Contacts of the helix formed by residues 702 - 709 (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 GLY 702 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469A HIS* 3.9 1.4 - - - -
642A GLN* 2.8 31.0 + - - +
645A ALA* 4.0 6.5 - - - -
698A LEU 3.2 21.1 + - - -
699A ILE 3.0 12.4 + - - -
700A LEU 3.4 0.4 - - - -
701A SER* 1.3 78.1 - - - +
703A ALA* 1.3 61.0 + - - +
704A GLN 3.1 0.2 - - - -
705A GLN* 3.2 18.5 + - - +
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Residues in contact with ALA 703 (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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469A HIS* 3.2 22.2 + - - -
472A MET* 4.6 26.3 - - + +
473A GLU* 6.0 0.2 - - - +
645A ALA* 3.9 14.0 - - + +
649A ARG* 5.4 9.4 - - + -
700A LEU 5.1 0.6 + - - -
701A SER 3.0 1.6 + - - -
702A GLY* 1.3 75.9 - - - +
704A GLN* 1.3 71.9 + - - +
705A GLN 3.4 0.2 - - - -
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Residues in contact with GLN 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A LEU 4.4 4.9 + - - -
701A SER* 3.0 25.9 + - - +
703A ALA* 1.3 92.9 - - - +
705A GLN* 1.3 68.9 + - - +
706A PRO* 3.7 5.4 - - - +
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Residues in contact with GLN 705 (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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469A HIS* 3.0 14.9 + - - -
642A GLN* 5.2 0.7 - - - +
698A LEU* 5.5 2.0 - - + +
701A SER* 3.1 36.9 + - - +
702A GLY* 3.2 14.9 + - - +
704A GLN* 1.3 86.0 + - - +
706A PRO* 1.3 68.5 - - + +
708A GLY 2.8 18.8 + - - -
709A TYR 3.5 28.2 - - - +
712A PRO* 4.0 18.2 - - - +
713A ILE* 3.6 31.7 - - + +
716A ARG* 4.9 4.3 + - - +
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Residues in contact with PRO 706 (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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58A ASP* 3.9 22.0 - - - +
344A LEU* 4.3 25.4 - - + -
469A HIS* 4.8 0.4 - - - +
704A GLN 3.7 4.9 - - - +
705A GLN* 1.3 92.0 - - + +
707A ASN* 1.3 66.5 + - - +
708A GLY 2.9 6.2 + - - -
709A TYR* 3.0 24.6 + - + +
712A PRO* 4.5 15.3 - - + -
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Residues in contact with ASN 707 (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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57A ARG* 3.4 40.6 + - - +
58A ASP* 4.8 1.4 - - - +
61A GLN* 4.3 17.6 + - - +
401A HIS* 3.7 22.3 + - + -
466A ASP* 4.1 9.0 + - - +
469A HIS* 3.4 25.9 + - - +
470A THR* 5.5 0.6 + - - -
638A ARG* 2.7 35.3 + - - +
705A GLN 3.1 2.4 + - - -
706A PRO* 1.3 77.3 - - - +
708A GLY* 1.3 57.3 + - - +
709A TYR* 3.3 18.6 - - + -
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Residues in contact with GLY 708 (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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469A HIS* 3.4 3.7 + - - -
638A ARG* 3.2 20.9 - - - +
641A SER* 5.2 0.9 + - - -
642A GLN* 3.3 39.4 + - - +
705A GLN* 2.8 16.1 + - - -
707A ASN* 1.3 80.2 - - - +
709A TYR* 1.3 64.1 + - - +
710A THR* 3.7 3.3 + - - +
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Residues in contact with TYR 709 (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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57A ARG* 3.6 22.4 - - - -
344A LEU* 3.8 31.0 - - + -
399A LYS* 3.4 42.4 + - + +
401A HIS* 2.8 18.0 + - - -
435A GLU* 2.7 18.6 + - - -
638A ARG* 3.3 36.1 - - + +
698A LEU* 5.1 0.3 - - - +
705A GLN* 3.5 23.7 - - - +
706A PRO* 3.0 22.8 + - + +
707A ASN* 3.7 11.9 - - + -
708A GLY* 1.3 76.6 - - - +
710A THR* 1.3 63.1 + - - +
711A GLU* 3.4 11.2 - - - +
712A PRO* 3.7 8.2 - - + +
713A ILE* 5.3 0.3 + - - +
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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