Contacts of the helix formed by residues 689 - 701 (chain B) in PDB entry 2GQ3
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 SER 689 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610B VAL* 5.1 0.2 - - - +
614B ASP* 5.4 2.1 + - - -
680B ARG* 5.4 7.8 + - - +
681B PRO 4.9 3.1 - - - -
682B MET* 3.1 26.6 - - - +
685B ASN 3.7 7.6 + - - -
686B PHE 3.1 13.5 + - - +
687B ASP 3.2 0.6 - - - -
688B ASP* 1.4 80.5 - - - +
690B ILE* 1.3 54.0 + - - +
691B ALA* 3.7 5.9 + - - +
692B PHE* 2.8 27.4 + - - -
693B LEU* 2.8 39.4 + - - +
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Residues in contact with ILE 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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613B VAL* 3.8 11.4 - - + -
614B ASP* 5.4 0.6 + - - +
688B ASP 3.6 3.1 + - - +
689B SER* 1.3 68.9 - - - +
691B ALA* 1.3 53.0 + - - +
693B LEU* 2.8 12.4 + - + +
694B ALA* 2.6 34.6 + - - +
717B ARG* 3.5 31.2 - - - +
720B GLU* 3.4 45.5 - - + +
721B PHE* 4.0 26.5 - - + +
724B ARG* 3.9 33.7 - - + +
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Residues in contact with ALA 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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606B LEU* 4.9 0.2 - - - +
609B VAL* 3.4 13.8 - - - +
610B VAL* 3.4 42.8 - - + +
613B VAL* 4.1 12.3 - - + +
614B ASP* 3.5 20.8 + - - +
682B MET* 4.5 2.2 - - - -
689B SER* 3.2 4.0 - - - +
690B ILE* 1.3 77.7 - - - +
692B PHE* 1.4 65.8 + - - +
694B ALA 3.3 0.3 + - - -
695B ALA* 3.1 19.9 + - - +
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Residues in contact with PHE 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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606B LEU* 4.0 17.0 - - + -
659B ARG* 3.5 35.0 - - - -
662B LEU* 3.6 42.8 - - + +
663B GLU* 4.3 1.3 - - + -
666B ALA* 4.1 6.1 - - + -
682B MET* 3.9 13.8 - - + -
686B PHE* 3.4 57.9 - + + +
687B ASP* 4.4 1.1 - - - -
689B SER* 2.8 25.0 + - - +
691B ALA* 1.4 71.4 - - - +
693B LEU* 1.3 63.2 + - + +
695B ALA* 3.1 7.4 + - - +
696B GLN* 3.1 33.2 + - + -
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Residues in contact with LEU 693 (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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686B PHE 4.4 2.0 - - - +
687B ASP* 3.5 46.2 - - + +
689B SER 2.8 23.2 + - - +
690B ILE* 2.8 12.4 + - + +
692B PHE* 1.3 73.3 - - + +
694B ALA* 1.3 58.8 + - - +
696B GLN* 3.6 22.6 + - - +
697B GLU* 3.0 29.5 + - - +
717B ARG* 3.5 32.2 + - - +
720B GLU* 5.8 0.7 - - - +
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Residues in contact with ALA 694 (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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609B VAL* 3.8 15.3 - - + -
613B VAL* 4.0 11.4 - - + -
690B ILE 2.6 18.4 + - - +
691B ALA 3.7 5.2 - - - +
693B LEU* 1.3 72.1 - - - +
695B ALA* 1.3 58.7 + - - +
697B GLU* 3.2 3.6 + - - +
698B LEU* 2.8 40.0 + - + +
713B ILE* 4.5 4.9 - - + -
714B LEU* 4.9 2.5 - - + -
717B ARG* 3.7 30.2 - - + +
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Residues in contact with ALA 695 (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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605B ILE* 3.9 19.9 - - + +
