Contacts of the helix formed by residues 656 - 664 (chain B) in PDB entry 4K6J
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 ASP 656 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652B GLN* 3.7 32.4 + - - +
654B PHE 3.1 0.6 - - - -
655B THR* 1.3 83.9 + - - +
657B ASP* 1.3 65.4 + - - +
658B ILE 2.9 10.3 + - - -
659B GLU* 3.3 16.6 + - - +
660B TYR* 4.0 7.0 + - - +
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Residues in contact with ASP 657 (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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652B GLN 3.9 9.4 + - - +
653B GLU* 3.6 23.1 - - - +
654B PHE* 3.3 2.6 + - - -
656B ASP* 1.3 78.3 - - - +
658B ILE* 1.3 61.0 + - - +
659B GLU 3.5 0.2 - - - -
660B TYR* 3.2 40.2 + - + +
661B LEU* 3.2 24.5 + - + +
684B LYS* 3.6 24.5 + - - -
690B PHE* 5.1 2.2 - - + -
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Residues in contact with ILE 658 (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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654B PHE* 2.8 41.2 + - + +
655B THR* 3.3 11.2 - - - +
656B ASP 2.9 0.2 + - - -
657B ASP* 1.3 77.6 - - - +
659B GLU* 1.3 86.2 - - - +
661B LEU* 4.6 2.9 - - + -
662B LEU* 3.0 49.4 + - + +
681B LEU* 4.5 9.0 - - + -
690B PHE* 4.2 14.1 - - + -
694B LEU* 3.6 29.2 - - + -
699B MET* 3.8 15.9 - - + -
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Residues in contact with GLU 659 (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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655B THR* 3.5 16.9 - - - +
656B ASP* 3.3 6.3 + - - +
658B ILE* 1.3 93.4 - - - +
660B TYR* 1.3 57.2 + - - +
662B LEU* 4.0 14.0 - - - +
663B SER* 3.2 25.6 + - - -
699B MET* 4.5 8.2 - - - +
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Residues in contact with TYR 660 (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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656B ASP 4.0 4.4 + - - +
657B ASP* 3.2 53.3 + - + -
658B ILE 3.2 0.2 - - - -
659B GLU* 1.3 79.2 - - - +
661B LEU* 1.3 92.1 + - + +
662B LEU 3.2 0.2 - - - -
663B SER* 2.8 19.9 + - - -
664B GLY* 3.2 9.4 + - - -
677B SER* 4.9 0.7 + - - -
680B SER* 4.1 7.4 + - - -
684B LYS* 4.1 6.9 + - - -
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Residues in contact with LEU 661 (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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657B ASP* 3.2 21.6 + - + +
658B ILE* 3.5 4.9 + - + +
660B TYR* 1.3 103.9 - - + +
662B LEU* 1.3 62.4 + - - +
664B GLY* 3.3 9.9 + - - -
665B LEU* 3.3 17.8 + - - +
677B SER* 3.7 22.5 - - - +
680B SER* 3.4 32.5 - - - +
681B LEU* 4.0 29.2 - - + -
684B LYS* 3.9 29.4 - - + -
690B PHE* 4.5 4.5 - - + -
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Residues in contact with LEU 662 (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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658B ILE* 3.0 37.9 + - + +
659B GLU* 4.0 12.8 - - - +
661B LEU* 1.3 73.5 - - - +
663B SER* 1.3 65.7 + - - +
664B GLY 3.0 1.6 - - - -
665B LEU* 2.9 31.6 + - + +
666B LYS* 3.9 10.5 + - - +
681B LEU* 5.3 3.1 - - + -
699B MET* 3.7 32.1 - - + -
702B MET* 3.6 40.1 - - + +
703B VAL* 4.1 19.1 - - + -
706B THR* 4.9 0.9 - - - +
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Residues in contact with SER 663 (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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659B GLU 3.2 14.4 + - - -
660B TYR* 2.8 24.6 + - - +
662B LEU* 1.3 77.6 - - - +
664B GLY* 1.3 59.3 + - - +
665B LEU 3.1 1.7 + - - -
666B LYS* 3.4 30.2 + - - +
669B GLN* 3.7 11.5 - - - +
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Residues in contact with GLY 664 (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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660B TYR 3.2 12.3 + - - -
661B LEU 3.7 1.6 - - - -
662B LEU 3.0 1.6 - - - -
663B SER* 1.3 77.0 + - - +
665B LEU* 1.3 58.2 + - - +
666B LYS 3.4 0.7 - - - -
669B GLN* 3.9 14.9 - - - +
673B THR* 3.6 5.1 - - - +
674B ARG* 3.3 23.4 + - - +
677B SER* 3.2 28.6 + - - -
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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
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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