Contacts of the strand formed by residues 1555 - 1558 (chain A) in PDB entry 4C6C
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 LEU1555 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1534A PHE* 4.3 2.7 - - - -
1535A LEU 3.5 9.4 - - - +
1536A GLY 3.8 3.1 - - - -
1537A ALA* 3.6 25.1 - - - +
1545A LEU* 4.0 21.3 - - + -
1554A GLY* 1.3 72.3 - - - -
1556A KCX 1.3 58.4 - - - +
1557A LEU* 3.7 24.0 - - + -
1577A HIS* 3.8 22.9 - - + +
1581A TRP* 3.4 46.2 - - + +
1586A PRO 2.9 7.8 + - - +
1587A ILE* 3.3 9.5 - - + +
1588A VAL* 2.9 28.6 + - - +
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Residues in contact with KCX1556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1471A HIS* 3.0 8.1 + - - -
1473A HIS* 3.0 8.8 + - - -
1503A MET* 3.4 16.4 - - - +
1504A PRO* 4.0 11.7 - - + -
1534A PHE* 4.3 3.3 - - + -
1535A LEU 2.8 17.9 + - - +
1536A GLY* 3.6 1.4 - - - -
1537A ALA* 2.9 26.0 + - - +
1555A LEU* 1.3 70.3 - - - +
1557A LEU* 1.3 65.9 + - - +
1558A TYR* 3.0 51.5 + - + -
1588A VAL* 3.5 25.1 - - + +
1590A HIS* 3.1 24.4 + - - +
1613A CYS* 4.2 5.4 - - - -
1614A HIS* 3.3 2.3 + - - -
2822A ZN 2.1 29.5 - - - -
2823A ZN 1.9 34.7 - - - -
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Residues in contact with LEU1557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1537A ALA* 3.8 15.7 - - + -
1555A LEU* 3.7 31.4 - - + -
1556A KCX 1.3 76.6 - - - +
1558A TYR* 1.3 61.9 + - - +
1559A LEU* 3.6 29.1 + - + -
1568A LEU* 4.5 4.5 - - + -
1574A TRP* 4.6 14.4 - - + +
1577A HIS* 4.6 4.9 - - + -
1578A PHE* 3.6 32.1 - - + -
1587A ILE* 3.9 14.1 - - + -
1588A VAL 2.9 13.1 + - - +
1589A ALA* 3.3 4.1 - - + +
1590A HIS 2.9 26.3 + - - -
1599A VAL* 4.8 1.6 - - + -
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Residues in contact with TYR1558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1473A HIS* 3.5 13.9 - + - -
1503A MET* 3.7 8.8 - - - +
1504A PRO* 3.7 8.4 - - + +
1505A ASN* 3.5 20.2 - - + +
1537A ALA 5.4 1.4 + - - -
1556A KCX 3.0 64.7 + - + -
1557A LEU* 1.3 69.6 - - - +
1559A LEU* 1.3 65.8 + - - +
1560A ASN 3.5 7.3 + - - +
1562A THR* 4.1 20.0 - - - +
1566A LEU* 3.6 57.9 + - + +
1568A LEU* 4.5 10.3 + - - +
1590A HIS* 4.3 11.4 - + + -
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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