Contacts of the helix formed by residues 673 - 682 (chain C) 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 GLN 673 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C THR* 3.6 7.0 - - - +
641C ARG* 2.7 45.0 + - + +
642C GLY* 3.0 30.6 - - - +
643C GLY 4.5 3.0 + - - +
646C GLY* 4.8 16.0 + - - +
671C THR* 3.8 14.0 + - - +
672C VAL* 1.3 74.2 - - - +
674C GLY* 1.3 67.7 + - - +
675C GLU* 3.0 21.5 - - + +
676C VAL* 3.0 27.2 + - + +
677C ILE* 3.2 7.9 + - - +
968C ASN* 4.7 11.7 - - - +
970C GLY 4.7 1.8 + - - +
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Residues in contact with GLY 674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C THR* 3.8 17.8 + - - -
176C ALA 4.2 2.0 + - - -
177C HIS* 3.1 34.6 - - - -
672C VAL 3.8 0.2 + - - -
673C GLN* 1.3 70.3 - - - +
675C GLU* 1.3 69.0 + - - +
676C VAL 3.0 1.7 + - - -
677C ILE* 3.2 27.6 + - - +
678C GLU* 4.4 3.3 + - - +
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Residues in contact with GLU 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ALA 4.9 0.7 - - - +
177C HIS* 3.7 15.3 + - + +
178C PRO* 3.6 24.4 - - + +
641C ARG* 2.5 36.8 + - - -
673C GLN* 3.0 21.3 - - + +
674C GLY* 1.3 81.0 + - - +
676C VAL* 1.3 65.0 + - + +
678C GLU* 5.2 2.6 + - - +
679C PHE* 5.4 0.9 + - - +
963C ALA 5.3 2.9 - - - +
967C GLN* 3.6 55.7 - - - +
968C ASN* 4.2 2.9 - - - +
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Residues in contact with VAL 676 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646C GLY 4.3 18.6 - - - +
648C GLY* 5.2 0.9 - - - +
672C VAL* 3.9 12.6 - - + -
673C GLN* 3.0 33.2 + - + +
675C GLU* 1.3 85.8 - - + +
677C ILE* 1.3 64.8 + - - +
678C GLU 3.2 2.7 - - - -
679C PHE* 3.0 21.4 + - + +
680C CYS* 3.1 27.4 + - - -
967C GLN* 4.9 2.5 - - - +
968C ASN* 3.8 38.1 - - + +
1003C FLC 4.8 5.8 - - - +
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Residues in contact with ILE 677 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C PHE* 3.7 26.2 - - + -
175C THR 4.0 12.8 - - - +
244C GLY* 5.9 6.1 - - - +
247C TYR* 3.8 38.1 - - + -
672C VAL* 3.6 21.1 - - + +
673C GLN 3.2 13.8 + - - +
674C GLY* 3.2 20.9 + - - +
676C VAL* 1.3 77.1 - - - +
678C GLU* 1.3 58.4 + - - +
680C CYS 3.8 0.2 - - - -
681C PHE* 2.9 42.1 + - + +
682C GLY 3.8 0.2 + - - -
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Residues in contact with GLU 678 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU* 4.8 1.4 - - + +
114C GLU* 2.9 29.1 - - - +
187C LEU* 3.7 10.4 - - - +
190C ASN* 4.2 11.1 + - - -
194C ARG* 3.3 21.6 + - - -
247C TYR* 2.8 41.9 + - - +
674C GLY 4.4 2.4 + - - -
675C GLU 5.2 2.7 - - - +
676C VAL 3.2 0.8 - - - -
677C ILE* 1.3 78.6 - - - +
679C PHE* 1.3 59.2 + - - +
682C GLY* 3.0 28.3 + - - -
683C GLU 4.7 0.3 + - - -
686C LEU* 5.0 0.3 - - - +
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Residues in contact with PHE 679 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ASN* 5.8 2.0 - - + -
113C GLU* 3.8 26.2 - - + -
114C GLU* 4.3 18.8 - - + -
117C ILE* 3.5 30.5 - - + -
649C GLY* 4.3 15.4 - - - -
675C GLU 5.4 0.6 + - - +
676C VAL* 3.0 12.5 + - + +
678C GLU* 1.3 79.6 - - - +
680C CYS* 1.3 61.2 + - - +
686C LEU* 3.3 26.8 - - + +
690C THR* 5.3 0.2 - - - +
894C ARG* 4.3 2.0 - - - -
967C GLN* 4.0 27.6 - - - +
1003C FLC 3.0 45.3 - - + -
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Residues in contact with CYS 680 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648C GLY* 3.6 35.2 - - - -
649C GLY* 3.9 5.8 - - - -
672C VAL* 5.6 1.3 - - - -
676C VAL* 3.1 33.6 + - - +
679C PHE* 1.3 84.4 - - - +
681C PHE* 1.3 76.3 + - + +
682C GLY 3.9 0.4 - - - -
686C LEU* 3.2 23.4 - - - +
687C CYS* 3.3 8.7 + - - -
690C THR* 3.3 21.3 - - + +
1003C FLC 5.3 0.7 - - - -
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Residues in contact with PHE 681 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C LEU* 3.9 24.0 - - + -
174C PHE* 4.1 18.4 - + - -
247C TYR* 4.0 14.9 - - + -
251C THR* 2.7 33.7 + - - +
252C VAL* 3.6 26.2 - - + -
285C PHE* 4.7 4.9 - + - -
672C VAL* 4.1 22.4 - - + -
677C ILE* 2.9 21.0 + - + +
680C CYS* 1.3 89.4 - - + +
682C GLY* 1.3 66.2 + - - +
683C GLU 3.2 4.0 - - - -
687C CYS* 3.8 13.9 - - - -
690C THR* 3.6 20.0 - - - -
691C LEU* 4.2 17.9 - - + -
694C PHE* 5.8 2.2 - + - -
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Residues in contact with GLY 682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LEU* 6.0 0.4 - - - -
194C ARG* 2.9 22.5 + - - -
247C TYR* 4.0 13.9 - - - -
250C GLU* 3.8 9.2 - - - +
251C THR* 3.8 9.4 - - - +
677C ILE 3.8 1.8 + - - -
678C GLU* 3.0 33.5 + - - -
679C PHE 4.8 0.2 - - - -
681C PHE* 1.3 78.0 - - - +
683C GLU* 1.3 57.9 + - - +
686C LEU* 5.3 0.2 - - - +
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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