Contacts of the helix formed by residues 1471 - 1479 (chain B) 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 TYR1471 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1473A LYS 4.5 0.2 - - - -
1474A TYR* 3.6 34.3 - + + -
1477A ASP* 2.4 39.7 + - + +
1478A HIS* 3.6 27.3 - + - -
1467B CYS* 5.0 2.7 - - - -
1468B ASN* 2.7 42.1 + - + +
1470B VAL* 1.3 92.3 - - + +
1472B GLU* 1.3 65.2 + - - +
1473B LYS 3.3 2.7 - - - -
1474B TYR* 3.1 10.1 + - - +
1475B CYS* 3.0 28.1 + - - -
1487B GLY 5.4 4.0 - - - +
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Residues in contact with GLU1472 (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 CYS* 3.8 21.2 - - - +
1468B ASN 2.9 14.1 + - - +
1469B PRO* 3.8 15.5 - - + +
1470B VAL 3.5 1.6 - - - -
1471B TYR* 1.3 76.7 - - - +
1473B LYS* 1.3 64.4 + - - +
1475B CYS* 3.3 1.3 + - - +
1476B ALA* 3.0 22.9 + - - +
1533B GLN* 2.6 38.9 + - - +
1534B ARG* 3.5 39.8 + - - +
1537B ALA* 5.4 2.1 - - - +
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Residues in contact with LYS1473 (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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1470A VAL* 3.3 34.5 - - + +
1471A TYR* 4.9 0.2 - - - -
1469B PRO 4.7 2.2 + - - -
1470B VAL 5.0 2.4 + - - +
1471B TYR 3.3 0.6 - - - -
1472B GLU* 1.3 81.0 - - + +
1474B TYR* 1.3 63.8 + - - +
1476B ALA* 3.5 6.1 + - + +
1477B ASP* 3.1 47.8 + - - +
1530B ASP* 5.0 11.1 + - - +
1534B ARG* 5.4 6.1 - - - +
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Residues in contact with TYR1474 (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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1470A VAL 5.0 2.5 + - - +
1471A TYR* 3.7 33.5 - - + -
1474A TYR* 3.2 68.1 - + + -
1485A ASP* 4.2 2.1 - - - +
1487A GLY* 3.0 19.0 + - - -
1488A CYS* 3.5 13.4 + - - -
1470B VAL 5.6 0.6 + - - +
1471B TYR 3.1 9.9 + - - +
1473B LYS* 1.3 79.2 - - - +
1475B CYS* 1.3 63.7 + - - +
1477B ASP 3.2 1.2 + - - -
1478B HIS* 2.8 62.8 + + + +
1485B ASP* 2.6 29.1 + - - -
1488B CYS* 3.6 9.2 - - - -
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Residues in contact with CYS1475 (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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1474A TYR* 4.4 5.4 - - - -
1467B CYS* 4.1 16.8 - - - -
1471B TYR* 3.0 20.3 + - - -
1472B GLU 3.8 7.2 - - - +
1474B TYR* 1.3 76.2 - - - +
1476B ALA* 1.3 57.4 + - - +
1478B HIS* 3.3 2.1 + - - -
1479B PHE* 2.9 31.4 + - - +
1487B GLY 4.6 0.9 - - - -
1488B CYS* 2.0 56.6 - - + +
1493B CYS* 4.3 3.6 - - - +
1496B ASP* 4.9 1.6 - - - +
1533B GLN* 3.8 19.1 - - - +
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Residues in contact with ALA1476 (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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1472B GLU* 3.0 20.2 + - - +
1473B LYS* 3.7 8.3 - - + +
1474B TYR 3.2 0.2 - - - -
1475B CYS* 1.3 79.3 - - - +
1477B ASP* 1.3 65.0 + - - +
1478B HIS 3.4 0.5 + - - -
1479B PHE* 3.5 5.7 + - - +
1529B ALA* 3.3 24.2 - - - +
1530B ASP* 3.5 30.7 - - + +
1533B GLN* 3.6 24.6 - - - +
1534B ARG* 5.3 0.2 - - - +
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Residues in contact with ASP1477 (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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1470A VAL* 5.0 0.3 - - - +
1471A TYR* 2.4 41.0 + - + +
1473B LYS* 3.1 46.8 + - - +
1474B TYR 3.2 3.6 + - - +
1476B ALA* 1.3 82.9 - - - +
1478B HIS* 1.3 63.2 + - + +
1479B PHE 3.8 1.4 + - - +
1481B ASP* 5.0 4.5 - - - +
1529B ALA* 4.5 9.1 - - - +
1530B ASP* 5.4 3.8 - - - +
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Residues in contact with HIS1478 (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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1471A TYR* 3.5 34.7 - + - -
1487A GLY* 3.7 30.8 + - - -
1474B TYR* 2.8 60.2 + + + +
1475B CYS* 3.6 2.7 - - - +
1477B ASP* 1.3 78.7 - - + +
1479B PHE* 1.3 58.6 + - - +
1481B ASP* 2.9 26.6 - - - +
1483B ARG* 6.1 0.9 - - - -
1485B ASP* 3.5 16.8 - - + +
1496B ASP* 3.6 3.1 - - - +
5003B CA 2.4 30.7 - - - -
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Residues in contact with PHE1479 (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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1475B CYS 2.9 15.8 + - - +
1476B ALA 3.6 10.8 - - - +
1477B ASP 3.4 2.1 - - - +
1478B HIS* 1.3 74.2 - - - +
1480B ALA* 1.3 82.4 + - + +
1481B ASP* 3.3 2.1 + - - +
1494B GLY 3.3 23.8 - - - -
1496B ASP* 3.8 9.4 - - - -
1497B GLY* 3.3 23.1 - - - -
1529B ALA* 3.9 27.2 - - - +
1532B LEU* 3.5 27.6 - - + -
1533B GLN* 3.6 29.6 - - + -
1536B SER* 3.6 21.8 - - - -
1542B SER* 4.8 2.5 - - - -
1543B LEU 4.0 12.8 - - - -
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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