Contacts of the helix formed by residues 702 - 709 (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 GLY 702 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469B HIS* 4.1 0.2 - - - -
642B GLN* 3.0 29.7 + - - +
645B ALA* 4.0 3.4 - - - -
698B LEU 3.1 21.9 + - - -
699B ILE 3.2 11.3 + - - -
700B LEU 3.3 0.6 - - - -
701B SER* 1.3 79.4 - - - +
703B ALA* 1.3 61.8 + - - +
705B GLN* 3.2 20.5 + - - +
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Residues in contact with ALA 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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469B HIS* 3.2 23.6 + - - -
472B MET* 4.4 19.2 - - + +
473B GLU* 5.6 0.4 - - - +
645B ALA* 3.7 12.8 - - + +
649B ARG* 4.4 24.7 - - + -
700B LEU 6.1 0.4 - - - +
701B SER 3.3 0.6 - - - -
702B GLY* 1.3 75.5 - - - +
704B GLN* 1.3 72.9 + - - +
705B GLN 3.4 0.2 - - - -
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Residues in contact with GLN 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B HIS* 5.5 0.2 - - - -
700B LEU 5.2 2.8 + - - -
701B SER* 3.1 27.9 + - - +
703B ALA* 1.3 92.1 - - - +
705B GLN* 1.3 71.5 + - - +
706B PRO* 3.5 5.7 - - - +
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Residues in contact with GLN 705 (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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469B HIS* 3.0 14.7 + - - -
642B GLN* 5.3 0.9 - - - +
698B LEU* 5.1 2.2 - - + +
701B SER* 3.0 34.9 + - - +
702B GLY* 3.2 15.7 + - - +
704B GLN* 1.3 86.3 + - - +
706B PRO* 1.4 68.4 - - + +
708B GLY* 2.8 17.6 + - - -
709B TYR 3.3 23.0 - - - +
710B THR* 5.7 0.7 - - - -
712B PRO* 3.9 18.5 - - - +
713B ILE* 3.3 34.0 + - + +
716B ARG* 5.4 0.4 + - - +
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Residues in contact with PRO 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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58B ASP* 3.8 22.7 - - - +
344B LEU* 4.2 31.9 - - + -
469B HIS* 4.6 1.1 - - - +
704B GLN 3.5 6.2 - - - +
705B GLN* 1.4 87.1 - - + +
707B ASN* 1.3 66.8 + - - +
708B GLY 2.8 10.6 + - - -
709B TYR* 2.9 18.0 + - + +
712B PRO* 4.7 10.8 - - + -
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Residues in contact with ASN 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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57B ARG* 3.4 42.8 - - - +
58B ASP* 5.1 0.2 + - - -
61B GLN* 4.1 21.1 - - - +
401B HIS* 3.8 18.4 + - + -
466B ASP* 4.1 7.7 - - - +
469B HIS* 3.2 29.0 + - - +
470B THR* 5.4 0.2 + - - -
638B ARG* 2.7 34.9 + - - +
705B GLN 3.0 2.8 + - - -
706B PRO* 1.3 79.4 - - - +
708B GLY* 1.3 56.7 + - - +
709B TYR* 3.2 17.6 - - + -
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Residues in contact with GLY 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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469B HIS* 3.4 2.9 - - - -
638B ARG* 3.0 22.3 - - - +
641B SER* 5.0 0.2 + - - -
642B GLN* 3.4 36.8 + - - +
705B GLN* 2.8 16.9 + - - +
706B PRO 2.8 0.8 + - - -
707B ASN* 1.3 79.1 - - - +
709B TYR* 1.3 64.9 + - - +
710B THR* 3.7 6.1 + - - +
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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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57B ARG* 3.7 22.0 - - - -
344B LEU* 3.8 32.5 - - + -
399B LYS* 3.3 41.2 + - + +
401B HIS* 2.8 18.5 + - - -
435B GLU* 2.6 24.4 + - - -
638B ARG* 3.3 31.0 - - - +
705B GLN* 3.3 21.5 - - - +
706B PRO* 2.9 21.1 + - + +
707B ASN* 3.8 13.0 - - + -
708B GLY* 1.3 78.5 - - - +
710B THR* 1.3 58.8 + - - +
711B GLU* 3.6 11.7 - - - +
712B PRO* 3.7 9.4 - - + +
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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