Contacts of the helix formed by residues 674 - 682 (chain B) in PDB entry 1JQO
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 674 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B THR 3.1 22.5 + - - -
176B ALA* 4.6 1.1 - - - -
177B HIS 4.0 10.8 - - - +
179B THR* 3.5 8.0 - - - +
180B GLN* 4.3 2.9 - - - -
243B TYR* 2.9 29.6 + - - -
672B VAL 3.2 1.0 + - - -
673B GLN* 1.3 66.5 - - - +
675B GLU* 1.3 62.8 + - - -
677B ILE* 2.8 21.1 + - - +
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Residues in contact with GLU 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B THR* 2.9 39.1 + - + +
180B GLN* 3.8 20.5 - - - +
181B SER* 3.9 5.9 + - - -
643B GLY* 5.4 2.3 - - - -
673B GLN 2.6 4.0 + - - +
674B GLY* 1.3 69.4 - - - -
676B VAL* 1.3 62.2 + - + +
678B GLU* 3.2 17.0 + - - +
679B PHE* 3.3 35.3 + - + -
963B ALA 5.0 1.2 - - - +
968B ASN* 3.2 23.4 + - - +
969B THR* 3.0 43.2 + - - -
970B GLY 4.5 1.2 + - - +
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Residues in contact with VAL 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B GLY 4.6 3.6 - - - +
643B GLY* 3.8 29.6 - - - +
671B THR 5.7 0.7 - - - +
672B VAL* 3.6 20.9 - - + -
673B GLN 2.7 25.6 + - - +
675B GLU* 1.3 71.4 - - + +
677B ILE* 1.3 56.6 + - - +
679B PHE* 3.1 18.5 + - + -
680B CYS* 2.7 56.0 + - - +
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Residues in contact with ILE 677 (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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174B PHE* 3.4 42.6 - - + -
175B THR 3.6 22.9 - - - +
243B TYR* 4.2 5.8 - - + +
244B GLY* 4.5 12.6 - - - +
247B TYR* 3.3 39.2 - - + -
289B MET* 5.0 1.1 - - - -
672B VAL* 3.4 27.1 - - + +
674B GLY* 2.8 15.4 + - - +
676B VAL* 1.3 78.2 - - - +
678B GLU* 1.3 58.4 + - - +
680B CYS* 5.0 0.2 - - - -
681B PHE* 2.8 28.6 + - + +
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Residues in contact with GLU 678 (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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114B GLU* 5.6 0.3 - - - +
180B GLN* 3.8 9.6 - - - +
187B LEU* 3.4 39.4 - - + +
190B ASN* 5.0 2.3 - - - +
194B ARG* 3.4 25.9 + - - -
247B TYR* 2.8 25.7 + - - +
674B GLY 3.6 1.4 + - - -
675B GLU 3.2 11.0 + - - +
677B ILE* 1.3 77.3 - - - +
679B PHE* 1.3 66.2 + - + +
682B GLY* 2.7 38.3 + - - -
686B LEU* 4.4 1.7 - - - +
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Residues in contact with PHE 679 (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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643B GLY 6.0 0.4 - - - -
675B GLU* 3.5 40.6 - - + -
676B VAL* 3.1 26.8 + - + +
678B GLU* 1.3 88.8 - - + +
680B CYS* 1.3 64.2 + - - +
681B PHE 2.9 5.0 + - - -
682B GLY 3.3 4.2 + - - -
686B LEU* 3.3 19.9 - - - +
967B GLN* 4.1 28.9 - - + -
968B ASN* 4.8 3.8 - - - -
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Residues in contact with CYS 680 (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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652B THR* 5.3 7.4 - - - -
672B VAL* 4.8 3.4 - - + -
676B VAL* 2.7 38.3 + - + +
679B PHE* 1.3 76.1 - - - +
681B PHE* 1.3 80.9 + - + +
686B LEU* 3.7 9.4 - - - +
687B CYS 3.7 1.2 + - - -
690B THR* 2.7 38.5 + - + +
694B PHE* 5.6 2.7 - - - -
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Residues in contact with PHE 681 (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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172B LEU* 3.8 28.5 - - + -
174B PHE* 4.2 17.3 - + - -
247B TYR* 3.2 25.4 - - + -
251B THR* 4.2 12.0 + - + -
252B VAL* 3.4 32.3 - - + -
285B PHE* 4.0 12.1 - + - -
672B VAL* 5.2 7.4 - - + -
677B ILE* 2.8 23.7 + - + +
679B PHE 2.9 0.4 + - - -
680B CYS* 1.3 98.0 - - + +
682B GLY* 1.3 66.7 + - - +
683B GLU 3.5 11.2 - - - +
687B CYS* 3.7 27.8 - - + +
690B THR* 3.7 21.8 - - + -
691B LEU* 4.5 5.8 - - + -
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Residues in contact with GLY 682 (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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191B ALA* 5.5 3.5 - - - +
194B ARG* 4.6 3.8 + - - -
247B TYR* 4.1 4.4 - - - -
251B THR* 4.5 6.1 + - - -
678B GLU* 2.7 43.5 + - - +
679B PHE 3.3 3.0 + - - -
681B PHE* 1.3 76.4 - - - +
683B GLU* 1.3 68.7 + - - +
686B LEU* 3.8 3.1 - - - +
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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