Contacts of the strand formed by residues 1542 - 1545 (chain A) in PDB entry 4ZLP
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 SER1542 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1479A PHE* 6.3 1.3 - - - -
1494A GLY 4.8 2.8 + - - -
1495A TRP* 3.8 18.8 - - - +
1497A GLY* 5.9 1.8 - - - -
1498A LEU* 3.3 43.9 + - - +
1536A SER* 4.0 3.6 - - - -
1541A THR* 1.3 80.3 + - - +
1543A LEU* 1.3 65.6 + - - +
1544A ARG* 5.4 1.1 - - - -
1585A GLU 3.8 0.2 - - - +
1586A ILE* 3.6 0.5 - - - -
1587A ASP* 2.8 44.1 + - - +
1590A LEU* 5.1 0.5 - - - +
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Residues in contact with LEU1543 (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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1479A PHE* 4.0 15.6 - - - -
1513A LEU* 4.1 13.7 - - + -
1532A LEU* 4.1 16.7 - - + +
1535A LEU* 4.6 10.1 - - + -
1536A SER* 3.0 24.0 + - - +
1539A LEU* 3.6 33.9 - - + -
1541A THR* 3.7 23.8 - - + +
1542A SER* 1.3 82.4 - - - +
1544A ARG* 1.3 65.7 + - - +
1584A LEU* 4.2 14.4 - - + -
1585A GLU 3.4 14.4 - - - +
1586A ILE* 3.7 19.1 - - + -
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Residues in contact with ARG1544 (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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1479A PHE* 6.3 0.2 - - + -
1498A LEU* 3.6 22.2 - - - +
1506A ALA* 4.0 6.1 - - - +
1508A LEU* 3.6 12.1 - - - +
1532A LEU* 3.9 13.9 - - + -
1542A SER* 5.4 1.6 - - - +
1543A LEU* 1.3 78.1 - - - +
1545A PHE* 1.3 69.3 + - - +
1584A LEU* 3.3 9.4 - - - -
1585A GLU* 2.7 62.4 + - + +
1587A ASP* 2.9 35.8 + - - +
1589A ARG* 3.8 7.2 - - - +
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Residues in contact with PHE1545 (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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1524A LEU* 3.9 24.2 - - + -
1525A LEU* 3.6 15.9 - - + -
1528A SER* 3.3 36.6 - - - -
1531A PHE* 4.5 6.5 - + - -
1532A LEU* 3.9 21.3 - - + +
1544A ARG* 1.3 85.3 - - - +
1546A ARG* 1.3 69.2 + - - +
1547A LEU* 3.6 15.7 + - + +
1553A ALA* 4.1 16.6 - - + -
1554A MET 5.0 0.7 - - - +
1555A VAL* 4.0 9.0 - - + -
1582A VAL* 3.8 23.1 - - + -
1583A MET 4.4 1.3 - - - +
1584A LEU* 3.4 17.9 - - + -
1585A GLU* 4.9 2.1 - - - -
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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