Contacts of the helix formed by residues 676 - 682 (chain G) in PDB entry 6V3O
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 VAL 676 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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646G GLY 4.2 18.6 - - - +
648G GLY* 5.1 2.7 - - - +
672G VAL* 3.8 14.1 - - + -
673G GLN* 2.9 34.5 + - + +
675G GLU* 1.3 86.3 - - + +
677G ILE* 1.3 66.2 + - - +
678G GLU 3.3 2.5 - - - -
679G PHE* 3.0 19.1 + - + +
680G CYS* 3.1 27.4 + - - -
967G GLN* 4.6 0.9 - - - +
968G ASN* 3.8 37.2 - - + +
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Residues in contact with ILE 677 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G PHE* 3.8 35.9 - - + -
175G THR 3.7 15.3 - - - +
177G HIS* 5.5 2.2 - - + +
244G GLY* 6.1 3.1 - - - +
247G TYR* 4.1 30.2 - - + -
289G MET* 5.6 3.6 - - + -
672G VAL* 4.3 10.1 - - + +
673G GLN 3.0 16.8 + - - +
674G GLY* 3.2 25.6 + - - +
676G VAL* 1.3 74.8 - - - +
678G GLU* 1.3 58.4 + - - +
680G CYS 3.8 0.2 - - - -
681G PHE* 2.8 37.0 + - + +
682G GLY 3.8 0.3 + - - -
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Residues in contact with GLU 678 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G LEU* 4.6 7.0 - - - +
114G GLU* 3.8 24.5 - - - +
187G LEU* 3.6 13.0 - - - +
190G ASN* 3.2 30.7 + - - +
194G ARG* 4.6 4.3 + - - +
247G TYR* 3.4 36.1 + - + +
674G GLY 4.6 2.0 + - - -
675G GLU 5.3 0.4 + - - -
676G VAL 3.3 0.4 - - - -
677G ILE* 1.3 76.5 - - - +
679G PHE* 1.3 62.6 + - - +
682G GLY* 3.0 27.3 + - - -
683G GLU 4.6 0.3 + - - -
686G LEU* 4.9 0.9 - - - +
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Residues in contact with PHE 679 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G ASN* 5.7 0.7 - - + -
113G GLU* 4.0 24.0 - - + -
114G GLU* 4.5 20.2 + - + -
117G ILE* 3.5 33.4 - - + -
649G GLY* 4.1 27.7 - - - -
675G GLU 5.2 0.6 + - - +
676G VAL* 3.0 13.6 + - + +
678G GLU* 1.3 80.8 - - - +
680G CYS* 1.3 57.8 + - - +
686G LEU* 3.3 26.8 - - + +
894G ARG* 4.5 6.3 - - - -
967G GLN* 4.0 26.5 - - - +
1001G GOL 3.6 28.3 - - - -
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Residues in contact with CYS 680 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648G GLY* 3.6 35.0 - - - -
649G GLY* 3.9 4.7 - - - -
672G VAL* 5.4 0.9 - - - -
676G VAL* 3.1 31.0 + - - +
679G PHE* 1.3 83.7 - - - +
681G PHE* 1.3 77.8 + - + +
682G GLY 3.8 0.2 - - - -
686G LEU* 3.2 15.5 - - - +
687G CYS* 3.3 8.5 + - - -
690G THR* 3.1 31.0 + - + +
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Residues in contact with PHE 681 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172G LEU* 4.0 19.7 - - + -
174G PHE* 4.1 16.8 - + - -
247G TYR* 3.8 19.5 - - + -
251G THR* 2.8 29.7 + - - +
252G VAL* 3.6 24.2 - - + -
285G PHE* 4.6 5.8 - + - -
672G VAL* 4.1 15.3 - - + -
677G ILE* 2.8 28.4 + - + +
680G CYS* 1.3 92.5 - - + +
682G GLY* 1.3 65.4 + - - +
683G GLU 3.3 3.8 - - - -
687G CYS* 4.0 12.6 - - - -
690G THR* 3.7 21.5 - - + -
691G LEU* 3.8 24.9 - - + -
694G PHE* 6.3 0.4 - + - -
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Residues in contact with GLY 682 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G GLU* 4.9 0.4 - - - -
194G ARG* 2.8 25.8 + - - -
247G TYR* 4.1 15.9 - - - -
250G GLU* 3.8 12.8 - - - +
251G THR* 3.8 5.8 - - - +
677G ILE 3.8 0.4 + - - -
678G GLU* 3.0 28.0 + - - -
680G CYS 3.8 0.4 - - - -
681G PHE* 1.3 80.4 - - - +
683G GLU* 1.3 59.1 + - - +
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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