Contacts of the helix formed by residues 1473 - 1481 (chain B) in PDB entry 5ZCS
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 ASP1473 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1466B LYS* 5.6 0.7 - - - +
1467B MET* 4.4 3.9 - - - +
1470B ASN* 5.3 7.4 + - - +
1471B LYS* 3.1 36.9 + - - +
1472B ASP* 1.3 71.9 - - - +
1474B PRO* 1.3 67.8 - - + +
1475B GLU* 4.5 2.2 - - + +
1476B LEU* 3.3 38.5 - - + +
1477B MET* 2.8 29.1 + - - +
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Residues in contact with PRO1474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1471B LYS* 3.7 17.7 - - - +
1472B ASP 3.9 2.7 - - - +
1473B ASP* 1.3 86.1 - - + +
1475B GLU* 1.3 61.4 + - + +
1477B MET* 3.2 15.1 + - + +
1478B LEU* 2.9 34.3 + - + +
1504B VAL* 5.7 2.5 - - + -
1505B ASN* 5.7 7.0 - - - +
1508B THR* 4.2 22.6 - - + +
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Residues in contact with GLU1475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1473B ASP* 3.4 1.9 - - + +
1474B PRO* 1.3 81.5 - - + +
1476B LEU* 1.3 60.6 + - + +
1478B LEU* 3.3 14.4 + - + +
1479B GLY* 2.9 23.9 + - - -
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Residues in contact with LEU1476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1447B ALA* 4.5 11.7 - - + -
1463B TYR* 3.9 27.5 - - + -
1466B LYS* 3.8 29.4 - - + -
1467B MET* 3.3 28.2 - - + +
1473B ASP* 3.3 36.1 + - + +
1474B PRO 3.3 0.2 - - - -
1475B GLU* 1.3 77.1 - - + +
1477B MET* 1.3 60.5 + - - +
1479B GLY* 3.8 2.0 - - - +
1480B ARG* 2.9 30.5 + - - +
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Residues in contact with MET1477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1467B MET* 3.8 12.8 - - + +
1472B ASP* 5.5 3.6 - - + +
1473B ASP 2.8 19.8 + - - +
1474B PRO* 3.5 9.9 - - + +
1475B GLU 3.2 0.4 - - - -
1476B LEU* 1.3 74.4 - - - +
1478B LEU* 1.3 64.3 + - - +
1480B ARG* 3.5 2.4 + - - +
1481B MET* 3.3 39.8 + - + +
1500B LYS* 3.8 39.0 - - + +
1504B VAL* 3.9 31.6 - - + -
1508B THR* 4.4 8.7 - - + -
1512B MET* 3.8 24.7 - - + -
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Residues in contact with LEU1478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1474B PRO* 2.9 20.4 + - + +
1475B GLU* 3.3 13.4 + - + +
1477B MET* 1.3 76.2 - - - +
1479B GLY* 1.3 61.6 + - - +
1481B MET* 3.8 9.8 + - - +
1482B ARG* 3.8 23.2 + - - +
1508B THR* 3.8 38.6 - - + +
1511B LYS* 4.6 23.8 - - + +
1512B MET* 4.2 9.4 - - + -
1515B MET* 3.8 30.5 - - + +
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Residues in contact with GLY1479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1451B GLU* 5.4 4.3 - - - -
1456B TRP* 3.2 32.1 - - - -
1463B TYR* 4.7 10.1 - - - -
1475B GLU 2.9 15.8 + - - -
1476B LEU* 3.4 2.9 + - - -
1477B MET 3.3 0.2 - - - -
1478B LEU* 1.3 76.2 - - - +
1480B ARG* 1.3 62.7 + - - +
1481B MET 3.4 0.2 - - - -
1482B ARG* 3.6 20.0 + - - +
1483B CYS* 4.0 0.5 - - - -
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Residues in contact with ARG1480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1460B LEU* 5.0 11.6 - - + +
1463B TYR* 4.9 13.9 - - + -
1464B ASP* 4.0 20.9 + - - -
1467B MET* 3.7 29.1 - - + +
1476B LEU 2.9 18.7 + - - +
1477B MET* 3.5 4.7 + - + +
1478B LEU 3.4 0.2 - - - -
1479B GLY* 1.3 78.2 - - - +
1481B MET* 1.3 61.7 + - + +
1483B CYS* 3.2 28.7 + - - +
1484B LEU* 4.4 3.1 + - - +
1496B GLN* 3.4 35.9 + - - +
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Residues in contact with MET1481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477B MET* 3.3 25.4 + - + +
1478B LEU 3.8 4.2 + - - +
1479B GLY 3.4 0.2 - - - -
1480B ARG* 1.3 79.8 - - + +
1482B ARG* 1.3 60.4 + - - +
1483B CYS 3.3 0.4 - - - -
1484B LEU* 3.8 5.4 + - - +
1485B GLU* 3.7 14.5 - - - +
1493B LEU* 3.7 29.1 - - + +
1496B GLN* 4.3 20.6 - - + +
1497B CYS* 3.7 37.7 - - - +
1512B MET* 3.7 37.9 - - - +
1515B MET* 4.4 18.1 - - + +
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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