Contacts of the helix formed by residues 596 - 607 (chain B) in PDB entry 2H5G
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 LYS 596 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593B SER* 3.0 20.0 + - - +
595B ASP* 1.3 83.7 - - + +
597B VAL* 1.3 65.8 + - - +
598B THR 3.4 2.2 - - - -
599B ARG* 3.4 13.4 - - + +
600B LEU* 3.3 36.3 + - + +
700B VAL* 4.8 4.3 - - + -
702B GLU* 2.6 40.0 + - - +
722B ASN* 3.6 23.5 - - + +
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Residues in contact with VAL 597 (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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588B VAL* 4.0 13.5 - - + -
592B ALA* 3.7 25.8 - - + -
593B SER 3.2 17.4 + - - +
594B VAL 4.2 3.2 + - - +
595B ASP 3.9 0.4 - - - -
596B LYS* 1.3 76.6 - - - +
598B THR* 1.3 64.7 + - - +
600B LEU* 3.2 4.8 + - - +
601B VAL* 3.0 31.5 + - + +
629B LEU* 3.9 17.5 - - + -
633B ILE* 3.3 34.3 - - + -
700B VAL* 4.0 14.6 - - + -
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Residues in contact with THR 598 (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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594B VAL 5.0 5.8 + - - -
595B ASP 5.5 0.8 + - - -
596B LYS 3.4 0.2 - - - -
597B VAL* 1.3 78.6 - - - +
599B ARG* 1.3 57.4 + - - +
601B VAL* 3.2 1.1 + - - -
602B ARG* 2.8 53.9 + - - +
629B LEU 4.9 0.7 + - - -
632B GLN* 3.9 31.0 + - + +
633B ILE* 4.1 5.7 + - - +
636B MSE 3.5 37.1 - - + +
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Residues in contact with ARG 599 (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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306B SO4 3.0 39.6 + - - +
595B ASP 4.3 16.1 + - - +
596B LYS* 3.4 16.8 - - - +
598B THR* 1.3 76.7 - - - +
600B LEU* 1.3 67.6 + - + +
602B ARG* 3.5 25.8 + - - +
603B ASP* 3.0 31.7 + - - +
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Residues in contact with LEU 600 (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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586B MSE 4.0 13.5 - - + -
596B LYS* 3.3 27.6 - - + +
597B VAL 3.2 4.4 + - - +
598B THR 3.2 0.6 - - - -
599B ARG* 1.3 83.9 - - + +
601B VAL* 1.3 60.5 + - - +
603B ASP* 4.1 2.8 - - - +
604B SER* 2.7 34.8 + - - -
700B VAL* 3.8 31.9 - - + -
722B ASN* 4.0 17.0 - - + +
723B ALA* 3.7 13.9 - - - +
724B SER* 3.6 29.9 + - - +
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Residues in contact with VAL 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B MSE 3.8 21.3 - - - -
588B VAL* 4.7 0.2 - - + -
597B VAL* 3.0 34.0 + - + +
598B THR* 4.6 0.4 - - - -
600B LEU* 1.3 72.6 - - - +
602B ARG* 1.3 68.0 + - - +
604B SER* 3.4 1.0 + - - -
605B LYS* 3.0 24.6 + - + +
615B LEU* 3.9 17.4 - - + +
618B LEU* 3.9 29.8 - - + -
633B ILE* 4.7 4.9 - - + -
636B MSE 3.6 21.5 - - + -
637B LEU* 4.3 12.6 - - + -
673B LEU* 4.9 1.3 - - + -
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Residues in contact with ARG 602 (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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306B SO4 3.0 28.5 + - - -
598B THR* 2.8 40.9 + - - +
599B ARG* 3.7 20.9 + - - +
601B VAL* 1.3 76.0 - - - +
603B ASP* 1.3 54.9 + - - +
606B CYS* 2.7 44.4 + - + +
607B GLU 3.7 0.3 + - - -
636B MSE 3.5 28.4 - - - +
640B GLU* 3.5 29.9 + - + +
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Residues in contact with ASP 603 (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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599B ARG 3.0 18.3 + - - +
600B LEU* 4.1 2.2 - - - +
602B ARG* 1.3 75.4 - - - +
604B SER* 1.3 63.9 + - - +
607B GLU* 3.0 52.9 + - - +
724B SER* 2.7 32.3 + - - +
726B ARG* 3.7 13.2 - - - +
727B PHE* 5.3 1.9 - - - -
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Residues in contact with SER 604 (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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586B MSE 3.3 12.0 - - - +
600B LEU 2.7 23.2 + - - -
601B VAL 3.8 3.1 - - - -
603B ASP* 1.3 77.6 - - - +
605B LYS* 1.3 57.9 + - - +
608B TYR 5.4 0.2 - - - +
614B ALA* 3.3 11.4 - - - +
615B LEU* 2.8 38.1 + - - -
724B SER* 3.3 7.0 + - - -
725B THR* 3.2 38.2 + - - -
726B ARG* 4.2 4.8 - - - +
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Residues in contact with LYS 605 (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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601B VAL* 3.0 19.0 + - + +
604B SER* 1.3 77.1 - - - +
606B CYS* 1.3 73.6 + - - +
607B GLU 3.7 0.7 - - - -
608B TYR 4.3 0.6 - - - -
609B PRO* 3.5 26.0 + - - +
614B ALA* 4.6 2.9 - - - +
615B LEU* 2.7 38.1 + - + +
616B GLU* 3.5 17.8 + - - +
637B LEU* 5.1 1.3 - - + -
642B VAL* 4.2 16.2 - - + -
670B ASP 3.2 24.3 + - - +
671B LEU* 4.7 2.0 - - + +
672B GLU 2.8 27.2 + - - +
673B LEU* 3.9 18.2 - - + -
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Residues in contact with CYS 606 (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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602B ARG* 2.7 30.9 + - + +
605B LYS* 1.3 79.0 - - - +
607B GLU* 1.3 64.0 + - - +
608B TYR 3.2 3.0 + - - -
609B PRO* 3.6 9.7 - - - +
636B MSE 4.7 2.5 - - - -
637B LEU* 5.4 0.7 - - - -
640B GLU* 3.7 43.1 - - - +
642B VAL* 3.8 19.3 - - - -
671B LEU* 4.3 13.9 - - + +
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Residues in contact with GLU 607 (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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424B LYS* 5.2 3.5 + - - -
602B ARG 3.7 1.6 + - - -
603B ASP* 3.0 46.0 + - - +
606B CYS* 1.3 79.0 - - - +
608B TYR* 1.3 58.9 + - - +
609B PRO* 4.3 0.7 - - - +
726B ARG* 2.8 43.9 + - - +
732B ARG* 5.9 1.5 + - - -
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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