Contacts of the helix formed by residues 688 - 703 (chain A) in PDB entry 2HWK
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 HIS 688 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A LEU* 3.8 37.9 - - + +
600A VAL* 5.1 8.6 - - + +
610A LEU* 3.8 23.8 - - + -
611A VAL 6.1 0.9 - - - -
685A TYR* 3.4 18.0 - - - -
687A TYR* 1.3 93.9 - - + +
689A HIS* 1.3 71.6 + - + +
690A TYR* 2.8 35.2 + - + +
691A GLN* 3.0 20.5 + - + +
692A GLN* 3.0 10.9 + - - +
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Residues in contact with HIS 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A LEU* 3.6 28.4 - - + +
611A VAL* 3.3 25.9 + - + +
685A TYR* 3.4 13.4 + - - -
688A HIS* 1.3 80.3 + - + +
690A TYR* 1.3 64.3 + - - +
692A GLN* 3.1 3.0 + - - +
693A CYS* 2.9 25.8 + - + +
722A TYR* 2.7 30.5 + - + -
755A THR* 3.7 27.6 - - + +
784A TYR* 3.5 42.1 - + - -
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Residues in contact with TYR 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ASN* 4.0 11.6 + - - -
521A VAL* 4.3 9.1 - - + +
527A ASP* 4.9 2.4 + - - -
599A LEU 3.4 23.3 - - - +
600A VAL* 4.1 9.6 - - + -
601A PRO* 3.5 37.3 - - + +
604A ARG* 5.0 0.2 - - - -
606A LEU* 4.2 4.5 - - + -
610A LEU* 4.4 4.6 - - + +
688A HIS* 2.8 22.4 + - + +
689A HIS* 1.3 78.7 - - - +
691A GLN* 1.3 63.4 + - - +
693A CYS* 3.3 1.2 + - - +
694A GLU* 2.9 45.0 + - - +
725A ALA* 3.6 44.2 - - + -
726A ASP* 3.5 20.0 - - + +
727A ARG 4.8 0.5 + - - -
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Residues in contact with GLN 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ARG* 5.1 2.9 - - - +
599A LEU 4.9 1.7 + - - +
683A THR* 5.1 0.2 - - - +
684A PRO 3.3 20.4 + - - -
685A TYR* 3.9 1.4 - - - -
686A LYS* 2.9 40.0 + - + +
687A TYR* 3.3 48.4 + - + +
688A HIS* 3.0 20.0 + - + +
690A TYR* 1.3 84.2 - - - +
692A GLN* 1.3 57.5 + - - +
694A GLU* 3.4 3.4 + - - +
695A ASP* 2.8 59.9 + - - +
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Residues in contact with GLN 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A THR* 2.7 32.8 + - - +
684A PRO 3.8 9.6 - - - +
685A TYR* 3.2 22.2 - - + +
688A HIS 3.0 11.8 + - - +
689A HIS 3.1 6.5 + - - +
691A GLN* 1.3 83.6 - - - +
693A CYS* 1.3 66.6 + - - +
695A ASP* 3.5 1.7 + - - +
696A HIS* 3.1 23.2 + - - +
722A TYR* 3.4 26.7 + - + +
753A GLU* 2.9 22.9 + - - +
755A THR* 2.6 30.7 + - - +
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Residues in contact with CYS 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A HIS* 2.9 17.2 + - + +
690A TYR 3.8 3.1 - - - +
692A GLN* 1.3 78.7 - - - +
694A GLU* 1.3 61.6 + - - +
696A HIS* 3.2 13.6 + - - +
697A ALA 3.4 8.0 + - - -
700A LEU* 5.7 0.4 - - - +
722A TYR* 3.8 23.1 - - + +
723A GLY 3.5 25.8 - - - -
724A TYR* 3.7 1.3 - - - -
725A ALA* 3.4 30.7 - - + -
726A ASP* 3.3 18.5 - - - +
729A SER* 3.7 4.9 + - - -
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Residues in contact with GLU 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A HIS* 5.7 1.2 + - - -
514A ILE* 3.9 17.8 - - + +
517A ASN* 2.7 34.6 + - - +
518A GLN* 3.7 41.4 + - - +
521A VAL* 4.8 2.1 - - - +
690A TYR* 2.9 39.9 + - + +
691A GLN* 4.1 3.5 - - - +
693A CYS* 1.3 77.9 - - - +
695A ASP* 1.3 60.3 + - - +
697A ALA* 3.3 14.4 + - - +
698A ILE 4.6 0.7 + - - -
726A ASP* 3.3 26.4 + - + +
728A ALA* 6.2 0.6 - - + +
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Residues in contact with ASP 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ASP* 5.5 8.9 + - - +
503A TYR* 5.5 1.2 - - - -
510A HIS* 5.4 6.4 + - - -
518A GLN* 3.4 28.6 + - - +
522A ARG* 4.9 3.8 + - - -
683A THR* 3.4 21.7 - - + +
686A LYS* 4.8 6.2 + - - +
691A GLN* 2.8 44.5 + - - +
692A GLN 3.5 0.4 + - - +
693A CYS 3.3 0.2 - - - -
694A GLU* 1.3 76.5 - - - +
696A HIS* 1.3 60.2 + - - +
697A ALA 3.2 0.6 + - - -
698A ILE* 3.9 17.9 - - - +
699A LYS* 4.0 9.4 - - - -
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Residues in contact with HIS 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A VAL* 6.1 2.4 - - + +
