Contacts of the helix formed by residues 685 - 696 (chain B) in PDB entry 4KSP
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 PRO 685 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549B MET* 4.4 12.1 - - + -
553B ILE* 4.4 15.9 - - + -
683B ASN 3.3 10.2 - - - +
684B CYS* 1.3 90.7 - - - +
686B LYS* 1.3 65.5 + - - +
687B ALA* 4.4 7.0 - - + +
688B MET* 2.8 33.4 + - + +
689B LYS 3.4 4.0 + - - -
716B LEU* 4.6 14.1 - - + -
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Residues in contact with LYS 686 (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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684B CYS 4.4 7.0 - - - +
685B PRO* 1.3 78.3 - - - +
687B ALA* 1.3 63.3 + - - +
688B MET 3.2 0.2 + - - -
689B LYS* 3.3 17.8 + - + +
690B ARG* 3.0 24.8 + - - +
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Residues in contact with ALA 687 (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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685B PRO* 4.4 4.0 - - + +
686B LYS* 1.3 78.4 - - - +
688B MET* 1.3 55.0 + - - +
690B ARG* 3.4 11.5 - - - +
691B LEU* 2.9 27.4 + - - +
712B SER 5.7 0.7 - - - +
715B LEU* 6.3 2.7 - - + -
716B LEU* 3.6 31.9 - - + -
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Residues in contact with MET 688 (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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553B ILE* 4.2 23.3 - - + -
556B ALA* 5.1 2.2 - - + -
645B LEU* 3.8 28.9 - - + -
649B MET* 3.9 16.8 - - + -
684B CYS* 3.6 20.4 - - - -
685B PRO* 2.8 20.0 + - + +
687B ALA* 1.3 77.1 - - - +
689B LYS* 1.3 58.9 + - - +
691B LEU* 3.1 14.3 + - + +
692B MET* 2.8 31.6 + - + +
713B ILE* 4.5 14.1 - - + -
716B LEU* 3.7 32.0 - - + +
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Residues in contact with LYS 689 (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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677B LEU* 3.5 46.0 + - + +
678B SER* 4.5 5.5 - - - +
680B VAL* 3.6 28.3 - - + +
684B CYS* 4.3 15.3 - - - +
685B PRO 3.4 3.7 + - - +
686B LYS* 3.3 20.1 + - + +
688B MET* 1.3 77.5 - - - +
690B ARG* 1.3 58.8 + - - +
692B MET* 3.3 11.4 - - + +
693B ALA* 3.0 28.4 + - - +
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Residues in contact with ARG 690 (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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686B LYS 3.0 15.0 + - - +
687B ALA* 3.4 9.6 - - - +
689B LYS* 1.3 78.7 - - - +
691B LEU* 1.3 61.9 + - - +
693B ALA* 3.3 15.5 + - + +
694B GLU* 3.3 31.0 + - + +
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Residues in contact with LEU 691 (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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645B LEU* 4.2 18.6 - - + -
687B ALA 2.9 15.7 + - - +
688B MET* 3.1 17.5 + - + +
690B ARG* 1.3 74.1 - - - +
692B MET* 1.3 66.2 + - - +
694B GLU* 3.2 8.5 + - + +
695B CYS* 3.1 25.1 + - - -
704B PRO* 5.2 6.3 - - + -
708B GLN 5.7 0.2 - - - -
709B ILE* 4.1 26.5 - - + +
712B SER* 4.3 24.0 - - - +
713B ILE* 3.6 37.2 - - + -
716B LEU* 5.8 1.8 - - + -
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Residues in contact with MET 692 (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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642B GLY 4.1 6.5 - - - +
645B LEU* 3.5 32.5 - - + +
646B TYR* 3.9 24.9 - - - -
649B MET* 3.7 29.8 - - + -
677B LEU* 4.2 22.0 - - + -
680B VAL* 3.7 19.5 - - + -
684B CYS* 4.5 0.7 - - - -
688B MET* 2.8 14.2 + - + +
689B LYS* 3.3 25.1 - - + +
691B LEU* 1.3 72.3 - - - +
693B ALA* 1.3 63.9 + - - +
695B CYS* 3.3 4.2 + - - +
696B LEU* 3.1 32.2 + - + +
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Residues in contact with ALA 693 (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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677B LEU* 4.2 20.2 - - + -
689B LYS 3.0 13.8 + - - +
690B ARG* 3.5 12.8 - - + +
691B LEU 3.2 0.4 - - - -
692B MET* 1.3 74.9 - - - +
694B GLU* 1.3 65.5 + - - +
696B LEU* 3.3 13.5 + - - +
697B LYS* 3.3 22.6 + - - +
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Residues in contact with GLU 694 (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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690B ARG* 3.4 27.9 + - + +
691B LEU* 3.2 10.9 + - + +
693B ALA* 1.3 77.0 - - - +
695B CYS* 1.3 65.5 + - - +
696B LEU 3.3 0.7 + - - -
697B LYS* 3.4 44.3 + - - +
702B GLU 4.4 5.7 - - - +
703B ARG* 3.7 4.5 - - - -
704B PRO* 3.5 29.7 - - + +
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Residues in contact with CYS 695 (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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638B VAL* 4.0 15.0 - - - +
639B TYR* 3.4 14.7 - - - -
641B PHE* 4.1 14.6 - - - -
642B GLY* 3.7 19.1 - - - -
645B LEU* 4.4 3.1 - - - -
691B LEU* 3.1 25.4 + - - -
692B MET* 3.6 8.1 - - - +
694B GLU* 1.3 79.5 - - - +
696B LEU* 1.3 59.6 + - - +
703B ARG* 3.1 19.9 - - - -
704B PRO* 4.4 2.5 - - - -
709B ILE* 3.8 33.2 - - - -
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Residues in contact with LEU 696 (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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639B TYR* 3.5 28.7 - - + +
642B GLY* 3.6 27.1 - - - +
643B ILE* 3.5 29.8 - - + +
646B TYR* 5.2 2.7 - - + -
675B PRO* 3.8 27.4 - - + +
677B LEU* 4.2 22.9 - - + -
692B MET* 3.1 23.3 + - + +
693B ALA* 3.3 7.4 + - - +
694B GLU 3.1 0.4 - - - -
695B CYS* 1.3 75.8 - - - +
697B LYS* 1.3 69.6 + - - +
698B LYS* 3.5 7.3 + - - +
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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