Contacts of the helix formed by residues 67 - 78 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56C ILE* 4.2 14.1 - - + -
60C VAL* 4.3 14.4 - - + -
65C LEU* 3.3 8.0 - - + +
66C PHE* 1.3 87.5 - - + +
68C ALA* 1.3 57.9 + - - +
70C GLN* 3.2 22.4 + - + +
71C VAL* 2.9 34.3 + - + +
111C SER* 5.4 0.2 - - - -
112C THR* 3.6 26.2 - - - +
115C ILE* 3.8 18.6 - - + -
235C GLY 3.8 8.3 - - - +
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C PHE* 2.9 33.3 + - + +
67C PRO* 1.3 72.3 - - - +
69C ALA* 1.3 63.4 + - - +
70C GLN* 4.0 0.4 + - - -
71C VAL* 3.4 2.9 + - - +
72C LYS* 3.2 22.2 + - - +
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Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PRO 3.5 0.4 - - - -
68C ALA* 1.3 77.7 - - - +
70C GLN* 1.3 76.6 + - - +
72C LYS* 3.4 7.7 + - - +
73C LYS* 3.1 28.3 + - + +
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Residues in contact with GLN 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PHE* 3.9 3.7 - - + -
52C GLU* 3.7 28.5 + - + +
53C LEU* 4.1 17.7 - - + -
56C ILE* 3.4 39.1 - - + +
67C PRO* 3.4 27.4 - - + +
68C ALA 3.2 0.4 + - - -
69C ALA* 1.3 84.4 + - - +
71C VAL* 1.3 60.2 + - - +
73C LYS* 3.3 8.1 + - - +
74C MET* 2.9 37.3 + - - +
112C THR* 5.3 0.7 - - + +
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C PHE* 4.0 24.0 - - + -
67C PRO* 2.9 33.3 + - + +
68C ALA 3.4 5.1 + - - +
70C GLN* 1.3 74.3 - - - +
72C LYS* 1.3 57.4 + - - +
74C MET* 3.4 15.6 + - - +
75C GLY 2.8 23.6 + - - -
80C LEU* 3.5 26.4 - - + +
112C THR* 5.1 3.4 - - + -
115C ILE* 4.1 17.3 - - + -
146C GLY 4.9 5.4 - - - +
149C ILE* 4.3 16.8 - - + -
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Residues in contact with LYS 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ALA 3.2 11.1 + - - +
69C ALA* 3.6 10.1 - - - +
70C GLN 3.2 0.4 - - - -
71C VAL* 1.3 77.5 - - - +
73C LYS* 1.3 64.4 + - + +
75C GLY* 3.2 2.0 + - - +
76C GLY* 3.1 18.4 + - - -
145C SER* 3.8 7.2 + - - +
146C GLY* 4.0 21.5 - - - +
147C ASP* 2.3 41.2 + - - +
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Residues in contact with LYS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PHE* 3.8 20.2 - - + -
52C GLU* 3.6 29.1 + - - +
69C ALA* 3.1 17.9 + - + +
70C GLN* 3.6 8.7 - - - +
72C LYS* 1.3 76.5 - - + +
74C MET* 1.3 62.7 + - - +
76C GLY* 3.1 4.4 + - - -
77C LEU* 3.1 24.1 + - - +
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Residues in contact with MET 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PHE* 3.4 27.8 - - + -
53C LEU* 5.1 0.4 - - - -
70C GLN 2.9 20.1 + - - +
71C VAL* 3.4 15.5 - - - +
73C LYS* 1.3 75.0 - - - +
75C GLY* 1.3 62.1 + - - +
77C LEU* 3.1 14.3 + - - +
78C GLY 3.2 0.2 + - - -
79C LEU* 3.1 37.8 + - + +
80C LEU* 4.4 7.9 - - + -
105C ILE* 3.7 12.6 - - + -
112C THR* 3.2 35.4 - - + -
116C MET* 3.5 41.1 - - + -
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Residues in contact with GLY 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C VAL 2.8 11.1 + - - -
72C LYS 3.2 2.0 + - - -
73C LYS 3.2 0.4 - - - -
74C MET* 1.3 75.9 - - - +
76C GLY* 1.3 59.3 + - - +
78C GLY* 3.3 11.1 + - - -
80C LEU* 3.6 18.1 - - - +
144C THR 3.7 6.1 - - - +
145C SER* 3.2 41.0 - - - -
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LYS 3.1 12.3 + - - -
73C LYS* 3.1 5.5 + - - -
75C GLY* 1.3 75.4 - - - +
77C LEU* 1.3 62.6 + - - +
78C GLY 3.6 0.5 + - - -
145C SER* 3.6 4.6 + - - -
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C THR* 4.8 19.5 - - + -
48C PHE* 3.5 41.5 - - + -
73C LYS* 3.1 13.2 + - + +
74C MET 3.1 11.0 + - - +
76C GLY* 1.3 79.0 - - - +
78C GLY* 1.3 59.8 + - - +
79C LEU* 3.4 20.3 + - + +
91C ALA* 5.3 1.7 - - - +
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Residues in contact with GLY 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C MET 3.2 2.4 + - - -
75C GLY 3.3 10.7 + - - -
76C GLY 3.3 1.4 + - - -
77C LEU* 1.3 78.1 - - - +
79C LEU* 1.3 60.9 + - - +
80C LEU 3.3 3.1 - - - -
81C ALA* 3.2 28.9 + - - -
82C MET* 3.4 4.4 + - - +
90C GLY 5.7 0.9 - - - -
91C ALA* 3.6 22.7 - - - +
144C THR 5.1 3.1 - - - -
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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