Contacts of the helix formed by residues 63 - 72 (chain B) in PDB entry 2VUT
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 ASN 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B GLY* 4.4 1.6 - - - -
59B PRO* 2.5 43.0 + - + +
60B LEU 3.3 6.8 + - - +
61B LEU 3.0 7.2 - - - +
62B ASN* 1.3 77.6 - - - +
64B VAL* 1.3 62.1 + - - +
65B PRO* 3.6 10.8 - - - +
66B LEU* 3.2 33.3 + - - +
67B MET* 3.3 26.1 + - - +
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Residues in contact with VAL 64 (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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62B ASN* 3.8 3.7 - - - -
63B ASN* 1.3 70.5 - - - +
65B PRO* 1.3 75.4 - - + +
67B MET* 2.9 19.7 + - + +
68B ASP* 2.9 29.2 + - - +
94B ASP* 4.8 19.5 - - + +
101B ARG* 3.6 19.7 - - - +
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Residues in contact with PRO 65 (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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62B ASN 5.5 0.2 - - - +
63B ASN* 3.5 12.3 - - - +
64B VAL* 1.3 97.3 - - + +
66B LEU* 1.3 59.5 + - - +
68B ASP* 3.5 8.4 + - + +
69B THR* 3.0 29.3 + - - -
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Residues in contact with LEU 66 (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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35B GLN* 3.7 29.2 - - + -
56B PHE* 3.5 39.7 - - + +
57B GLN 5.5 1.8 - - - +
58B GLY* 3.9 10.3 - - - +
59B PRO 3.4 10.3 - - - +
60B LEU* 4.1 9.2 - - + -
63B ASN* 3.2 36.4 + - + +
64B VAL 3.2 0.6 - - - -
65B PRO* 1.3 76.1 - - - +
67B MET* 1.3 63.7 + - - +
69B THR* 3.3 6.3 + - - -
70B LEU* 2.9 32.5 + - + +
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Residues in contact with MET 67 (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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60B LEU* 3.1 38.1 - - + +
63B ASN 3.3 15.5 + - - +
64B VAL* 2.9 11.5 + - + +
66B LEU* 1.3 78.3 - - + +
68B ASP* 1.3 62.5 + - - +
70B LEU* 3.3 5.9 + - - +
71B PHE* 3.2 30.5 + - - -
91B ILE* 4.1 12.6 - - + +
94B ASP* 3.4 40.4 - - + +
95B LEU* 3.4 38.4 - - + -
98B ALA* 3.8 14.6 - - + -
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Residues in contact with ASP 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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64B VAL* 2.9 27.3 + - - +
65B PRO* 3.9 8.5 - - + +
67B MET* 1.3 75.2 - - - +
69B THR* 1.3 64.4 + - - +
71B PHE* 3.3 5.8 + - - +
72B GLU* 3.3 25.3 + - + +
98B ALA* 3.9 8.8 - - - +
101B ARG* 2.7 36.4 + - - +
102B ALA* 5.7 0.7 - - - +
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Residues in contact with THR 69 (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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33B ARG* 2.6 33.2 + - - +
56B PHE* 3.9 30.3 - - + -
65B PRO 3.0 17.6 + - - -
66B LEU* 3.6 7.6 - - - -
68B ASP* 1.3 77.4 - - - +
70B LEU* 1.3 60.0 + - - +
72B GLU* 3.2 26.9 + - - +
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Residues in contact with LEU 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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9B ALA* 3.7 16.1 - - + +
10B VAL 3.6 22.4 - - - +
11B VAL* 3.6 22.2 - - + -
33B ARG* 2.9 61.0 + - - +
34B ALA 3.8 10.5 - - - +
35B GLN* 3.9 8.5 - - + +
56B PHE* 3.9 15.0 - - + -
60B LEU* 5.7 0.9 - - + -
66B LEU* 2.9 18.8 + - + +
67B MET* 3.5 6.5 - - - +
69B THR* 1.3 77.9 - - - +
71B PHE* 1.3 63.8 + - + +
74B ALA* 4.2 0.2 - - - +
79B ILE* 5.4 0.2 - - + -
95B LEU* 4.8 9.0 - - + -
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Residues in contact with PHE 71 (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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9B ALA* 3.8 24.7 - - + -
67B MET 3.2 22.8 + - - +
68B ASP* 3.3 5.6 + - - +
69B THR 3.2 0.4 - - - -
70B LEU* 1.3 80.5 - - + +
72B GLU* 1.3 58.8 + - - +
73B GLY 3.1 1.2 + - - -
74B ALA* 2.9 23.2 + - - +
77B ALA* 4.0 16.6 - - + -
79B ILE* 4.4 12.3 - - + -
95B LEU* 3.2 44.0 - - + -
98B ALA* 3.8 9.0 - - + +
99B ALA* 3.7 27.4 - - + -
102B ALA* 3.9 21.3 - - + +
104B THR* 3.9 8.7 + - - -
105B ILE* 4.0 15.4 - - + +
108B TYR* 4.1 8.1 - + - -
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Residues in contact with GLU 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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7B THR* 5.1 0.2 - - - +
33B ARG* 3.3 28.4 + - - +
68B ASP* 3.3 14.7 + - - +
69B THR* 3.2 35.1 + - - +
71B PHE* 1.3 74.0 - - - +
73B GLY* 1.3 58.7 + - - +
74B ALA 3.0 4.2 + - - -
102B ALA* 5.5 2.0 - - - -
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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