Contacts of the strand formed by residues 27 - 34 (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 HIS 27 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22V GLN 5.1 2.4 + - - -
23V ARG* 3.4 26.9 - - - -
25V TYR 2.7 20.9 + - - +
26V CYS* 1.3 74.9 - - - +
28V PRO* 1.3 95.0 + - + +
29V ILE* 3.3 17.6 + - + +
58V GLY* 3.0 27.3 + - - +
102V CYS* 3.7 11.7 - - - -
30W GLU* 5.6 1.7 + - - -
32W LEU* 3.8 16.9 - - + +
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Residues in contact with PRO 28 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27V HIS* 1.3 102.9 - - + +
29V ILE* 1.3 59.7 + - - +
55V MET* 4.1 19.2 - - + +
56V ARG 3.6 8.3 - - - +
99V HIS 3.5 25.1 - - - +
100V ASN 3.8 18.4 - - - +
101V LYS* 4.2 1.3 - - - +
102V CYS* 3.5 23.5 - - + +
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Residues in contact with ILE 29 (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* 4.1 17.0 - - + +
28V PRO* 1.3 76.0 - - - +
30V GLU* 1.3 69.4 + - + +
31V THR* 2.8 27.7 + - - +
55V MET* 4.0 6.5 - - - -
56V ARG 2.9 27.3 + - - +
58V GLY* 4.3 17.9 - - - -
30W GLU* 3.8 41.5 - - + +
31W THR* 5.2 0.4 - - - -
32W LEU* 4.0 29.4 - - + +
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Residues in contact with GLU 30 (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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29V ILE* 1.3 82.3 - - + +
31V THR* 1.3 64.2 + - - +
32V LEU* 5.1 0.4 - - + +
53V PRO* 3.7 25.7 - - + +
54V LEU 3.6 7.2 - - - +
55V MET* 3.7 19.6 - - + +
23W ARG* 2.9 35.6 + - - +
27W HIS* 5.4 0.9 + - - -
29W ILE* 3.5 34.1 - - + +
30W GLU 4.3 8.3 - - - +
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Residues in contact with THR 31 (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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29V ILE* 2.8 22.7 + - - +
30V GLU* 1.3 74.1 + - - +
32V LEU* 1.3 67.5 + - - +
33V VAL* 3.3 23.5 + - + +
54V LEU 2.8 34.7 + - - +
56V ARG* 3.9 18.4 + - + +
57V CYS 5.6 0.2 + - - -
29W ILE* 5.6 0.4 - - - -
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Residues in contact with LEU 32 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30V GLU* 5.1 0.4 - - + +
31V THR* 1.3 75.4 - - - +
33V VAL* 1.3 61.5 + - - +
34V ASP* 4.0 3.3 + - - +
51V CYS* 4.6 5.4 - - - -
52V VAL 4.1 1.3 - - - -
53V PRO* 3.6 33.7 - - + -
23W ARG 3.9 12.8 - - - +
24W SER* 4.0 10.1 - - - +
27W HIS* 3.6 26.2 - - + -
29W ILE* 4.0 26.5 - - + +
58W GLY* 3.7 4.5 - - - -
59W GLY* 3.4 40.0 + - - +
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Residues in contact with VAL 33 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31V THR* 3.7 28.7 - - + +
32V LEU* 1.3 75.9 - - - +
34V ASP* 1.3 77.5 + - - +
37V GLN* 4.2 17.7 - - + -
38V GLU* 4.5 10.8 - - + +
51V CYS* 3.9 2.9 - - - -
52V VAL* 2.9 35.9 + - + +
54V LEU* 3.9 29.8 - - + -
56V ARG* 4.4 16.8 - - + +
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Residues in contact with ASP 34 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32V LEU 4.0 3.3 + - - +
33V VAL* 1.3 79.3 - - - +
35V ILE* 1.4 66.0 + - - +
36V PHE* 3.6 34.6 - - + -
37V GLN* 3.0 27.1 + - + +
38V GLU* 4.2 1.7 + - - +
50V SER* 3.6 9.5 + - - +
51V CYS* 3.5 16.0 - - - +
52V VAL* 5.7 0.2 - - - -
59W GLY 5.4 1.9 - - - +
60W CYS* 5.0 4.0 - - - +
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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