Contacts of the helix formed by residues 1468 - 1479 (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 ASN1468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1466A THR 3.4 5.1 + - - -
1467A CYS* 1.3 72.4 - - - +
1469A PRO* 1.3 70.2 - - - +
1470A VAL* 3.2 22.6 + - - +
1471A TYR* 2.7 70.9 + - + +
1472A GLU* 3.1 9.2 + - - -
1493A CYS* 4.5 1.2 - - - -
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Residues in contact with PRO1469 (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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1466A THR* 5.6 4.7 - - + -
1467A CYS 3.1 9.8 - - - +
1468A ASN* 1.3 90.8 - - - +
1470A VAL* 1.3 61.8 + - + +
1471A TYR 3.5 0.3 + - - -
1472A GLU* 3.6 18.2 + - + +
1473A LYS* 4.7 2.1 + - - +
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Residues in contact with VAL1470 (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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1468A ASN* 2.9 17.6 + - - +
1469A PRO* 1.3 82.5 - - + +
1471A TYR* 1.3 72.9 + - + +
1472A GLU 3.5 0.2 - - - -
1473A LYS* 5.0 3.0 + - - +
1474A TYR* 5.4 1.6 + - - +
1470B VAL 5.7 1.2 - - - +
1473B LYS* 3.3 42.7 - - + +
1474B TYR* 5.0 4.3 + - - +
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Residues in contact with TYR1471 (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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1467A CYS* 4.9 4.0 - - - -
1468A ASN* 2.7 46.4 + - + +
1470A VAL* 1.3 91.6 - - + +
1472A GLU* 1.3 55.5 + - - -
1473A LYS 3.4 2.2 - - - -
1474A TYR* 3.2 8.8 + - - +
1475A CYS* 2.9 34.7 + - - -
1487A GLY 5.2 4.0 - - - +
1493A CYS* 6.0 1.6 - - - -
1474B TYR* 3.7 34.1 - + + -
1477B ASP* 2.4 43.5 + - + +
1478B HIS* 3.5 25.9 - + - -
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Residues in contact with GLU1472 (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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1467A CYS* 4.1 19.2 - - - +
1468A ASN 3.1 9.5 + - - +
1469A PRO* 3.7 18.2 - - + +
1470A VAL 3.5 1.6 - - - -
1471A TYR* 1.3 76.5 - - - +
1473A LYS* 1.3 59.5 + - - +
1475A CYS* 3.2 1.7 + - - -
1476A ALA* 2.8 30.8 + - - +
1533A GLN* 2.7 39.8 + - - +
1534A ARG* 3.3 44.6 + - - +
1537A ALA* 5.5 1.9 - - - +
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Residues in contact with LYS1473 (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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1469A PRO 4.7 2.0 + - - -
1470A VAL 5.0 2.6 + - - +
1471A TYR 3.4 0.4 - - - -
1472A GLU* 1.3 81.7 - - - +
1474A TYR* 1.3 62.2 + - - +
1476A ALA* 3.4 6.1 + - + +
1477A ASP* 2.8 60.5 + - - +
1530A ASP* 5.8 1.8 - - - +
1534A ARG* 5.9 3.4 - - - +
1470B VAL* 3.5 32.8 - - + +
1471B TYR* 4.8 0.2 - - - -
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Residues in contact with TYR1474 (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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1470A VAL 5.4 1.3 + - - +
1471A TYR* 3.2 10.3 + - - +
1473A LYS* 1.3 79.6 - - - +
1475A CYS* 1.3 62.6 + - - +
1477A ASP 3.2 1.7 + - - -
1478A HIS* 2.7 63.6 + + - -
1485A ASP* 2.7 27.4 + - - -
1488A CYS* 3.7 9.2 - - - -
1470B VAL 5.2 2.1 + - - +
1471B TYR* 3.6 33.5 - - + -
1474B TYR* 3.2 67.6 - + + -
1485B ASP* 4.3 1.6 - - - +
1487B GLY* 3.0 21.2 + - - -
1488B CYS* 3.6 11.9 + - - -
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Residues in contact with CYS1475 (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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1467A CYS* 4.1 16.4 - - - -
1471A TYR* 2.9 22.9 + - - +
1472A GLU* 3.7 5.8 - - - +
1474A TYR* 1.3 75.6 - - - +
1476A ALA* 1.3 63.1 + - - +
1478A HIS* 3.3 1.8 + - - +
1479A PHE* 3.0 26.7 + - - +
1487A GLY 4.5 0.2 - - - -
1488A CYS* 2.1 57.9 - - + +
1493A CYS* 4.2 5.2 - - - +
1496A ASP* 5.0 1.2 - - - +
1533A GLN* 3.8 19.2 - - - +
1474B TYR* 4.4 5.2 - - - -
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Residues in contact with ALA1476 (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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1472A GLU* 2.8 19.9 + - - +
1473A LYS* 3.8 8.3 - - + +
1475A CYS* 1.3 76.7 - - - +
1477A ASP* 1.3 66.0 + - - +
1478A HIS 3.5 0.2 + - - -
1479A PHE* 3.6 11.4 - - - +
1529A ALA* 3.6 18.4 - - - +
1530A ASP* 3.5 31.1 + - + +
1533A GLN* 3.6 23.9 - - - +
1534A ARG* 5.5 0.7 - - - +
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Residues in contact with ASP1477 (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 LYS* 2.8 46.0 + - - +
1474A TYR 3.2 3.8 + - - +
1476A ALA* 1.3 81.4 - - - +
1478A HIS* 1.3 61.8 + - + +
1479A PHE 3.4 2.5 + - - +
1481A ASP* 4.7 4.9 - - - +
1529A ALA* 5.3 3.5 - - - +
1530A ASP* 6.0 1.2 - - - +
1471B TYR* 2.4 37.0 + - + +
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Residues in contact with HIS1478 (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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1474A TYR* 2.7 65.7 + + + +
1475A CYS* 3.3 2.2 + - - +
1477A ASP* 1.3 78.6 - - + +
1479A PHE* 1.3 57.9 + - - +
1481A ASP* 2.8 25.0 - - - +
1485A ASP* 3.5 17.0 - - + +
1488A CYS* 5.6 0.2 - - - -
1496A ASP* 2.8 7.4 - - - +
5003A CA 2.4 30.1 - - - -
1471B TYR* 3.6 34.9 - + - -
1487B GLY* 3.9 25.1 + - - -
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Residues in contact with PHE1479 (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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1475A CYS 3.0 15.6 + - - +
1476A ALA 3.6 10.8 - - - +
1477A ASP 3.4 2.6 - - - +
1478A HIS* 1.3 75.3 - - - +
1480A ALA* 1.3 84.0 + - + +
1481A ASP* 3.2 2.3 + - - +
1493A CYS 5.1 0.2 - - - -
1494A GLY 3.4 14.1 - - - -
1496A ASP* 3.9 7.9 - - - +
1497A GLY* 3.3 31.4 - - - -
1529A ALA* 3.8 26.4 - - + +
1532A LEU* 3.6 38.1 - - + -
1533A GLN* 3.5 32.1 - - + -
1536A SER* 4.1 4.5 - - - -
1542A SER* 6.3 1.1 - - - -
1543A LEU 4.0 13.2 - - - -
1544A ARG* 6.3 0.4 - - + -
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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