Contacts of the helix formed by residues 1479 - 1483 (chain B) in PDB entry 3PT6
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 CYS1479 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B ZN 2.4 36.6 - - - -
1462B PHE* 3.2 25.8 - - - +
1478B VAL* 1.3 82.7 - - - +
1480B SER* 1.3 75.8 + - - +
1481B CYS* 3.0 5.8 + - - -
1482B ALA* 3.1 15.2 + - + +
1483B GLU 4.0 0.3 + - - -
1487B CYS* 3.6 18.6 - - - -
1488B ASP 4.2 13.2 - - - -
1491B SER* 4.3 3.6 - - - -
1500B TRP* 4.2 6.3 - - + -
1504B HIS* 3.6 15.0 - - + -
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Residues in contact with SER1480 (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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1462B PHE* 3.5 24.6 - - - -
1479B CYS* 1.3 76.0 - - - +
1481B CYS* 1.3 55.4 + - - +
1483B GLU* 2.9 36.5 + - - +
1485B LYS* 3.2 22.6 + - - -
1486B ALA 2.9 24.9 + - - -
1488B ASP* 3.7 19.1 - - - +
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Residues in contact with CYS1481 (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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3B ZN 2.4 35.4 - - - -
1479B CYS* 3.0 5.5 + - - -
1480B SER* 1.3 79.2 - - - +
1482B ALA* 1.3 60.2 + - - +
1483B GLU 3.1 0.7 - - - -
1484B GLY* 2.9 17.5 + - - -
1485B LYS 3.0 17.2 + - - +
1486B ALA 4.0 0.4 + - - -
1487B CYS* 3.8 9.6 - - - +
1504B HIS* 3.6 21.5 - - - -
1508B ARG* 5.4 14.8 + - - +
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Residues in contact with ALA1482 (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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1463B HIS 3.5 4.3 - - - +
1464B ASP* 3.3 31.1 - - + +
1465B VAL* 3.2 26.5 + - - +
1477B GLY* 4.3 12.3 - - - -
1478B VAL 5.0 1.6 - - - +
1479B CYS 3.1 12.9 + - - +
1481B CYS* 1.3 83.0 - - - +
1483B GLU* 1.3 57.8 + - - +
1484B GLY 3.2 0.4 + - - -
1503B PRO 6.1 0.7 - - - +
1504B HIS 6.1 1.1 - - - +
1507B ASN* 5.7 0.9 - - - +
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Residues in contact with GLU1483 (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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1461B THR 5.1 0.3 - - - +
1462B PHE* 3.5 34.2 - - + -
1463B HIS* 3.2 36.8 + - + +
1465B VAL* 5.2 7.6 - - - +
1479B CYS 4.0 0.2 + - - -
1480B SER* 2.9 14.8 + - - +
1482B ALA* 1.3 78.6 - - - +
1484B GLY* 1.3 54.5 + - - +
1485B LYS* 3.4 32.9 + - + +
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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