Contacts of the helix formed by residues 721 - 730 (chain B) in PDB entry 1GUX
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 PHE 721 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705B MET* 3.9 35.4 - - + -
706B CYS* 4.0 18.8 - - - -
709B TYR* 3.5 30.7 - + + -
719B LEU 3.7 2.0 + - - -
720B LYS* 1.3 70.3 - - - +
722B LYS* 1.3 58.2 + - - +
724B ILE* 2.9 15.8 + - + +
725B VAL* 2.8 38.1 + - + +
752B ILE* 3.8 28.0 - - + -
753B ILE* 3.9 22.4 - - + -
756B TYR* 3.7 26.5 - + + -
4E CYS* 4.0 11.2 - - + -
6E GLU* 2.9 17.8 + - - +
8E LEU* 5.1 0.7 - - - -
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Residues in contact with LYS 722 (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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720B LYS* 3.2 10.2 - - + +
721B PHE* 1.3 78.0 - - - +
723B ILE* 1.3 86.5 + - - +
725B VAL* 3.8 4.3 - - + +
726B THR* 2.9 43.1 + - - +
6E GLU* 3.2 16.5 + - - +
7E GLN 5.9 0.7 - - - +
8E LEU* 4.2 17.3 - - + +
9E ASN* 3.5 26.9 - - - +
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Residues in contact with ILE 723 (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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669B LEU* 4.0 14.5 - - + +
719B LEU* 3.9 20.9 - - + -
720B LYS* 3.1 30.9 + - + +
722B LYS* 1.3 100.1 - - - +
724B ILE* 1.3 65.9 + - - +
726B THR* 3.6 7.5 + - + +
727B ALA* 3.1 23.2 + - - +
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Residues in contact with ILE 724 (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 LEU* 4.6 3.1 - - + +
669B LEU* 3.8 10.9 - - + +
705B MET* 3.8 37.2 - - + +
708B MET* 4.4 15.5 - - + -
709B TYR* 3.7 38.6 - - + +
719B LEU* 3.8 29.4 - - + -
720B LYS 3.1 14.1 + - - +
721B PHE* 2.9 16.7 + - + +
723B ILE* 1.3 77.4 - - - +
725B VAL* 1.3 51.7 + - - +
727B ALA* 3.1 5.2 + - - +
728B TYR* 2.7 32.6 + - - +
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Residues in contact with VAL 725 (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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705B MET* 4.1 10.8 - - - -
721B PHE* 2.8 20.7 + - + +
722B LYS* 3.8 7.6 - - + +
724B ILE* 1.3 73.9 - - - +
726B THR* 1.3 67.7 + - - +
728B TYR* 3.4 8.6 - - - +
729B LYS* 3.2 20.2 + - - +
739B PHE* 3.4 64.7 - - + -
752B ILE* 4.1 7.6 - - + -
8E LEU* 4.1 22.4 - - + -
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Residues in contact with THR 726 (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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722B LYS* 2.9 33.7 + - - +
723B ILE* 3.8 9.0 - - + +
725B VAL* 1.3 75.6 - - - +
727B ALA* 1.3 63.1 + - - +
729B LYS* 3.5 38.3 + - - +
730B ASP* 4.1 8.5 + - - +
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Residues in contact with ALA 727 (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 LEU* 3.9 7.4 - - + +
668B ARG* 2.5 37.9 + - - +
669B LEU* 3.5 31.9 - - + -
723B ILE 3.1 17.1 + - - +
724B ILE 3.1 5.2 + - - +
726B THR* 1.3 74.5 - - - +
728B TYR* 1.3 67.8 + - - +
730B ASP* 3.0 9.4 + - - -
731B LEU 4.1 0.5 + - - -
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Residues in contact with TYR 728 (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 LEU* 3.8 11.0 - - + +
699B HIS* 4.0 2.3 - - - -
701B ASP* 2.5 46.5 + - + +
704B MET* 4.1 9.0 - - + -
705B MET* 3.6 27.6 - - + -
724B ILE 2.7 15.9 + - - +
725B VAL 3.4 6.1 - - - +
726B THR 3.3 0.2 - - - -
727B ALA* 1.3 77.3 - - - +
729B LYS* 1.3 61.6 + - - +
731B LEU* 3.0 31.5 + - + +
733B HIS* 3.7 6.5 - + - -
734B ALA* 3.0 36.3 - - + +
735B VAL 4.1 16.1 + - - -
738B THR* 3.8 14.7 + - - +
739B PHE* 3.6 24.0 - + - -
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Residues in contact with LYS 729 (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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725B VAL* 3.2 13.7 + - - +
726B THR* 3.5 42.3 + - - +
727B ALA 3.2 0.6 - - - -
728B TYR* 1.3 76.3 - - + +
730B ASP* 1.3 65.4 + - - +
731B LEU 3.2 7.4 + - - +
734B ALA* 3.8 14.4 - - - +
735B VAL 5.6 0.2 - - - -
736B GLN* 4.6 22.1 - - + +
739B PHE* 3.7 26.6 - - + -
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Residues in contact with ASP 730 (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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668B ARG* 3.6 29.5 + - - +
726B THR 4.5 7.2 - - - +
727B ALA* 3.0 5.9 + - - -
729B LYS* 1.3 81.4 - - - +
731B LEU* 1.3 66.9 + - - +
732B PRO* 3.4 4.3 - - - +
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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