Contacts of the strand formed by residues 51 - 58 (chain V) in PDB entry 1VPP
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 CYS 51 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32V LEU* 4.6 7.0 - - - -
33V VAL 3.2 17.7 - - - +
34V ASP* 3.5 17.3 - - - +
35V ILE 3.9 1.3 - - - +
49V PRO* 3.3 9.3 - - - +
50V SER* 1.3 79.1 - - - +
52V VAL* 1.3 71.2 + - - +
24W SER* 3.3 27.5 - - - -
59W GLY* 3.7 9.0 - - - -
60W CYS* 2.1 54.1 - - + -
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Residues in contact with VAL 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31V THR 3.4 1.2 - - - +
32V LEU* 4.1 4.5 - - - -
33V VAL* 2.9 34.6 + - + +
35V ILE* 4.0 5.8 - - + -
38V GLU* 6.0 0.2 - - + -
51V CYS* 1.3 79.7 - - - +
53V PRO* 1.3 70.7 - - + +
54V LEU* 3.4 27.9 + - + +
78V MET* 3.9 7.6 - - - -
80V ILE* 3.7 30.1 - - + -
96V PHE* 3.9 30.1 - - + -
20W VAL* 3.9 8.5 - - + -
24W SER* 4.4 0.7 - - - -
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Residues in contact with PRO 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30V GLU* 3.7 30.3 - - + +
31V THR 3.7 1.3 - - - +
32V LEU* 3.6 18.5 - - + -
52V VAL* 1.3 86.2 - - + +
54V LEU* 1.3 59.7 + - - +
76V ILE* 5.5 0.9 - - - +
78V MET* 3.2 24.5 - - + +
15W VAL* 6.1 0.2 - - + -
20W VAL* 4.2 17.0 - - + +
23W ARG* 3.6 37.9 + - + +
24W SER* 4.3 9.9 - - - -
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Residues in contact with LEU 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30V GLU* 4.3 3.1 - - - -
31V THR* 2.8 41.3 + - - +
33V VAL* 3.9 20.2 - - + -
38V GLU* 4.8 0.7 - - - -
52V VAL* 3.7 16.6 - - + +
53V PRO* 1.3 84.1 - - - +
55V MET* 1.3 63.5 + - - +
56V ARG* 3.4 35.3 + - + +
76V ILE* 3.7 30.3 - - + -
78V MET* 3.7 8.3 - - + -
96V PHE* 3.7 21.5 - - + -
97V LEU 3.7 11.0 - - - +
98V GLN* 5.1 0.9 - - + -
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Residues in contact with MET 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28V PRO* 4.1 16.2 - - + +
29V ILE* 3.7 3.8 - - - -
30V GLU* 3.7 30.5 - - + +
54V LEU* 1.3 71.2 - - - +
56V ARG* 1.3 65.4 + - - +
98V GLN* 3.4 22.5 + - + +
99V HIS 2.8 42.9 + - - +
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Residues in contact with ARG 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28V PRO* 4.0 1.8 - - - -
29V ILE* 2.9 31.7 + - - +
31V THR* 3.9 20.9 + - + +
33V VAL* 4.4 15.3 - - + +
38V GLU* 2.8 34.4 + - - -
54V LEU* 3.4 23.6 + - + +
55V MET* 1.3 80.5 + - - +
57V CYS* 1.3 71.2 + - - +
58V GLY 3.3 0.5 + - - -
97V LEU* 3.0 42.4 + - - +
99V HIS* 3.4 29.2 + - + +
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Residues in contact with CYS 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V HIS 3.7 1.3 - - - -
31V THR* 5.6 0.2 + - - -
56V ARG* 1.3 75.6 - - - +
58V GLY* 1.3 59.1 + - - +
68V CYS* 4.1 14.8 - - - +
69V VAL 4.4 5.6 - - - -
70V PRO* 3.5 25.1 - - + -
99V HIS* 2.8 30.8 + - + +
102V CYS* 2.0 54.3 - - + -
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Residues in contact with GLY 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26V CYS* 3.4 2.6 - - - -
27V HIS 3.0 33.4 + - - +
29V ILE* 4.3 10.5 - - - -
56V ARG 3.3 1.9 + - - -
57V CYS* 1.3 76.2 - - - +
59V GLY* 1.3 62.5 + - - -
68V CYS* 3.7 5.9 - - - -
32W LEU* 3.8 9.8 - - - +
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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