Contacts of the helix formed by residues 656 - 661 (chain A) in PDB entry 3PTA
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 CYS 656 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ZN 2.3 38.6 - - - -
653A CYS* 3.4 2.5 - - - -
655A VAL* 1.3 91.6 - - - +
657A GLU* 1.3 65.5 + - - +
658A VAL* 4.0 14.1 - - + +
659A CYS* 3.3 19.6 + - - +
660A GLN* 3.6 6.6 + - - +
691A CYS* 4.2 1.3 - - - -
692A PRO* 4.4 3.6 - - + -
693A ASN* 3.2 25.1 - - - +
1531A GLU* 3.4 17.2 + - - +
1533A MET* 5.2 1.6 - - - -
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Residues in contact with GLU 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A CYS* 1.3 68.5 - - - +
658A VAL* 1.3 61.2 + - + +
659A CYS 3.0 2.5 - - - -
660A GLN* 2.6 42.5 + - + +
661A GLN* 3.0 37.8 + - + +
1418A SER* 3.1 34.3 + - - -
1420A LEU* 3.7 27.0 - - + +
1421A VAL* 3.6 18.7 - - + +
1424A ARG* 4.9 4.3 + - - +
1533A MET* 4.8 4.1 - - + +
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Residues in contact with VAL 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A CYS* 3.3 6.3 - - + -
657A GLU* 1.3 78.5 - - + +
659A CYS* 1.3 59.1 + - - +
661A GLN* 4.1 18.1 + - - +
688A GLU* 3.6 24.2 - - - +
689A ARG* 3.6 21.1 - - - +
690A ARG* 3.4 33.0 - - + +
691A CYS* 4.9 0.4 - - - -
692A PRO* 4.1 25.1 - - + -
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Residues in contact with CYS 659 (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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2A ZN 2.4 35.4 - - - -
652A ARG* 3.7 22.9 - - - +
653A CYS 3.0 18.6 - - - +
654A GLY* 4.8 6.3 - - - -
656A CYS* 3.3 9.1 + - - +
657A GLU 3.0 0.8 - - - -
658A VAL* 1.3 78.8 - - - +
660A GLN* 1.3 64.2 + - + +
689A ARG* 3.3 22.0 + - - -
691A CYS* 3.6 18.6 - - - -
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Residues in contact with GLN 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A GLY 5.5 3.6 - - - +
655A VAL 3.8 4.7 + - - +
656A CYS 3.6 10.5 - - - +
657A GLU* 2.6 27.9 + - + +
659A CYS* 1.3 72.0 - - + +
661A GLN* 1.3 68.6 + - - +
662A PRO* 3.3 4.5 - - - +
689A ARG* 4.4 0.9 + - - -
1424A ARG* 4.2 8.8 + - - -
1492A PHE* 4.5 9.1 - - - -
1497A PRO* 4.9 2.8 - - - +
1499A CYS* 3.2 33.9 - - - +
1533A MET* 3.1 36.9 - - - +
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Residues in contact with GLN 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A GLU* 3.0 46.0 + - + +
658A VAL* 4.2 18.9 - - - +
659A CYS 3.6 0.2 - - - -
660A GLN* 1.3 75.4 - - - +
662A PRO* 1.3 70.2 - - + +
688A GLU* 3.5 37.3 + - + +
689A ARG* 2.7 35.0 + - - +
1492A PHE* 4.9 1.6 - - + -
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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
------------------------------------------------------------
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