Contacts of the helix formed by residues 680 - 692 (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 ASN 680 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587B TYR* 3.6 6.3 - - - -
621B HIS* 3.9 14.8 + - + -
622B ARG* 5.2 3.0 - - - +
678B VAL* 3.6 3.2 - - - +
679B ASP* 1.3 92.5 + - - +
681B VAL* 1.3 68.8 + - + +
682B GLN* 3.2 13.2 + - - +
683B ASP* 2.9 33.8 + - - +
684B ALA* 3.0 20.1 + - - +
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Residues in contact with VAL 681 (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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587B TYR* 3.3 31.0 + - + +
589B ASP* 4.2 1.8 - - - +
621B HIS* 5.2 0.4 - - + -
680B ASN* 1.3 73.5 - - + +
682B GLN* 1.3 56.9 + - - +
684B ALA* 3.2 3.8 + - - +
685B ILE* 2.8 41.5 + - + +
699B ILE* 4.3 0.2 - - + -
706B THR* 3.4 35.4 - - + +
709B PHE* 4.5 12.6 - - + -
710B PHE* 4.1 22.9 - - + -
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Residues in contact with GLN 682 (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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680B ASN* 3.2 11.2 + - - +
681B VAL* 1.3 77.7 - - - +
683B ASP* 1.3 53.0 + - - +
685B ILE* 3.3 18.7 + - - +
686B ASP* 2.8 72.0 + - - +
709B PHE* 3.7 28.2 - - + -
713B HIS* 5.6 2.6 - - - +
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Residues in contact with ASP 683 (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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649B LYS* 4.1 9.6 + - - -
678B VAL* 3.6 13.0 - - + +
679B ASP* 2.9 41.8 + - - +
680B ASN* 2.9 23.0 + - - +
682B GLN* 1.3 72.3 - - - +
684B ALA* 1.3 58.6 + - - +
686B ASP* 3.3 11.0 + - - +
687B HIS* 2.8 31.7 + - - +
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Residues in contact with ALA 684 (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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587B TYR* 3.5 46.7 - - + -
619B LEU* 4.1 11.0 - - + -
678B VAL* 4.1 6.4 - - + +
680B ASN 3.0 9.6 + - - +
681B VAL 3.3 8.7 - - - +
683B ASP* 1.3 76.2 - - - +
685B ILE* 1.3 57.4 + - - +
687B HIS* 3.2 3.5 + - - +
688B ILE* 2.9 35.1 + - - +
710B PHE* 4.6 3.4 - - + -
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Residues in contact with ILE 685 (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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681B VAL* 2.8 24.2 + - + +
682B GLN* 3.5 20.9 - - - +
684B ALA* 1.3 71.9 - - - +
686B ASP* 1.3 59.5 + - - +
688B ILE* 3.2 8.3 + - - +
689B HIS* 2.9 54.5 + - + +
709B PHE* 3.7 37.0 - - + -
710B PHE* 4.0 16.2 - - + -
713B HIS* 3.9 21.8 - - + +
714B VAL* 3.9 18.4 - - + -
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Residues in contact with ASP 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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682B GLN* 2.8 51.6 + - - +
683B ASP* 3.6 11.3 - - - +
685B ILE* 1.3 73.9 - - - +
687B HIS* 1.3 57.2 + - - +
689B HIS* 3.3 7.7 + - - +
690B LYS* 2.9 32.0 + - - +
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Residues in contact with HIS 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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585B HIS* 3.3 33.1 + + - -
617B THR* 3.9 6.0 + - + +
619B LEU* 3.7 30.0 - - + +
664B LEU* 4.0 24.8 + - + +
676B GLU* 4.3 10.8 - - + +
678B VAL* 4.8 4.7 - - + +
683B ASP 2.8 18.1 + - - +
684B ALA* 3.4 4.5 - - - +
686B ASP* 1.3 77.2 - - - +
688B ILE* 1.3 56.6 + - - +
690B LYS* 3.2 1.6 + - - -
691B TYR* 2.9 61.9 + + - +
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Residues in contact with ILE 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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585B HIS* 3.7 35.7 - - + +
587B TYR* 5.0 2.2 - - + -
619B LEU* 4.0 7.9 - - + -
684B ALA 2.9 21.4 + - - +
685B ILE* 3.2 5.6 + - - +
687B HIS* 1.3 74.3 - - - +
689B HIS* 1.3 62.4 + - + +
692B GLY* 2.8 28.7 + - - -
694B SER 5.7 0.8 + - - +
697B ASP* 3.6 31.0 - - + +
698B VAL 5.4 0.2 - - - +
710B PHE* 3.5 38.8 - - + -
714B VAL* 4.1 18.4 - - + -
716B SER* 4.2 2.5 - - - +
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Residues in contact with HIS 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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685B ILE* 2.9 33.6 + - + +
686B ASP* 3.8 7.1 + - - +
688B ILE* 1.3 87.5 - - + +
690B LYS* 1.3 64.2 + - - +
692B GLY 4.4 5.5 + - - +
713B HIS 2.9 24.0 + - - -
714B VAL* 3.4 4.6 - - + -
715B ASP* 3.0 47.0 + - + -
716B SER* 5.7 0.7 - - - -
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Residues in contact with LYS 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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665B ARG* 2.3 43.4 + - - +
686B ASP 2.9 17.7 + - - +
687B HIS* 3.7 3.8 - - - +
689B HIS* 1.3 80.7 - - - +
691B TYR* 1.3 94.7 + - + +
692B GLY 5.0 0.5 - - - +
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Residues in contact with TYR 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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581B GLU* 5.2 0.3 - - - +
583B ILE* 4.0 13.0 - - - +
585B HIS* 4.3 3.6 - - - +
664B LEU* 3.4 52.7 - - + +
665B ARG* 3.6 54.4 - - + +
687B HIS* 2.9 58.1 + + + +
690B LYS* 1.3 105.8 - - + +
692B GLY* 1.3 66.6 + - - +
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Residues in contact with GLY 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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581B GLU* 4.5 3.5 - - - +
583B ILE* 3.7 5.6 - - - -
585B HIS* 3.5 20.7 - - - -
688B ILE* 2.8 22.4 + - - +
689B HIS 4.6 4.7 - - - +
690B LYS 3.8 0.9 - - - +
691B TYR* 1.3 81.8 - - - +
693B SER* 1.3 59.6 + - - -
694B SER* 3.4 6.1 + - - -
697B ASP* 5.5 0.7 - - - -
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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