Contacts of the strand formed by residues 1524 - 1528 (chain C) in PDB entry 5ZCJ
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 GLU1524 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLU* 5.7 3.5 - - - +
19A ARG* 4.4 15.4 + - - +
1507C THR* 3.3 25.6 + - - +
1516C LYS* 3.7 24.9 - - + +
1517C LEU 3.2 14.4 - - - +
1518C LEU* 4.0 21.2 - - + +
1522C GLY 3.5 3.2 + - - +
1523C TYR* 1.3 84.9 - - - +
1525C CYS* 1.3 65.7 + - - +
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Residues in contact with CYS1525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 3.6 17.9 - - - +
1495C TRP* 3.7 12.3 - - - -
1516C LYS* 3.5 7.2 - - - +
1517C LEU* 2.8 32.3 + - - +
1519C PHE* 4.2 4.9 - - - -
1523C TYR* 3.5 36.6 - - + +
1524C GLU* 1.3 77.7 - - - +
1526C ASP* 1.3 66.7 + - - +
1527C VAL* 3.8 13.0 + - - -
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Residues in contact with ASP1526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 4.8 5.0 + - - -
1495C TRP 5.6 0.5 - - - +
1510C VAL* 3.7 24.1 - - - +
1514C LYS* 4.3 20.0 - - + +
1515C TYR 3.2 4.7 - - - +
1516C LYS* 2.9 40.7 + - - +
1525C CYS* 1.3 79.8 - - - +
1527C VAL* 1.3 62.3 + - - +
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Residues in contact with VAL1527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1493C ALA* 4.5 2.7 - - + -
1494C LYS 3.5 26.0 - - - +
1495C TRP* 4.4 4.0 - - - -
1514C LYS* 4.6 2.2 - - - -
1515C TYR* 2.6 38.5 + - - +
1517C LEU* 4.1 19.7 - - + -
1519C PHE* 4.4 8.5 - - + -
1525C CYS* 3.8 18.6 - - - -
1526C ASP* 1.3 80.3 - - - +
1528C LEU* 1.3 78.3 + - - +
1529C GLY 3.7 0.2 + - - -
1531C ASP* 3.7 7.6 - - + +
1532C ILE* 3.6 21.3 - - + -
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Residues in contact with LEU1528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512C ALA 5.0 3.4 - - - +
1513C GLY 3.6 8.5 - - - +
1514C LYS* 3.6 30.7 - - + +
1527C VAL* 1.3 86.1 - - - +
1529C GLY* 1.3 60.6 + - - +
1530C LYS* 3.1 33.7 - - + -
1531C ASP* 2.8 27.9 + - - +
1532C ILE* 3.6 1.8 - - - +
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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