Contacts of the helix formed by residues 682 - 703 (chain B) in PDB entry 3K23
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 SER 682 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B LEU* 3.4 18.1 - - - +
588B HIS* 3.7 13.5 + - - -
591B ASP* 2.6 22.6 + - - -
680B LEU* 2.7 9.3 + - - -
681B LYS* 1.3 77.0 - - - +
683B GLN* 1.3 62.5 + - - +
684B GLU* 3.2 4.0 - - - -
685B LEU* 3.1 12.9 + - - +
686B PHE* 3.0 19.8 + - - +
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Residues in contact with GLN 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B VAL* 4.5 10.9 - - - +
679B GLY* 3.4 10.1 - - - -
680B LEU* 2.7 49.4 + - - +
682B SER* 1.3 72.9 - - - +
684B GLU* 1.3 67.4 + - - +
686B PHE* 3.1 33.0 + - - -
687B ASP* 3.1 45.9 + - - +
772B LEU* 6.0 1.2 - - - +
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Residues in contact with GLU 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B SER* 3.2 2.2 - - - -
683B GLN* 1.3 78.8 - - - +
685B LEU* 1.3 60.5 + - - +
687B ASP* 4.1 1.8 + - - +
688B GLU* 3.5 31.5 + - - +
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Residues in contact with LEU 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B GLY* 4.6 2.9 - - - +
586B ASN* 3.6 39.3 - - + +
587B LEU* 4.0 13.9 - - + +
682B SER* 3.1 16.0 + - - +
684B GLU* 1.3 77.3 - - - +
686B PHE* 1.3 67.1 + - - +
688B GLU* 3.3 13.1 + - + +
689B ILE* 3.1 36.8 + - + +
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Residues in contact with PHE 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B LEU* 3.9 16.0 - - + +
595B LEU* 3.8 31.2 - - + -
672B LEU* 3.5 43.2 - - + +
675B VAL* 3.7 13.0 - - + -
680B LEU* 3.1 28.5 - - + -
682B SER 3.0 11.4 + - - +
683B GLN* 3.1 19.9 + - - +
685B LEU* 1.3 75.4 - - - +
687B ASP* 1.3 77.7 + - - +
689B ILE* 3.0 8.4 + - - +
690B ARG* 2.9 33.4 + - - +
772B LEU* 3.8 15.9 - - + -
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Residues in contact with ASP 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B GLN* 3.1 39.0 + - - +
684B GLU* 4.7 1.8 - - - +
686B PHE* 1.3 98.0 - - - +
688B GLU* 1.3 59.0 + - + +
690B ARG* 3.9 10.1 - - - +
691B MET* 3.1 35.0 + - + +
772B LEU* 5.3 2.9 - - - +
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Residues in contact with GLU 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B GLU* 3.5 19.1 + - - +
685B LEU* 3.3 14.6 + - + +
686B PHE 3.2 0.6 - - - -
687B ASP* 1.3 78.2 - - + +
689B ILE* 1.3 64.3 + - - +
691B MET* 3.4 14.9 - - + +
692B THR* 3.3 24.6 - - - +
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Residues in contact with ILE 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B ILE* 6.1 0.4 - - + -
582B PRO 4.6 5.8 - - - +
583B GLY* 2.9 41.3 - - - +
584B PHE* 4.1 1.8 - - + +
587B LEU* 4.0 22.0 - - + -
672B LEU* 4.0 19.5 - - + -
685B LEU* 3.1 32.1 + - + +
686B PHE* 3.0 7.5 + - - +
688B GLU* 1.3 72.3 - - - +
690B ARG* 1.3 67.6 + - - +
691B MET 3.0 2.3 + - - -
692B THR* 3.1 22.7 + - - -
693B TYR* 3.2 29.4 - - + -
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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
----------------------------------------------------------
669B LEU* 3.6 15.0 + - + +
672B LEU* 3.1 42.4 + - + +
673B SER* 4.8 3.8 - - - +
686B PHE* 2.9 24.6 + - + +
687B ASP* 3.9 11.4 - - - +
688B GLU 3.5 0.2 - - - -
689B ILE* 1.3 77.0 - - - +
691B MET* 1.3 61.6 + - - +
693B TYR 3.6 0.9 + - - -
694B ILE* 3.1 45.2 + - + +
772B LEU* 3.6 35.8 + - - +
773B LEU 4.5 6.3 + - - -
774B PHE* 3.1 42.0 - - - -
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Residues in contact with MET 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B ASP* 3.1 21.9 + - + +
688B GLU* 3.4 17.7 - - + +
689B ILE 3.0 0.6 - - - -
690B ARG* 1.3 75.0 - - - +
692B THR* 1.3 63.2 + - + +
694B ILE* 2.8 40.3 + - + +
695B LYS* 3.1 14.0 + - + +
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Residues in contact with THR 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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532B LEU* 4.0 12.5 - - - +
688B GLU 3.3 16.2 - - - +
689B ILE* 3.1 14.3 + - - -
691B MET* 1.3 78.1 - - + +
693B TYR* 1.3 69.5 + - - +
695B LYS* 3.3 27.4 - - - +
696B GLU* 2.9 28.4 + - - +
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Residues in contact with TYR 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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532B LEU* 3.5 29.4 - - + +
536B LEU* 4.1 20.4 - - + +
581B ILE* 3.4 16.1 - - + +
582B PRO* 3.2 36.4 + - - +
665B CYS* 4.6 7.4 - - - +
668B THR* 3.9 25.1 - - + -
669B LEU* 3.5 34.0 - - + +
