Contacts of the strand formed by residues 60 - 67 (chain C) in PDB entry 3VJR
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 GLU 60 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C ILE 6.0 0.4 - - - +
7C LYS* 6.5 0.7 - - + -
55C VAL 4.3 0.2 - - - -
56C THR* 3.4 7.1 - - - +
57C LEU 3.1 30.5 + - - +
58C GLY 3.9 8.6 - - - +
59C GLY* 1.3 88.8 - - - +
61C ASP* 1.3 71.8 + - - +
62C VAL* 3.4 3.9 + - + +
180C PHE* 6.3 0.4 - - + -
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Residues in contact with ASP 61 (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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7C LYS* 4.4 15.6 - - - +
54C ARG* 3.1 37.1 + - + -
55C VAL 3.6 2.7 - - - -
56C THR* 4.7 0.7 + - - -
60C GLU* 1.3 79.0 + - - +
62C VAL* 1.3 64.6 + - - +
63C ARG* 4.2 20.1 + - - +
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Residues in contact with VAL 62 (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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6C ILE 3.4 21.3 - - - +
7C LYS 3.6 12.6 - - - +
9C ILE* 3.8 31.2 - - + -
53C SER 3.9 0.2 - - - +
54C ARG* 3.5 3.2 - - - +
55C VAL* 2.8 49.7 + - + +
57C LEU* 4.0 17.5 - - + +
60C GLU* 4.0 5.2 - - + +
61C ASP* 1.3 78.3 - - - +
63C ARG* 1.3 72.1 + - - +
64C LEU* 4.7 0.2 - - + -
180C PHE* 3.7 20.0 - - + -
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Residues in contact with ARG 63 (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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7C LYS 2.9 15.2 + - - +
8C LEU* 3.4 7.3 - - + +
9C ILE* 2.8 31.4 + - - -
52C THR* 6.1 0.2 - - - -
53C SER 3.4 11.1 + - - +
54C ARG* 3.8 35.3 - - - +
61C ASP* 4.2 18.2 + - - +
62C VAL* 1.3 80.1 - - - +
64C LEU* 1.3 58.8 + - - +
81C MET* 3.8 20.1 - - + +
85C PHE* 3.4 58.7 - - + -
87C ILE* 5.3 2.5 - - + -
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Residues in contact with LEU 64 (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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8C LEU* 4.9 0.4 - - - -
9C ILE* 3.4 28.9 - - + -
31C VAL* 4.0 11.0 - - + +
34C LEU* 4.3 14.6 - - + +
35C ALA* 3.7 40.4 - - + +
38C LEU* 5.0 0.7 - - + -
42C LEU* 3.9 15.9 - - + -
51C TYR 4.2 0.2 - - - -
52C THR* 3.0 31.2 - - - -
53C SER* 3.0 17.6 + - - +
55C VAL* 4.3 30.5 - - + -
62C VAL* 4.7 0.2 - - + -
63C ARG* 1.3 79.0 - - - +
65C LEU* 1.3 60.8 + - - +
81C MET* 4.7 0.9 - - - +
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Residues in contact with LEU 65 (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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8C LEU* 4.2 8.7 - - + -
9C ILE 2.8 11.2 + - - +
10C VAL* 3.2 20.5 - - + +
11C GLY 2.8 26.0 + - - -
31C VAL* 4.4 1.5 - - - +
48C PHE 4.1 10.3 - - - +
50C GLY* 4.1 12.3 - - - -
51C TYR 3.3 9.4 - - - +
52C THR* 4.0 4.9 - - + -
64C LEU* 1.3 75.5 - - - +
66C VAL* 1.3 67.2 + - - +
67C PRO* 4.0 15.5 - - + -
77C ALA* 3.7 31.0 - - + +
78C VAL* 3.9 10.3 - - + +
81C MET* 3.7 29.2 - - + -
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Residues in contact with VAL 66 (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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11C GLY 3.5 14.8 - - - +
13C ALA* 4.1 7.0 - - + -
28C ALA* 3.8 20.6 - - + -
31C VAL* 3.7 29.2 - - + -
32C ASP* 4.0 9.0 - - - +
42C LEU* 3.8 18.4 - - + +
51C TYR* 2.9 44.6 + - + +
65C LEU* 1.3 77.3 - - - +
67C PRO* 1.3 73.2 - - - +
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Residues in contact with PRO 67 (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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10C VAL* 3.9 17.9 - - + -
11C GLY 3.3 16.2 - - - +
12C LEU* 4.6 4.0 - - + -
13C ALA* 4.4 13.3 - - - +
14C ASN 5.8 0.9 - - - -
15C PRO* 5.9 0.2 - - - +
49C PHE 3.3 8.7 - - - +
50C GLY* 3.9 1.3 - - - -
65C LEU* 3.8 8.2 - - + +
66C VAL* 1.3 98.6 - - - +
68C THR* 1.3 60.9 + - - +
69C THR* 3.6 22.4 - - - +
74C SER* 4.4 20.0 - - - +
77C ALA* 3.7 22.9 - - + -
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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