Contacts of the strand formed by residues 31 - 37 (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 SER 31 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29V HIS 3.6 1.2 - - - -
30V ARG* 1.3 81.0 - - - +
32V VAL* 1.3 67.9 + - - +
33V SER 4.8 0.2 + - - -
48V GLU* 2.6 33.6 + - - +
49V TYR 2.8 10.9 + - - -
50V PHE* 4.3 1.3 - - - -
55V ARG* 4.2 7.9 - - - -
93V ALA 3.5 0.8 - - - +
94V SER* 3.1 29.1 - - - -
95V SER* 3.1 21.0 + - - -
97V ALA* 4.4 6.1 - - - -
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Residues in contact with VAL 32 (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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23V CYS* 4.1 2.2 - - - +
25V PRO* 3.9 29.4 - - + -
30V ARG 5.5 0.4 - - - -
31V SER* 1.3 81.9 + - - +
33V SER* 1.3 57.7 + - - +
34V TRP* 3.7 14.8 - - - +
48V GLU* 3.4 2.3 - - - -
49V TYR* 2.7 47.8 + - + +
69V GLN* 4.8 1.3 - - - +
73V SER 3.9 18.4 - - - +
75V SER* 4.0 17.9 - - - -
92V CYS* 3.0 34.1 - - - -
93V ALA 3.5 2.0 - - - -
94V SER* 4.7 0.9 - - - -
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Residues in contact with SER 33 (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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102U TYR 4.8 2.5 - - - -
32V VAL* 1.3 74.1 - - - +
34V TRP* 1.3 66.8 + - - +
35V TYR* 3.2 26.4 + - - -
45V PHE* 3.3 19.3 - - - -
47V PHE 3.2 4.3 - - - -
48V GLU* 3.7 21.5 - - - -
91V LEU 3.7 0.2 - - - +
92V CYS* 3.4 5.5 - - - -
93V ALA* 3.0 35.9 + - - -
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Residues in contact with TRP 34 (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* 4.7 5.4 - - - -
21V LEU* 3.3 39.9 - - + -
22V SER 3.9 11.4 - - - -
23V CYS* 3.6 22.2 - - + -
32V VAL* 3.7 15.4 - - + +
33V SER* 1.3 85.8 + - - +
35V TYR* 1.3 71.1 + - - +
45V PHE* 3.9 0.2 - - - -
46V LEU* 2.9 42.1 + - + -
47V PHE* 2.9 25.1 + + + -
49V TYR* 5.1 2.0 - + - -
75V SER* 3.5 22.5 + - - -
77V MET* 2.9 50.4 - - + +
90V TYR* 4.1 15.7 - - + -
91V LEU 3.3 14.6 - - - -
92V CYS* 4.3 2.2 - - + -
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Residues in contact with TYR 35 (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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103U LYS* 3.7 8.7 - - - +
104U LEU* 3.4 33.4 + - - +
106U PHE* 4.1 15.5 - + - -
33V SER* 3.2 31.7 + - - -
34V TRP* 1.3 82.7 - - - +
36V GLN* 1.3 58.1 + - - +
37V GLN 3.9 0.7 - - - -
43V LEU* 4.3 23.8 - - + -
44V GLN 3.6 4.9 - - - -
45V PHE* 3.7 35.0 - + + -
46V LEU* 3.4 6.5 - - - +
89V LEU 3.6 0.2 - - - +
90V TYR* 3.3 5.0 - - - +
91V LEU* 2.8 44.4 + - + +
93V ALA* 4.7 4.0 - - + -
106V ALA* 5.9 1.1 - - + -
108V PHE* 3.3 34.8 - + + -
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Residues in contact with GLN 36 (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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35V TYR* 1.3 71.3 - - - +
37V GLN* 1.3 57.6 + - - +
38V THR* 3.3 34.8 + - + +
43V LEU* 3.7 1.1 + - - -
44V GLN* 2.9 38.2 + - - +
46V LEU* 3.3 18.1 - - + +
60V PHE* 3.1 34.5 - - + -
65V PHE* 4.5 1.2 - - - -
85V GLY 4.5 3.6 + - - -
86V ASP* 4.4 14.6 + - - +
88V ALA* 4.0 15.9 - - + -
89V LEU 3.7 3.1 - - - -
90V TYR* 3.5 28.8 + - + +
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Residues in contact with GLN 37 (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* 2.8 41.9 + - - +
89U PHE* 3.8 22.8 - - - -
35V TYR 3.9 1.4 - - - -
36V GLN* 1.3 69.0 - - - +
38V THR* 1.3 63.0 + - - +
39V PRO* 4.7 0.9 - - - +
42V GLY* 5.4 1.0 - - - -
43V LEU* 3.6 30.3 - - + +
88V ALA* 3.1 18.0 - - - +
89V LEU* 2.9 35.3 + - + +
91V LEU* 3.5 16.7 - - + +
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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