672B LEU* 4.2 8.5 - - + -
689B ILE* 3.2 40.4 + - + -
690B ARG 3.9 0.7 - - - +
691B MET 3.2 0.8 - - - -
692B THR* 1.3 81.2 + - - +
694B ILE* 1.3 63.8 + - - +
696B GLU* 3.7 9.5 - - + +
697B LEU* 3.3 17.5 + - - +
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Residues in contact with ILE 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B LEU* 4.1 16.6 - - + -
690B ARG* 3.1 46.2 + - + +
691B MET* 2.8 31.5 + - - +
693B TYR* 1.3 79.4 - - - +
695B LYS* 1.3 59.6 - - + +
697B LEU* 3.6 4.7 - - - +
698B GLY 3.3 13.0 + - - -
715B PHE* 3.6 34.7 - - + -
774B PHE* 4.2 12.6 - - + -
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Residues in contact with LYS 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B MET* 3.1 10.0 + - + +
692B THR* 3.3 33.1 - - - +
694B ILE* 1.3 76.5 - - + +
696B GLU* 1.3 57.6 + - - +
697B LEU 3.2 0.4 - - - -
698B GLY* 2.8 6.6 + - - +
699B LYS* 2.6 69.7 + - + +
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Residues in contact with GLU 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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531B THR* 4.4 4.0 - - - -
532B LEU* 3.3 35.9 + - + +
533B VAL* 3.2 33.7 + - + +
665B CYS* 3.7 18.4 - - - -
692B THR 2.9 20.0 + - - +
693B TYR* 3.8 14.1 - - + +
694B ILE 3.4 0.2 - - - -
695B LYS* 1.3 74.9 - - - +
697B LEU* 1.3 60.0 + - - +
699B LYS* 3.5 32.0 + - - +
700B ALA* 2.9 25.6 + - - +
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Residues in contact with LEU 697 (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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662B GLU* 3.4 44.6 - - + +
665B CYS* 3.6 15.3 - - + -
666B MET* 3.9 20.6 - - + +
669B LEU* 4.9 11.0 - - + -
693B TYR 3.3 11.8 + - - +
694B ILE* 3.6 10.3 - - - +
695B LYS 3.2 0.2 - - - -
696B GLU* 1.3 78.3 - - - +
698B GLY* 1.3 50.5 + - - +
700B ALA* 2.9 5.7 + - - +
701B ILE* 2.7 51.8 + - + +
715B PHE* 4.7 12.6 - - + -
718B LEU* 4.8 10.5 - - + -
719B THR* 4.8 11.9 - - + +
722B LEU* 5.6 2.7 - - + -
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Residues in contact with GLY 698 (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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694B ILE 3.3 7.4 + - - -
695B LYS* 2.8 11.4 + - - -
697B LEU* 1.3 78.8 - - - +
699B LYS* 1.3 49.4 + - - -
701B ILE* 3.2 13.4 + - - +
702B VAL* 2.7 45.2 + - - +
715B PHE* 4.8 6.2 - - - -
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Residues in contact with LYS 699 (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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695B LYS* 2.6 56.5 + - + +
696B GLU* 3.7 30.2 + - - +
698B GLY* 1.3 73.7 - - - +
700B ALA* 1.3 58.2 + - - +
702B VAL* 4.2 6.7 - - - +
703B LYS* 2.9 33.3 + - - +
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Residues in contact with ALA 700 (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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533B VAL* 5.6 2.7 - - + -
659B SER* 4.9 1.7 + - - -
661B GLU* 4.1 33.0 - - + +
662B GLU* 3.9 25.2 - - + +
665B CYS* 4.4 2.2 - - - -
696B GLU 2.9 14.8 + - - +
697B LEU* 2.9 16.7 + - - +
699B LYS* 1.3 76.9 - - - +
701B ILE* 1.3 58.7 + - - +
703B LYS* 3.9 14.4 - - - +
704B ARG* 4.0 4.7 + - - +
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Residues in contact with ILE 701 (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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662B GLU* 3.2 22.0 - - + +
697B LEU* 2.7 33.3 + - + +
698B GLY* 3.2 6.9 + - - +
700B ALA* 1.3 72.2 - - - +
702B VAL* 1.3 58.7 + - + +
703B LYS 3.1 1.6 - - - -
704B ARG* 2.8 25.0 + - - +
711B ASN* 3.0 54.7 + - + +
714B ARG* 4.3 11.4 - - - -
715B PHE* 3.9 43.3 - - + +
718B LEU* 4.5 8.3 - - + -
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Residues in contact with VAL 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B GLY* 2.7 27.3 + - - +
699B LYS* 4.2 6.1 - - - +
701B ILE* 1.3 74.3 - - + +
703B LYS* 1.3 56.4 + - - +
704B ARG 3.2 2.9 + - - -
705B GLU 3.5 15.6 - - - +
711B ASN* 4.3 10.5 - - + +
712B TRP* 5.5 13.2 - - + -
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Residues in contact with LYS 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B GLU* 5.0 11.7 - - - +
699B LYS 2.9 20.5 + - - +
700B ALA* 3.9 8.6 - - - +
701B ILE 3.1 0.4 - - - -
702B VAL* 1.3 75.4 - - - +
704B ARG* 1.3 56.4 + - - -
705B GLU 5.0 0.4 - - - -
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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
------------------------------------------------------------
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