Contacts of the strand formed by residues 89 - 95 (chain V) in PDB entry 1ZGL
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 LEU 89 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37U GLN* 5.7 1.1 - - - +
40U GLY 5.8 0.4 - - - +
41U GLU 4.6 14.8 - - - +
36V GLN* 3.7 1.2 - - - -
37V GLN* 2.9 49.4 + - + +
88V ALA* 1.3 74.2 - - - +
90V TYR* 1.3 61.8 + - - +
91V LEU* 3.5 17.1 + - + -
110V GLN 3.6 10.1 - - - +
111V GLY* 3.3 16.8 - - - -
112V THR 3.1 36.8 - - - +
113V ARG* 3.9 35.4 - - + +
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Residues in contact with TYR 90 (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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6V GLN* 3.1 22.0 + - - -
21V LEU* 3.5 23.3 - - + -
34V TRP* 4.1 9.0 - - + -
35V TYR 3.3 5.8 - - - +
36V GLN* 3.5 30.3 + - + -
46V LEU* 4.6 4.5 - - + -
65V PHE* 4.3 13.1 - + - -
77V MET* 3.2 34.1 - - + -
79V VAL* 4.4 3.7 - - + +
86V ASP* 2.6 47.1 + - - +
88V ALA* 3.2 19.1 - - + -
89V LEU* 1.3 74.3 - - - +
91V LEU* 1.3 58.3 - - - +
112V THR* 3.2 15.0 + - - +
114V LEU* 3.7 24.7 - - + +
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Residues in contact with LEU 91 (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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37U GLN* 4.9 0.7 - - - +
42U GLY* 4.5 9.0 - - - -
43U LEU* 4.7 7.9 - - + -
6V GLN* 3.7 0.7 - - - +
33V SER 3.7 0.2 - - - +
34V TRP* 3.3 8.6 - - - +
35V TYR* 2.8 40.8 + - + +
37V GLN* 3.5 30.3 - - + +
43V LEU* 4.0 16.4 - - + -
89V LEU* 3.5 12.5 + - + +
90V TYR* 1.3 73.5 - - - +
92V CYS* 1.3 63.6 + - - +
108V PHE* 4.0 23.6 - - + -
109V GLY 4.4 7.9 - - - +
110V GLN* 3.7 9.6 - - - +
111V GLY* 3.4 28.0 - - - +
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Residues in contact with CYS 92 (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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4V VAL* 3.6 6.2 - - - +
6V GLN* 2.7 22.0 + - - +
23V CYS* 2.0 51.6 - - + -
32V VAL* 3.0 28.7 - - - -
33V SER 3.4 3.1 - - - +
34V TRP* 4.1 8.7 - - + -
91V LEU* 1.3 78.5 - - - +
93V ALA* 1.3 62.8 + - - +
94V SER* 5.9 0.7 - - - -
108V PHE* 3.6 2.4 - - - -
109V GLY 2.9 25.5 + - - -
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Residues in contact with ALA 93 (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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4V VAL* 5.6 0.4 - - - -
31V SER 3.5 0.7 - - - +
32V VAL* 3.5 5.2 - - - -
33V SER* 3.0 36.0 + - - +
35V TYR* 4.7 4.0 - - + -
92V CYS* 1.3 76.3 - - - +
94V SER* 1.3 60.1 + - - +
106V ALA* 4.2 8.1 - - + -
107V PHE 3.0 27.1 - - - +
108V PHE* 3.8 27.3 - - + -
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Residues in contact with SER 94 (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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4V VAL* 4.3 4.5 - - - +
25V PRO* 3.7 25.8 - - - -
26V ILE* 3.2 20.3 + - - +
29V HIS* 2.8 20.5 + - - -
31V SER 3.1 13.5 - - - -
32V VAL* 4.7 1.8 - - - -
92V CYS* 5.9 0.4 - - - -
93V ALA* 1.3 75.2 - - - +
95V SER* 1.3 63.2 + - - +
106V ALA* 4.7 1.1 - - - -
107V PHE* 2.8 36.9 + - - +
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Residues in contact with SER 95 (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 HIS* 3.4 14.4 - - - -
30V ARG 2.8 21.0 + - - -
31V SER* 3.1 19.6 + - - -
94V SER* 1.3 79.2 + - - +
96V LEU* 1.3 60.6 + - - +
97V ALA* 3.1 16.3 + - - -
102V THR* 5.4 5.7 - - - +
103V GLU* 4.6 11.0 + - - -
106V ALA* 4.1 17.9 - - - -
107V PHE* 4.7 3.6 - - - -
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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