Contacts of the helix formed by residues 674 - 682 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A THR 2.8 22.2 + - - -
176A ALA* 4.6 3.1 - - - -
177A HIS 3.8 10.0 - - - +
179A THR* 3.3 9.8 - - - +
180A GLN* 4.3 3.6 - - - -
243A TYR* 3.5 15.2 + - - -
673A GLN* 1.3 65.2 - - - +
675A GLU* 1.3 54.0 + - - +
677A ILE* 2.7 42.8 + - - +
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Residues in contact with GLU 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A THR* 2.8 42.6 + - - +
180A GLN* 3.6 23.4 - - - +
181A SER* 4.4 5.7 + - - -
643A GLY* 5.7 2.4 - - - -
674A GLY* 1.3 68.5 - - - -
676A VAL* 1.3 62.3 + - + +
678A GLU* 3.0 24.4 + - - +
679A PHE* 3.3 36.1 + - + -
963A ALA* 5.2 1.6 - - - +
967A GLN 4.5 0.7 - - - +
968A ASN* 3.6 13.9 + - - +
969A THR* 2.7 41.9 + - - -
970A GLY 4.4 1.4 + - - +
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Residues in contact with VAL 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A THR* 5.6 0.4 - - - +
642A GLY 4.3 6.5 - - - +
643A GLY* 3.6 31.6 - - - +
672A VAL* 4.0 14.8 - - + -
673A GLN* 2.9 21.8 + - + +
675A GLU* 1.3 70.7 - - + +
677A ILE* 1.3 59.2 + - - +
678A GLU 3.1 0.2 - - - -
679A PHE* 3.1 21.7 + - + -
680A CYS* 2.8 51.1 + - - +
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Residues in contact with ILE 677 (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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174A PHE* 3.6 40.8 - - + -
175A THR 3.9 11.7 - - - +
176A ALA* 5.9 0.2 - - - -
243A TYR* 4.2 14.8 - - + +
244A GLY* 4.6 5.4 - - - -
247A TYR* 3.5 35.2 - - + -
289A MET* 5.0 1.8 - - + -
672A VAL* 3.2 36.6 - - + +
674A GLY* 2.7 24.5 + - - +
676A VAL* 1.3 72.9 - - - +
678A GLU* 1.3 57.5 + - - +
681A PHE* 2.9 32.1 + - + -
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Residues in contact with GLU 678 (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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180A GLN* 3.5 15.5 - - - +
187A LEU* 3.2 41.4 - - + +
190A ASN* 5.1 0.7 - - - +
194A ARG* 2.8 27.4 + - - -
243A TYR* 4.0 0.2 + - - -
247A TYR* 3.1 25.7 + - - +
674A GLY 4.0 0.4 + - - -
675A GLU 3.0 12.5 + - - +
677A ILE* 1.3 77.0 - - - +
679A PHE* 1.3 67.5 + - + +
682A GLY* 2.8 43.0 + - - -
686A LEU* 4.5 1.6 - - - +
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Residues in contact with PHE 679 (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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114A GLU* 6.2 0.2 - - - -
180A GLN* 5.8 0.7 - - - -
675A GLU* 3.3 39.7 - - + -
676A VAL* 3.4 28.0 - - + +
678A GLU* 1.3 90.0 - - + +
680A CYS* 1.3 63.3 + - - +
686A LEU* 3.4 22.1 - - - +
967A GLN* 3.2 35.9 - - + -
968A ASN* 4.2 8.3 - - - -
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Residues in contact with CYS 680 (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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652A THR* 5.8 3.8 - - - -
672A VAL* 5.2 2.0 - - - -
676A VAL* 2.8 38.9 + - + +
679A PHE* 1.3 79.7 - - - +
681A PHE* 1.3 76.8 + - + +
686A LEU* 3.2 18.8 - - - -
687A CYS* 3.2 2.3 + - - -
690A THR* 2.9 39.9 + - + +
694A PHE* 5.9 1.3 - - - -
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Residues in contact with PHE 681 (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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172A LEU* 4.1 17.0 - - + -
174A PHE* 3.7 30.7 - + - -
247A TYR* 3.4 15.8 - - + -
251A THR* 3.2 23.1 + - - +
252A VAL* 3.6 26.7 - - + -
285A PHE* 4.1 14.8 - + - -
672A VAL* 4.4 9.4 - - + -
677A ILE* 2.9 22.7 + - + +
680A CYS* 1.3 85.9 - - + +
682A GLY* 1.3 67.3 + - - +
683A GLU 3.3 4.2 + - - -
687A CYS* 3.9 19.1 - - + +
690A THR* 3.8 28.3 - - + -
691A LEU* 4.2 12.3 - - + -
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Residues in contact with GLY 682 (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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191A ALA* 4.9 5.7 - - - +
194A ARG* 3.2 17.2 + - - -
247A TYR* 4.0 4.5 - - - -
251A THR* 4.5 6.6 - - - +
678A GLU* 2.8 38.0 + - - -
680A CYS 3.6 1.8 - - - -
681A PHE* 1.3 79.9 - - - +
683A GLU* 1.3 60.5 + - - +
686A LEU* 4.1 2.5 - - - +
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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