Contacts of the helix formed by residues 700 - 714 (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 LEU 700 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558A MET 4.5 1.8 - - - +
559A GLU* 2.9 30.4 + - + +
654B VAL* 4.1 17.5 - - + -
657B LEU* 4.2 20.4 - - + -
658B ALA* 4.0 25.6 - - + +
661B ARG* 4.5 6.3 - - - +
684B PHE* 3.6 21.1 - - + -
688B LEU* 3.6 35.4 - - + -
695B MET* 3.5 17.5 - - + +
699B HIS* 1.3 71.5 + - - +
701B ASP* 1.3 61.1 + - - +
702B GLN 3.1 0.5 + - - -
703B ILE* 3.1 6.4 + - - +
704B MET* 3.0 23.8 + - - +
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Residues in contact with ASP 701 (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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658B ALA* 6.1 0.2 - - - -
661B ARG* 2.9 29.9 + - - -
684B PHE* 5.9 0.3 - - - -
699B HIS* 3.1 18.3 + - - +
700B LEU* 1.3 76.4 - - - +
702B GLN* 1.3 60.3 + - - +
704B MET* 3.7 15.0 - - + +
705B MET* 3.1 34.9 + - + +
728B TYR* 2.5 44.1 + - + +
733B HIS* 2.9 21.1 - - - -
738B THR* 4.4 1.3 - - + -
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Residues in contact with GLN 702 (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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698B ARG* 3.4 13.2 - - - +
699B HIS* 2.8 37.7 + - - +
701B ASP* 1.3 77.0 - - - +
703B ILE* 1.3 66.5 + - + +
705B MET* 3.5 0.9 + - + -
706B CYS* 3.1 30.8 + - - -
738B THR* 2.7 45.6 + - + +
741B ARG 3.9 7.9 + - - -
742B VAL* 3.7 26.2 - - + +
752B ILE* 3.8 17.5 - - + +
755B PHE* 4.7 11.4 - - + -
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Residues in contact with ILE 703 (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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684B PHE* 3.6 23.3 - - + -
687B THR* 3.6 27.6 - - + -
688B LEU* 4.5 3.8 - - + -
694B LEU* 4.1 25.1 - - + +
695B MET* 3.5 30.1 - - + -
698B ARG* 5.6 1.6 - - + -
699B HIS 4.2 3.6 - - - +
700B LEU 3.1 7.2 + - - +
702B GLN* 1.3 77.9 - - + +
704B MET* 1.3 62.3 + - - +
706B CYS* 3.4 5.4 + - - +
707B SER* 2.9 30.2 + - - +
755B PHE* 3.9 28.5 - - + -
760B PHE* 4.2 8.6 - - + -
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Residues in contact with MET 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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658B ALA* 4.2 3.1 - - - +
661B ARG* 3.6 20.6 - - + +
662B LEU* 3.5 38.8 - - + -
665B LEU* 3.3 26.5 - - + -
680B ILE* 4.8 0.7 - - - +
684B PHE* 3.4 34.7 - - + -
700B LEU 3.0 9.3 + - - +
701B ASP* 3.7 22.4 - - + +
702B GLN 3.2 0.2 - - - -
703B ILE* 1.3 77.8 - - - +
705B MET* 1.3 64.6 + - + +
707B SER* 3.4 2.9 + - - -
708B MET* 3.1 25.0 + - - +
728B TYR* 4.1 20.0 - - + -
731B LEU* 4.6 0.7 - - + -
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Residues in contact with MET 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B LEU* 4.6 2.7 - - + -
701B ASP* 3.1 27.3 + - + +
702B GLN* 4.4 1.1 - - - -
703B ILE 3.4 0.2 - - - -
704B MET* 1.3 90.3 - - + +
706B CYS* 1.3 60.5 + - - +
708B MET* 3.4 6.3 + - - +
709B TYR* 3.0 29.1 + - - +
721B PHE* 3.9 10.0 - - + -
724B ILE* 3.8 19.6 - - + +
725B VAL* 4.1 20.0 - - - -
728B TYR* 3.6 48.7 - - + -
738B THR* 4.7 4.3 - - + -
739B PHE* 4.2 9.4 - - + -
752B ILE* 3.7 25.6 - - + -
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Residues in contact with CYS 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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702B GLN 3.1 23.2 + - - +
703B ILE 3.7 4.0 - - - +
705B MET* 1.3 77.7 - - - +
707B SER* 1.3 56.7 + - - +
709B TYR 3.5 0.5 + - - -
710B GLY 3.0 24.1 + - - -
721B PHE* 4.0 7.0 - - - -
752B ILE* 4.0 11.7 - - - -
755B PHE* 3.6 29.8 - - - -
756B TYR* 3.7 29.5 - - + -
760B PHE* 3.5 33.6 - - + -
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Residues in contact with SER 707 (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 ILE* 4.0 10.3 - - - -
683B LEU* 3.6 20.0 - - - +
