Contacts of the helix formed by residues 670 - 675 (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 CYS 670 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ZN 2.3 32.1 - - - -
667B CYS* 3.5 5.9 - - - -
669B LYS* 1.3 78.1 - - - +
671B LYS* 1.3 63.7 + - - +
672B ALA* 2.8 7.0 - - + +
673B CYS* 3.1 17.3 - - - +
674B LYS* 2.8 28.6 + - - +
689B CYS* 3.7 1.3 - - - -
690B LEU* 3.3 39.0 - - - -
691B LYS* 4.5 1.3 - - - -
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Residues in contact with LYS 671 (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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669B LYS 3.6 1.8 + - - -
670B CYS* 1.3 73.5 - - - +
672B ALA* 1.3 62.7 + - - +
674B LYS* 4.0 7.3 + - - +
675B ASP* 4.0 14.7 + - - +
685B SER* 5.5 3.3 + - - -
21J C 3.7 24.0 + - - +
22J T 3.9 33.0 + - - +
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Residues in contact with ALA 672 (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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670B CYS* 2.8 8.6 - - + +
671B LYS* 1.3 85.1 - - - +
673B CYS* 1.3 62.9 + - - +
674B LYS 3.3 0.2 - - - -
675B ASP* 3.3 13.2 + - - +
676B MET* 3.5 14.7 + - - +
685B SER* 5.1 9.4 - - - +
687B GLN* 4.6 17.2 - - + +
688B ALA 3.1 29.8 - - - +
689B CYS* 4.6 0.2 - - - -
690B LEU* 4.8 3.4 - - + +
693B ARG* 5.0 4.3 - - - +
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Residues in contact with CYS 673 (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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4B ZN 2.3 36.1 - - - -
666B GLU* 3.7 17.0 - - - -
668B GLY* 3.6 25.6 - - - -
670B CYS* 2.9 20.1 + - + +
672B ALA* 1.3 73.7 - - - +
674B LYS* 1.3 67.2 + - - +
676B MET* 3.2 15.4 + - - +
679B PHE* 3.1 27.4 - - + +
689B CYS* 3.7 13.2 - - - -
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Residues in contact with LYS 674 (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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668B GLY 3.2 20.7 + - - +
669B LYS* 3.3 23.1 - - - +
670B CYS 2.8 28.9 + - - +
671B LYS* 4.0 8.5 - - - +
673B CYS* 1.3 77.7 - - - +
675B ASP* 1.3 62.3 + - - +
676B MET 3.2 2.1 + - - +
679B PHE* 4.0 11.5 - - - +
681B GLY* 3.2 18.9 + - - -
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Residues in contact with ASP 675 (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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671B LYS 4.0 7.6 + - - +
672B ALA 3.3 10.3 + - - +
673B CYS 3.1 1.4 - - - -
674B LYS* 1.3 77.8 - - - +
676B MET* 1.3 60.6 + - - +
681B GLY* 3.2 6.3 - - - -
682B THR* 3.4 22.9 + - - -
683B GLY* 2.9 21.9 + - - -
684B ARG* 3.0 8.1 + - - +
685B SER* 2.5 48.6 + - - -
686B LYS 4.1 0.7 + - - -
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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