Contacts of the helix formed by residues 689 - 701 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614A ASP* 5.2 2.8 + - - -
681A PRO 5.2 2.5 - - - -
682A MET* 3.5 25.4 - - - +
685A ASN 3.7 6.3 + - - -
686A PHE 3.0 12.5 + - - +
687A ASP 3.2 0.4 - - - -
688A ASP* 1.3 79.3 - - - +
690A ILE* 1.3 58.0 + - - +
691A ALA* 3.5 6.1 + - - +
692A PHE* 2.9 24.4 + - - +
693A LEU* 2.9 34.2 + - - +
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Residues in contact with ILE 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A VAL* 3.8 11.4 - - + -
688A ASP 3.9 0.8 + - - -
689A SER* 1.3 71.6 - - - +
691A ALA* 1.3 53.1 + - - +
693A LEU* 3.3 11.4 + - + +
694A ALA* 2.7 34.1 + - - +
717A ARG* 3.5 32.6 - - - +
720A GLU* 3.6 36.1 - - + +
721A PHE* 3.8 34.9 - - + -
724A ARG* 3.5 44.6 - - + +
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Residues in contact with ALA 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A VAL* 3.4 8.2 - - - +
610A VAL* 3.7 34.8 - - + -
613A VAL* 3.8 18.0 - - + +
614A ASP* 3.2 26.3 + - - +
682A MET* 4.7 2.7 - - - -
689A SER* 3.2 6.0 + - - +
690A ILE* 1.3 79.0 - - - +
692A PHE* 1.3 62.2 + - - +
694A ALA* 3.2 4.3 + - - +
695A ALA* 3.1 19.2 + - - +
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Residues in contact with PHE 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A LEU* 4.0 16.6 - - + -
659A ARG* 3.8 31.6 - - - -
662A LEU* 3.7 47.0 - - + +
663A GLU* 4.3 1.6 - - + -
666A ALA* 4.1 5.8 - - + -
682A MET* 4.2 12.0 - - + -
686A PHE* 3.6 61.9 - + + +
689A SER* 2.9 20.2 + - - +
691A ALA* 1.3 76.0 - - - +
693A LEU* 1.3 64.9 + - + +
695A ALA* 3.1 4.2 + - - +
696A GLN* 2.9 32.1 + - + +
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Residues in contact with LEU 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A PHE 4.5 0.9 - - - +
687A ASP* 3.3 48.9 - - + +
688A ASP 5.3 0.2 - - - -
689A SER 2.9 21.6 + - - +
690A ILE* 3.6 9.6 - - + +
692A PHE* 1.3 76.2 - - + +
694A ALA* 1.3 60.3 + - - +
696A GLN* 3.6 22.8 + - - +
697A GLU* 2.8 31.7 + - - +
717A ARG* 3.8 29.9 + - - +
720A GLU* 6.0 0.2 - - - +
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Residues in contact with ALA 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A VAL* 3.6 15.7 - - + -
613A VAL* 3.9 11.0 - - + -
690A ILE 2.7 18.5 + - - +
691A ALA 3.2 9.4 + - - +
693A LEU* 1.3 71.2 - - - +
695A ALA* 1.3 58.7 + - - +
697A GLU* 3.3 1.7 + - - +
698A LEU* 2.9 37.3 + - + +
713A ILE* 3.9 6.6 - - + +
714A LEU* 5.1 2.0 - - + -
717A ARG* 3.7 27.1 - - + +
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Residues in contact with ALA 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A ILE* 3.7 23.6 - - + +
606A LEU* 3.6 28.9 - - + -
609A VAL* 4.3 7.2 - - + -
662A LEU* 4.6 3.4 - - + -
691A ALA 3.1 10.0 + - - +
692A PHE 3.1 8.0 + - - +
694A ALA* 1.3 77.1 - - - +
696A GLN* 1.3 63.0 + - - +
698A LEU* 3.5 7.4 + - - +
699A ILE* 3.3 30.3 + - - +
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Residues in contact with GLN 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A VAL* 5.6 0.4 - - + -
659A ARG* 2.8 49.5 + - - +
662A LEU* 3.8 21.2 - - + +
687A ASP* 4.8 0.2 + - - -
692A PHE* 2.9 18.7 + - + +
693A LEU* 3.6 24.5 + - - +
695A ALA* 1.3 77.0 - - - +
697A GLU* 1.3 56.5 + - - +
699A ILE* 3.2 2.9 + - - +
700A LEU* 2.8 52.5 + - + +
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Residues in contact with GLU 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693A LEU 2.8 19.3 + - - +
694A ALA 3.7 3.4 - - - +
696A GLN* 1.3 72.7 - - - +
698A LEU* 1.3 58.3 + - - +
700A LEU* 5.1 1.1 - - - +
701A SER* 2.7 52.2 + - - +
713A ILE* 3.6 18.6 - - + +
716A ARG* 2.8 33.9 + - - -
717A ARG* 2.8 42.1 + - - +
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Residues in contact with LEU 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A ILE* 5.0 1.1 - - + -
609A VAL* 3.7 29.4 - - + -
637A LEU* 4.0 12.6 - - + -
641A SER* 3.6 23.4 - - - +
642A GLN* 5.1 0.5 + - - -
694A ALA 2.9 24.9 + - - +
695A ALA* 3.8 6.7 - - - +
696A GLN 3.3 0.2 - - - -
697A GLU* 1.3 75.4 - - - +
699A ILE* 1.3 58.3 + - + +
702A GLY* 3.2 21.3 - - - -
705A GLN* 5.5 1.5 - - + +
709A TYR 5.1 1.1 - - - +
710A THR* 3.8 46.4 - - + +
713A ILE* 3.6 26.0 - - + +
714A LEU* 4.2 9.0 - - + -
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Residues in contact with ILE 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A CYS* 4.1 0.2 - - - -
605A ILE* 3.8 29.6 - - + -
641A SER* 4.4 8.3 - - - -
644A LEU* 3.9 35.2 - - + -
645A ALA* 3.7 12.8 - - - +
648A LEU* 4.2 6.3 - - + +
658A VAL* 3.7 32.1 - - + -
662A LEU* 3.7 27.1 - - + -
695A ALA 3.3 17.7 + - - +
696A GLN 3.2 3.9 + - - +
697A GLU 3.1 0.4 - - - -
698A LEU* 1.3 78.4 - - + +
700A LEU* 1.4 64.8 + - + +
702A GLY* 3.0 17.8 + - - -
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Residues in contact with LEU 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A LEU* 3.7 26.9 - - + +
655A SER* 3.9 26.5 - - - +
658A VAL* 3.9 27.4 - - + -
659A ARG* 6.2 2.0 - - + -
696A GLN* 2.8 47.5 + - + +
697A GLU* 5.2 0.9 - - - -
699A ILE* 1.4 71.1 - - - +
701A SER* 1.3 59.8 + - - +
702A GLY 3.4 0.4 + - - -
703A ALA* 5.1 0.5 + - - +
704A GLN* 4.4 7.4 + - - -
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Residues in contact with SER 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A GLU* 2.7 38.7 + - - +
700A LEU* 1.3 72.6 - - - +
702A GLY* 1.3 65.0 + - - +
703A ALA 3.1 3.6 - - - -
704A GLN* 3.0 24.6 + - - +
705A GLN* 3.1 27.6 + - - -
713A ILE* 4.3 0.2 - - - -
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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