Contacts of the helix formed by residues 703 - 714 (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 ASP 703 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591B GLU* 4.0 21.9 - - + +
701B THR* 3.2 18.2 + - - +
702B GLU* 1.3 75.3 - - - +
704B GLU* 1.3 65.4 + - - +
705B ASN* 3.0 17.7 + - - +
706B THR* 2.7 41.6 + - - +
707B ALA* 3.0 18.8 + - - -
721B TRP* 4.7 0.2 - - - -
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Residues in contact with GLU 704 (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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702B GLU 3.3 7.4 + - - +
703B ASP* 1.3 71.4 + - - +
705B ASN* 1.3 61.9 + - - +
707B ALA* 3.3 0.7 + - - +
708B GLU* 2.9 46.6 + - + +
721B TRP* 3.8 29.6 - - + -
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Residues in contact with ASN 705 (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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703B ASP* 3.0 12.8 + - - +
704B GLU* 1.3 80.5 - - - +
706B THR* 1.3 62.2 + - - +
708B GLU* 3.5 5.0 + - - +
709B PHE* 3.1 23.6 + - - +
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Residues in contact with THR 706 (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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589B ASP* 3.6 22.3 + - - +
591B GLU* 5.8 0.5 - - - +
681B VAL* 3.4 31.7 - - + +
699B ILE* 3.8 13.7 - - + -
701B THR* 4.5 0.7 - - - -
703B ASP* 2.7 35.1 + - - +
705B ASN* 1.3 70.5 - - - +
707B ALA* 1.3 65.1 + - - +
709B PHE* 3.1 8.6 + - - +
710B PHE* 3.0 22.7 + - - +
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Residues in contact with ALA 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B ILE* 4.1 8.5 - - - +
701B THR* 3.7 8.2 - - + +
703B ASP 3.0 10.1 + - - +
704B GLU 3.6 7.6 - - - +
706B THR* 1.3 76.2 - - - +
708B GLU* 1.3 57.9 + - - +
710B PHE* 3.3 3.1 + - - +
711B LEU* 2.9 34.3 + - - +
721B TRP* 3.2 52.0 - - + +
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Residues in contact with GLU 708 (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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704B GLU* 2.9 35.2 + - + +
705B ASN* 4.1 4.7 - - - +
707B ALA* 1.3 76.9 - - - +
709B PHE* 1.3 57.1 + - - +
711B LEU* 3.7 20.4 - - - +
712B GLN* 3.0 31.2 + - - +
721B TRP* 3.8 21.5 - - + -
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Residues in contact with PHE 709 (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* 4.5 15.3 - - + -
682B GLN* 3.7 27.1 - - + -
685B ILE* 3.7 20.9 - - + -
705B ASN 3.1 15.8 + - - +
706B THR* 3.3 11.2 - - - +
708B GLU* 1.3 76.3 - - - +
710B PHE* 1.3 56.2 + - - +
712B GLN* 3.3 2.5 + - - -
713B HIS* 2.8 68.1 + + - +
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Residues in contact with PHE 710 (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* 4.0 17.5 - + + -
681B VAL* 4.1 9.6 - - + -
684B ALA* 4.6 2.2 - - + -
685B ILE* 4.0 20.6 - - + -
688B ILE* 3.5 33.9 - - + -
697B ASP 4.1 2.5 - - - -
698B VAL 3.6 20.4 - - - -
699B ILE* 3.5 46.9 - - + -
706B THR 3.0 11.7 + - - +
707B ALA 3.5 7.9 - - - +
709B PHE* 1.3 72.0 - - - +
711B LEU* 1.3 61.8 + - + +
714B VAL* 2.9 47.0 + - + +
719B VAL* 3.6 23.8 - - + -
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Residues in contact with LEU 711 (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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699B ILE* 4.4 0.7 - - + -
707B ALA 2.9 19.9 + - - +
708B GLU* 3.7 31.0 - - - +
710B PHE* 1.3 80.3 - - + +
712B GLN* 1.3 61.8 + - - +
714B VAL 4.0 9.9 - - - +
719B VAL* 3.7 42.5 - - + +
720B PHE 3.8 20.4 - - - +
721B TRP* 4.0 21.5 - - + +
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Residues in contact with GLN 712 (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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708B GLU 3.0 18.0 + - - +
709B PHE* 3.7 5.4 - - - +
710B PHE 3.2 0.2 - - - -
711B LEU* 1.3 79.9 - - - +
713B HIS* 1.3 77.7 + - + +
714B VAL 3.6 3.3 - - - +
715B ASP* 5.0 2.6 - - - +
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Residues in contact with HIS 713 (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* 5.6 2.7 - - - +
685B ILE* 3.9 19.7 - - + -
689B HIS* 2.9 24.4 - - - -
709B PHE* 2.8 65.5 + + - +
712B GLN* 1.3 96.2 - - + +
714B VAL* 1.3 63.3 + - - +
715B ASP* 3.4 7.3 - - - +
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Residues in contact with VAL 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B ILE* 3.9 18.6 - - + -
688B ILE* 4.1 20.6 - - + -
689B HIS* 3.4 4.7 - - - +
697B ASP* 4.1 5.6 - - + -
710B PHE* 2.9 49.4 + - + +
711B LEU 4.0 6.2 - - - +
712B GLN 4.4 2.9 - - - +
713B HIS* 1.3 77.9 - - - +
715B ASP* 1.3 62.0 + - - +
716B SER* 3.3 27.1 + - - +
719B VAL* 3.6 28.6 - - + +
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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