A GLY* 3.0 3.5 + - - -
76A GLY* 3.0 18.2 + - - -
145A SER* 3.8 7.4 + - - +
146A GLY* 3.9 20.6 + - - +
147A ASP* 2.6 39.9 + - - +
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Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.9 13.7 - - + -
52A GLU* 3.8 36.2 + - - +
69A ALA* 3.1 31.5 + - - +
70A GLN* 3.2 11.8 + - + +
72A LYS* 1.3 77.0 - - + +
74A MET* 1.3 62.3 + - - +
76A GLY* 2.9 14.0 + - - +
77A LEU* 3.1 18.3 + - + +
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Residues in contact with MET 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.5 25.8 - - + -
53A LEU* 4.9 0.4 - - - -
70A GLN 2.9 23.0 + - - +
71A VAL* 3.5 14.8 - - + +
73A LYS* 1.3 72.2 - - - +
75A GLY* 1.3 62.9 + - - +
77A LEU* 3.1 11.3 + - - +
78A GLY 3.2 0.2 + - - -
79A LEU* 3.1 44.3 + - + +
80A LEU* 4.3 10.3 - - + -
105A ILE* 3.8 8.7 - - + -
112A THR* 3.0 38.6 - - + -
116A MET* 3.7 39.7 - - + -
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Residues in contact with GLY 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL 2.9 10.9 + - - -
72A LYS 3.0 3.3 + - - -
74A MET* 1.3 78.4 - - - +
76A GLY* 1.3 60.8 + - - +
78A GLY* 3.2 11.1 + - - -
80A LEU* 3.5 19.0 - - - +
144A THR 3.8 5.4 - - - +
145A SER* 3.3 37.7 - - - +
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS 3.0 8.5 + - - -
73A LYS* 2.9 9.9 + - - -
75A GLY* 1.3 75.8 - - - +
77A LEU* 1.3 62.1 + - - +
78A GLY 3.6 0.9 + - - -
145A SER* 3.6 5.0 + - - -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 5.2 18.6 - - + -
48A PHE* 3.7 36.3 - - + -
73A LYS* 3.1 12.8 + - + +
74A MET* 3.1 11.7 + - - +
76A GLY* 1.3 79.0 - - - +
78A GLY* 1.3 57.6 + - - +
79A LEU* 3.4 19.1 + - + +
82A MET* 5.9 0.7 - - - +
91A ALA* 5.3 1.6 - - - +
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLY 3.2 12.9 + - - -
76A GLY 3.4 1.8 + - - -
77A LEU* 1.3 77.2 - - - +
79A LEU* 1.3 64.4 + - - +
80A LEU 3.2 3.6 - - - -
81A ALA* 3.1 25.6 + - - -
82A MET* 3.5 8.3 + - - +
90A GLY 5.8 0.7 - - - -
91A ALA* 3.8 20.0 - - - +
144A THR 5.1 4.0 - - - -
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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