681A VAL* 3.4 30.5 - - + -
683A THR* 2.7 24.1 + - - +
692A GLN 3.1 17.5 + - - +
693A CYS* 3.5 6.3 - - - +
694A GLU 3.2 0.8 - - - -
695A ASP* 1.3 76.3 - - - +
697A ALA* 1.3 64.6 + - - +
698A ILE 3.3 1.6 - - - -
699A LYS* 3.0 21.6 + - + +
700A LEU* 3.0 41.6 + - + +
719A SER* 4.8 1.0 + - - -
720A ILE 3.1 21.8 + - - -
721A GLY* 4.0 4.5 - - - -
722A TYR* 3.5 27.1 - + + -
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Residues in contact with ALA 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 4.3 9.9 - - + -
693A CYS 3.4 2.4 + - - +
694A GLU 3.3 14.1 + - - +
695A ASP 3.2 1.4 - - - -
696A HIS* 1.3 78.5 - - - +
698A ILE* 1.3 64.3 + - - +
700A LEU* 2.9 19.6 + - - +
701A SER* 2.9 14.0 + - - -
726A ASP* 3.8 11.0 - - - +
728A ALA* 4.2 16.2 - - + -
729A SER* 3.4 25.6 - - - +
732A ILE* 3.7 2.7 - - + +
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Residues in contact with ILE 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A FMT 4.6 7.4 - - - -
503A TYR* 3.6 36.3 - - + +
509A ALA 4.7 1.3 - - - +
510A HIS* 3.5 34.3 - - + +
511A SER* 3.7 33.4 - - - +
514A ILE* 4.2 8.3 - - + +
664A ASP* 5.8 0.9 - - - +
694A GLU 4.6 1.0 + - - -
695A ASP 3.9 14.3 + - - +
697A ALA* 1.3 78.3 - - - +
699A LYS* 1.3 59.8 + - + +
701A SER* 3.4 4.4 + - - -
702A MET* 2.9 57.0 + - + +
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Residues in contact with LYS 699 (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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503A TYR* 3.2 35.4 - - - +
508A LYS* 6.1 0.4 - - - +
679A VAL* 6.1 1.8 - - + -
681A VAL* 3.6 26.4 - - + +
682A ARG 3.3 14.3 + - - -
683A THR* 3.0 35.4 + - - +
684A PRO* 4.6 4.6 - - - +
695A ASP 4.0 11.7 - - - +
696A HIS* 3.0 18.5 + - + +
698A ILE* 1.3 77.8 - - + +
700A LEU* 1.3 59.9 + - - +
702A MET* 4.5 3.6 - - - +
703A LEU* 2.9 44.2 + - + +
704A THR* 3.5 1.9 + - - -
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Residues in contact with LEU 700 (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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693A CYS* 6.2 0.2 - - - -
696A HIS* 3.0 40.1 + - + +
697A ALA* 2.9 9.9 + - - +
699A LYS* 1.3 77.7 - - - +
701A SER* 1.3 55.9 + - - +
704A THR* 3.2 24.0 + - + +
705A LYS* 2.8 29.6 + - - +
719A SER* 4.0 7.4 - - - +
720A ILE 4.3 2.7 - - - +
723A GLY 4.7 5.6 - - - +
729A SER* 3.8 35.7 - - - +
732A ILE* 3.8 15.2 - - + +
733A ILE* 4.1 26.7 - - + -
759A PHE* 4.9 6.5 - - + -
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Residues in contact with SER 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 5.5 3.4 - - - -
697A ALA 2.9 7.0 + - - -
698A ILE* 3.7 13.5 - - - -
700A LEU* 1.3 78.9 - - - +
702A MET* 1.3 78.8 + - - +
705A LYS* 3.4 29.6 + - - +
706A LYS* 3.9 9.4 + - - +
732A ILE* 3.6 24.0 - - - +
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Residues in contact with MET 702 (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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102A FMT 4.3 26.7 - - - -
663A LEU 4.4 5.8 - - - +
664A ASP* 4.0 21.3 - - - +
665A LEU* 4.6 6.7 - - - +
666A GLY* 3.2 28.9 - - - +
667A ILE 3.3 2.4 + - - -
698A ILE* 2.9 37.3 + - + +
699A LYS* 4.4 2.0 - - - +
701A SER* 1.3 98.2 - - - +
703A LEU* 1.3 62.0 + - + +
706A LYS* 3.2 36.8 - - - +
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Residues in contact with LEU 703 (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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637A VAL* 4.1 18.6 - - + -
663A LEU* 3.7 37.9 - - + +
666A GLY* 4.0 6.1 - - - -
667A ILE* 3.2 27.1 - - + +
679A VAL* 4.1 14.4 - - + -
681A VAL* 3.8 35.0 - - + -
699A LYS* 2.9 21.5 + - + +
702A MET* 1.3 89.4 - - + +
704A THR* 1.3 61.7 + - - +
705A LYS 3.4 1.1 - - - -
706A LYS 3.4 0.9 + - - -
707A ALA* 2.9 26.0 + - - +
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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