Contacts of the helix formed by residues 667 - 676 (chain B) in PDB entry 5J3V
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 ASN 667 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613B VAL* 4.1 14.8 - - - +
617B GLN* 3.9 19.3 + - - +
663B VAL 5.0 0.7 - - - -
666B SER* 1.3 83.3 - - - +
668B ILE* 1.3 63.5 + - - +
669B LEU* 3.2 4.9 - - - +
670B THR* 3.4 20.6 + - - +
671B LEU* 3.3 27.5 + - - +
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Residues in contact with ILE 668 (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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609B TYR* 3.1 44.4 - - + +
613B VAL* 3.9 12.5 - - + +
616B VAL* 6.4 0.4 - - + -
645B LEU* 5.2 3.1 - - + -
648B LEU* 3.8 22.7 - - + -
659B ILE* 5.9 0.7 - - + -
663B VAL* 4.7 13.5 + - + +
666B SER* 3.6 3.5 + - - +
667B ASN* 1.3 72.7 - - - +
669B LEU* 1.3 55.5 + - + +
671B LEU* 2.8 13.0 + - + -
672B MET* 2.3 63.2 + - + +
690B LEU* 3.7 15.9 - - + -
694B LEU* 4.9 9.0 - - + -
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Residues in contact with LEU 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B VAL* 4.7 13.0 - - + +
667B ASN* 3.2 2.4 - - - -
668B ILE* 1.3 77.9 - - + +
670B THR* 1.3 58.0 + - - +
672B MET* 4.3 19.5 - - + -
673B TYR* 3.0 27.2 + - - +
691B LEU* 5.7 0.4 - - + -
694B LEU* 4.6 7.0 - - + -
701B HIS* 3.2 34.8 - - + +
702B VAL* 4.3 22.7 - - + -
705B CYS* 4.2 20.3 - - - -
709B PHE* 3.8 24.4 - - + -
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Residues in contact with THR 670 (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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667B ASN* 3.4 24.4 + - - +
668B ILE 3.1 0.4 - - - -
669B LEU* 1.3 78.1 - - - +
671B LEU* 1.3 65.2 + - + +
673B TYR* 3.2 24.1 - - + +
674B GLN* 3.3 25.9 + - + +
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Residues in contact with LEU 671 (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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613B VAL* 3.6 42.6 - - + +
616B VAL* 4.2 15.7 - - + -
617B GLN* 3.8 35.0 - - + +
620B LEU* 3.8 19.6 - - + +
667B ASN* 3.3 18.3 + - - +
668B ILE* 2.8 10.6 + - + +
670B THR* 1.3 76.5 - - + +
672B MET* 1.3 65.8 - - - +
674B GLN* 3.2 15.0 + - - +
675B CYS* 3.0 27.6 + - - -
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Residues in contact with MET 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B LEU* 5.4 2.7 - - + +
668B ILE* 2.3 54.5 + - + +
669B LEU* 4.0 12.6 - - + +
671B LEU* 1.3 65.7 - - - +
673B TYR* 1.3 64.6 + - - +
675B CYS* 3.2 8.6 + - - +
676B MET* 3.1 43.3 + - + +
687B SER* 3.5 35.0 - - - +
690B LEU* 3.7 12.8 - - + -
691B LEU* 3.7 23.1 - - + -
694B LEU* 3.6 26.5 - - + -
709B PHE* 5.1 2.0 - - + -
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Residues in contact with TYR 673 (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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669B LEU 3.0 16.2 + - - +
670B THR* 3.2 18.4 - - + +
672B MET* 1.3 77.2 - - - +
674B GLN* 1.3 64.4 + - + +
676B MET* 3.3 12.3 + - - +
677B GLN* 3.5 24.8 + - - +
708B ASP* 4.0 34.8 + - + +
709B PHE* 4.0 20.6 - + + -
712B ILE* 3.4 29.2 - - + +
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Residues in contact with GLN 674 (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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620B LEU* 3.8 33.8 - - + +
624B MET* 4.9 12.0 - - - +
670B THR* 3.5 27.5 + - + +
671B LEU* 3.2 13.9 + - - +
673B TYR* 1.3 76.7 - - + +
675B CYS* 1.3 64.6 + - - +
677B GLN* 3.1 22.9 + - - +
678B ASP* 3.4 9.7 + - - +
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Residues in contact with CYS 675 (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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616B VAL* 3.7 26.5 - - - -
620B LEU* 4.0 9.9 - - - -
641B MET* 4.0 13.9 - - - -
645B LEU* 4.0 12.1 - - + -
671B LEU 3.0 23.6 + - - +
672B MET* 3.2 10.5 + - - +
674B GLN* 1.3 77.7 - - - +
676B MET* 1.3 61.2 + - - +
678B ASP* 3.3 18.5 + - - +
683B VAL* 3.7 14.3 - - + +
684B ARG* 3.6 8.0 - - - +
687B SER* 3.7 20.7 + - - -
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Residues in contact with MET 676 (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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672B MET* 3.1 41.0 + - + +
673B TYR* 3.6 7.6 - - - +
674B GLN 3.2 0.6 - - - -
675B CYS* 1.3 77.0 - - - +
677B GLN* 1.3 56.9 + - - +
678B ASP 3.4 1.6 - - - -
684B ARG* 3.3 24.1 - - - +
687B SER* 3.6 15.3 - - - +
688B PHE* 3.6 24.9 - - + -
691B LEU* 3.8 30.1 - - + -
709B PHE* 3.6 34.1 - - + -
712B ILE* 3.8 31.9 - - + +
716B ASN* 4.4 2.4 + - - -
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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