Contacts of the strand formed by residues 19 - 24 (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 VAL 19 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11V LEU* 3.3 34.8 - - + -
13V LYS* 3.6 24.5 - - + +
18V GLN* 1.3 73.6 - - - +
20V THR* 1.3 77.6 + - - +
21V LEU* 3.4 11.4 - - + -
78V ASN* 3.2 12.8 + - - -
79V VAL* 3.2 26.8 + - + -
82V LEU* 3.2 36.1 - - + -
114V LEU* 4.3 10.5 - - + -
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Residues in contact with THR 20 (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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68T ARG* 6.0 2.5 - - - +
7V THR 4.5 0.2 - - - +
8V PRO* 4.3 9.9 - - - +
11V LEU* 5.3 0.2 - - - +
18V GLN* 4.1 1.7 + - - -
19V VAL* 1.3 76.2 + - - +
21V LEU* 1.3 72.0 + - - +
22V SER* 4.1 0.9 + - - -
76V GLU* 4.1 22.9 - - + +
77V MET 3.2 11.2 - - - +
78V ASN* 2.6 32.5 + - + -
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Residues in contact with LEU 21 (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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7V THR 3.7 4.9 - - - +
8V PRO* 4.6 0.7 - - + -
11V LEU* 3.5 16.6 - - + -
19V VAL* 3.4 30.1 - - + -
20V THR* 1.3 76.4 - - - +
22V SER* 1.3 61.9 + - - +
34V TRP* 3.3 23.6 - - + -
76V GLU* 3.2 7.1 - - - +
77V MET* 2.7 42.9 + - + +
79V VAL* 6.1 1.6 - - + -
90V TYR* 3.5 39.5 - - + -
112V THR* 3.7 23.1 - - + +
114V LEU* 4.8 5.8 - - + -
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Residues in contact with SER 22 (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* 3.3 5.5 + - - +
7V THR* 2.7 50.3 + - - -
20V THR* 5.4 0.4 - - - -
21V LEU* 1.3 76.1 - - - +
23V CYS* 1.3 68.6 + - - +
24V SER* 4.8 0.9 + - - -
34V TRP* 3.9 5.5 - - - -
74V ARG* 3.2 29.2 + - - +
75V SER 3.6 4.5 - - - -
76V GLU* 4.5 2.5 - - - +
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Residues in contact with CYS 23 (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* 4.1 12.1 - - - -
5V THR 3.2 7.9 - - - +
6V GLN* 4.1 9.6 - - + -
22V SER* 1.3 83.1 + - - +
24V SER* 1.3 65.8 + - - +
25V PRO* 4.0 5.0 - - - +
32V VAL* 4.1 3.3 - - + +
34V TRP* 3.6 13.2 - - + -
74V ARG* 4.6 0.7 - - - -
75V SER* 3.0 31.4 + - - +
92V CYS* 2.0 52.3 - - + -
94V SER* 6.2 0.2 - - - -
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Residues in contact with SER 24 (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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0V GLY 4.6 14.9 + - - -
4V VAL* 4.0 0.9 - - - -
5V THR* 2.8 46.3 + - - -
22V SER* 4.8 1.5 + - - -
23V CYS* 1.3 71.6 - - - +
25V PRO* 1.3 80.6 + - - +
73V SER* 5.2 0.3 + - - -
74V ARG* 4.5 17.2 - - - +
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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