Contacts of the strand formed by residues 51 - 58 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24V SER* 3.2 30.9 + - - -
59V GLY* 3.8 7.6 - - - -
60V CYS* 2.1 54.0 - - + -
32W LEU* 4.4 7.0 - - - -
33W VAL 3.3 15.3 - - - +
34W ASP* 3.4 20.9 - - - +
35W ILE* 4.1 1.6 - - - +
49W PRO* 3.3 11.3 - - - +
50W SER* 1.3 78.5 - - - +
52W VAL* 1.3 63.1 - - - +
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Residues in contact with VAL 52 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V VAL* 3.7 20.0 - - + -
24V SER* 4.2 0.4 - - - -
31W THR 3.4 1.7 - - - +
32W LEU* 3.4 4.8 - - - -
33W VAL* 2.8 37.4 + - + +
35W ILE* 4.1 6.3 - - + -
51W CYS* 1.3 78.7 - - - +
53W PRO* 1.3 67.4 - - + +
54W LEU* 3.6 26.0 + - + -
78W MET* 3.9 12.3 - - - -
80W ILE* 3.7 20.4 - - + -
96W PHE* 4.0 25.8 - - + -
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Residues in contact with PRO 53 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V VAL* 4.0 18.4 - - + +
23V ARG* 3.8 41.2 + - + +
24V SER* 4.2 8.1 - - - -
30W GLU* 3.9 24.2 - - + +
31W THR 3.6 0.2 - - - +
32W LEU* 3.6 24.9 - - + -
52W VAL* 1.3 86.0 - - + +
54W LEU* 1.3 57.9 + - - +
78W MET* 3.3 23.7 - - + +
98W GLN* 4.8 2.3 + - - +
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Residues in contact with LEU 54 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W GLU* 4.3 3.1 - - - -
31W THR* 2.8 38.0 + - - +
33W VAL* 4.1 16.4 - - + -
52W VAL* 3.8 26.5 - - + +
53W PRO* 1.3 82.2 - - - +
55W MET* 1.3 63.0 + - - +
56W ARG* 3.4 35.1 + - + +
76W ILE* 3.9 4.3 - - + -
78W MET* 3.9 15.3 - - + -
96W PHE* 3.5 30.7 - - + -
97W LEU 3.8 4.0 - - - +
98W GLN* 3.4 14.8 - - - +
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Residues in contact with MET 55 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28W PRO* 4.2 19.7 - - + +
29W ILE 3.7 4.3 - - - -
30W GLU* 3.9 28.5 - - + +
54W LEU* 1.3 68.4 - - - +
56W ARG* 1.3 78.1 + - - +
98W GLN* 2.8 25.8 + - - +
99W HIS* 3.0 33.1 + - - +
100W ASN* 5.7 1.1 - - - +
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Residues in contact with ARG 56 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28W PRO* 4.2 1.8 - - - -
29W ILE* 2.8 34.6 + - - +
31W THR* 3.6 28.0 - - + +
33W VAL* 4.4 17.3 - - + +
54W LEU* 3.4 23.8 + - - +
55W MET* 1.3 88.9 + - - +
57W CYS* 1.3 70.9 - - - +
58W GLY 3.3 0.7 + - - -
97W LEU* 2.5 55.5 + - - +
98W GLN* 3.8 2.4 - - - +
99W HIS* 3.5 23.1 + - + +
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Residues in contact with CYS 57 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27W HIS 3.7 1.1 - - - -
56W ARG* 1.3 77.3 - - - +
58W GLY* 1.3 59.0 + - - +
68W CYS* 4.1 13.0 - - - +
69W VAL 4.3 0.9 - - - -
70W PRO* 3.5 33.2 - - + -
99W HIS* 2.8 29.9 + - + +
101W LYS 3.8 0.4 - - - -
102W CYS* 2.0 52.9 - - + -
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Residues in contact with GLY 58 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32V LEU* 3.7 8.7 - - - +
26W CYS* 3.2 2.8 - - - -
27W HIS* 2.9 35.3 + - - +
29W ILE* 4.4 9.0 - - - -
56W ARG 3.3 2.5 + - - -
57W CYS* 1.3 75.9 - - - +
59W GLY* 1.3 65.0 + - - -
68W CYS* 4.0 8.0 - - - -
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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