606B LEU* 3.8 25.1 - - + -
609B VAL* 4.0 6.7 - - + +
662B LEU* 4.7 4.9 - - + -
691B ALA 3.1 12.6 + - - +
692B PHE 3.3 9.2 - - - +
694B ALA* 1.3 79.9 - - - +
696B GLN* 1.3 63.1 + - - +
698B LEU* 3.5 16.7 + - - +
699B ILE* 3.5 22.0 + - - +
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Residues in contact with GLN 696 (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 VAL* 5.5 0.2 - - + -
659B ARG* 2.9 47.3 + - - +
662B LEU* 3.8 23.4 - - + +
687B ASP* 4.6 0.4 + - - -
692B PHE* 3.1 16.2 + - + +
693B LEU* 3.6 27.5 + - - +
695B ALA* 1.3 76.6 - - - +
697B GLU* 1.3 62.1 + - - +
699B ILE* 3.1 4.1 + - - +
700B LEU* 3.0 52.3 + - + +
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Residues in contact with GLU 697 (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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693B LEU 3.0 17.5 + - - +
694B ALA 3.7 2.9 - - - +
696B GLN* 1.3 75.5 - - - +
698B LEU* 1.3 64.8 + - - +
699B ILE 3.0 1.7 + - - -
700B LEU* 5.0 2.7 - - - -
701B SER* 2.8 45.7 + - - +
713B ILE* 3.8 17.8 - - + +
716B ARG* 3.2 36.7 + - - -
717B ARG* 3.3 25.0 + - - +
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Residues in contact with LEU 698 (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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605B ILE* 4.8 1.1 - - + -
609B VAL* 3.8 29.6 - - + -
637B LEU* 4.1 9.9 - - + -
641B SER* 3.6 22.2 + - - +
642B GLN* 5.2 0.2 + - - -
694B ALA 2.8 25.5 + - - +
695B ALA* 3.8 5.8 - - - +
696B GLN 3.3 0.2 - - - -
697B GLU* 1.3 77.4 - - - +
699B ILE* 1.3 57.3 + - + +
702B GLY* 3.1 22.7 - - - -
705B GLN* 5.1 2.0 - - + +
709B TYR 5.4 0.2 - - - +
710B THR* 3.7 46.9 - - + +
713B ILE* 3.8 27.3 - - + +
714B LEU* 4.1 12.8 - - + -
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Residues in contact with ILE 699 (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 CYS* 4.3 1.8 - - - -
605B ILE* 3.7 31.6 - - + -
641B SER* 4.4 10.3 - - - -
644B LEU* 3.8 32.5 - - + -
645B ALA* 3.4 18.5 - - - +
648B LEU* 3.9 6.7 - - + +
658B VAL* 3.8 28.7 - - + -
662B LEU* 3.9 26.2 - - + -
695B ALA 3.5 17.4 + - - +
696B GLN 3.1 4.8 + - - +
697B GLU 3.1 0.8 - - - -
698B LEU* 1.3 75.8 - - - +
700B LEU* 1.3 66.4 + - + +
701B SER 3.3 0.4 - - - -
702B GLY 3.2 12.1 + - - -
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Residues in contact with LEU 700 (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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648B LEU* 3.7 26.7 - - + +
655B SER* 3.7 27.1 - - - +
658B VAL* 3.8 21.8 - - + -
659B ARG* 6.1 2.0 - - + +
696B GLN* 3.0 46.6 + - + +
697B GLU* 4.5 2.2 - - - +
699B ILE* 1.3 77.0 - - + +
701B SER* 1.3 58.8 + - - +
702B GLY 3.3 0.4 - - - -
703B ALA* 5.4 0.7 + - - +
704B GLN* 5.2 3.8 + - - -
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Residues in contact with SER 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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697B GLU* 2.8 37.8 + - - +
700B LEU* 1.3 78.5 - - - +
702B GLY* 1.3 64.7 + - - +
703B ALA 3.3 2.9 - - - -
704B GLN* 3.1 25.6 + - - +
705B GLN* 3.0 29.8 + - - -
713B ILE* 3.8 1.7 - - - +
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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