684B PHE* 3.5 33.2 - - - -
687B THR* 4.5 0.2 + - - -
703B ILE* 2.9 22.0 + - - +
704B MET 3.6 5.4 - - - -
705B MET 3.3 0.2 - - - -
706B CYS* 1.3 74.3 - - - +
708B MET* 1.3 65.0 + - - +
711B ILE* 3.1 30.7 + - - +
760B PHE* 3.6 12.6 - - - -
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Residues in contact with MET 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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662B LEU* 3.8 24.2 - - + -
665B LEU* 3.5 52.5 - - + +
666B CYS* 4.5 8.3 - - - -
669B LEU* 4.3 18.2 - - + -
670B LEU* 4.8 4.9 - - + -
680B ILE* 3.8 14.6 - - + -
704B MET* 3.1 21.5 + - - +
705B MET* 3.6 6.5 - - - +
706B CYS 3.3 0.2 - - - -
707B SER* 1.3 75.9 - - - +
709B TYR* 1.3 64.9 + - - +
711B ILE* 4.1 1.2 - - - +
712B CYS* 3.2 29.0 + - - -
719B LEU* 4.6 12.1 - - + -
724B ILE* 4.4 18.4 - - + -
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Residues in contact with TYR 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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705B MET 3.0 13.5 + - - +
706B CYS 3.9 2.5 - - - +
708B MET* 1.3 81.9 - - - +
710B GLY* 1.3 55.0 + - - +
712B CYS* 3.6 4.1 + - - +
713B LYS* 3.0 68.7 + - + +
719B LEU 3.5 25.4 - - - -
720B LYS* 4.5 0.2 - - - -
721B PHE* 3.5 40.4 - + + -
724B ILE* 3.7 11.0 - - + +
756B TYR* 3.4 33.7 - + - -
4E CYS* 3.3 26.5 - - + -
5E TYR 4.4 1.0 + - - -
6E GLU* 3.8 7.7 + - - -
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Residues in contact with GLY 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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706B CYS 3.0 15.9 + - - -
707B SER* 3.9 1.1 - - - -
708B MET 3.4 0.2 - - - -
709B TYR* 1.3 74.2 - - - +
711B ILE* 1.3 63.1 + - - +
713B LYS* 3.2 15.9 - - - +
714B VAL* 3.2 10.6 + - - +
756B TYR* 3.5 21.3 - - - -
768B ILE* 3.6 24.8 - - - +
2E LEU* 4.2 0.4 - - - +
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Residues in contact with ILE 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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676B LEU* 4.2 11.2 - - + -
679B ILE* 3.7 22.4 - - + -
680B ILE* 3.7 35.0 - - + -
683B LEU* 4.1 18.4 - - + +
707B SER 3.1 17.7 + - - +
710B GLY* 1.3 74.2 - - - +
712B CYS* 1.3 64.7 + - - +
713B LYS 3.0 1.1 + - - -
714B VAL* 3.0 9.6 - - + +
715B LYS* 2.9 34.6 + - + +
768B ILE* 4.7 3.4 - - + -
771B TYR* 3.5 37.2 - - + -
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Residues in contact with CYS 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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670B LEU* 3.8 25.6 - - - -
676B LEU* 3.9 14.8 - - - -
680B ILE* 4.7 3.4 - - - -
708B MET 3.2 18.6 + - - +
709B TYR* 3.8 4.3 - - - +
711B ILE* 1.3 76.9 - - - +
713B LYS* 1.3 59.1 + - - +
715B LYS* 3.9 4.5 - - - -
716B ASN* 3.2 1.2 + - - -
717B ILE* 2.9 50.8 + - + +
719B LEU* 3.8 32.8 - - + +
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Residues in contact with LYS 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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709B TYR* 3.0 49.6 + - + +
710B GLY* 3.2 12.6 - - - +
711B ILE 3.0 0.8 - - - -
712B CYS* 1.3 73.6 - - - +
714B VAL* 1.3 66.9 + - - +
716B ASN* 3.1 22.1 + - - +
717B ILE 5.2 0.7 - - - +
756B TYR* 4.1 0.4 - - - +
1E ASP* 3.5 23.1 + - - +
2E LEU* 3.7 20.2 - - + +
3E TYR 3.0 29.8 + - - -
5E TYR* 5.2 6.3 - - - +
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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
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710B GLY 3.2 8.6 + - - +
711B ILE* 3.0 22.9 - - - +
713B LYS* 1.3 77.8 - - - +
715B LYS* 1.3 59.3 + - + +
716B ASN* 2.8 23.3 - - - +
768B ILE* 3.6 22.2 - - + +
769B LEU* 3.5 34.1 - - + -
771B TYR* 3.9 22.4 - - + -
772B ALA* 4.2 16.9 - - + +
2E LEU* 3.8 9.8 - - + +
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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