Contacts of the strand formed by residues 667 - 672 (chain H) 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 SER 667 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H THR* 3.5 9.4 - - - -
634H LYS* 3.8 22.4 - - - -
635H LEU 4.8 0.8 - - - +
636H THR* 2.6 43.4 + - - +
637H LEU 4.7 1.2 + - - -
663H THR 5.0 0.3 - - - +
664H ILE* 3.4 20.4 + - - +
665H ASN 3.3 3.0 - - - -
666H GLY* 1.3 80.7 - - - +
668H ILE* 1.3 63.1 + - - +
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Residues in contact with ILE 668 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H THR 3.4 5.0 + - - +
170H VAL* 3.8 31.2 - - + -
171H ASP* 3.2 22.6 + - - +
636H THR* 4.2 1.3 - - - -
637H LEU* 3.9 13.0 - - + +
639H HIS* 4.0 22.0 - - + +
645H VAL* 5.5 2.9 - - + -
656H ILE* 4.9 18.4 - - + -
659H GLN* 5.7 1.8 - - + -
664H ILE* 4.1 24.7 - - + -
667H SER* 1.3 77.9 + - - +
669H ARG* 1.3 79.3 + - - +
670H VAL* 4.1 14.1 - - + -
698H THR* 4.0 15.9 - - + +
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Residues in contact with ARG 669 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H ASP* 2.7 49.2 + - + +
173H VAL* 3.9 5.3 - - + +
286H SER* 3.3 16.2 + - - -
454H ASP* 2.4 37.9 + - - -
530H GLY* 5.7 0.6 - - - -
531H PRO* 3.6 18.1 - - - +
596H GLN* 3.2 23.8 + - - +
636H THR* 4.0 17.5 - - + -
637H LEU 3.1 6.2 + - - +
638H PHE* 3.4 34.4 - - + -
639H HIS* 2.9 26.3 + - - -
668H ILE* 1.3 79.1 - - - +
670H VAL* 1.3 66.7 + - - +
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Residues in contact with VAL 670 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170H VAL* 5.1 1.3 - - + -
171H ASP 3.0 6.4 + - - +
172H LEU* 3.6 11.7 - - + -
173H VAL* 2.9 25.5 + - - +
638H PHE* 4.1 3.8 - - - -
639H HIS* 3.7 5.4 - - + +
645H VAL* 3.5 43.7 - - + +
646H GLY* 4.5 0.9 - - - -
656H ILE* 5.4 0.9 - - + -
668H ILE* 4.1 24.5 - - + -
669H ARG* 1.3 80.7 - - - +
671H THR* 1.3 75.5 + - - +
672H VAL* 3.6 1.3 + - + +
694H PHE* 4.0 27.8 - - + -
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Residues in contact with THR 671 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H VAL* 3.7 5.5 - - + +
175H THR* 3.7 28.3 - - + -
288H TRP* 5.4 2.3 - - + -
598H MET* 4.9 1.0 - - - +
638H PHE* 3.4 16.5 - - - -
639H HIS 2.9 20.7 + - - -
640H GLY* 3.3 18.3 - - - +
641H ARG* 4.3 10.8 - - + +
646H GLY* 4.3 13.0 - - - +
670H VAL* 1.3 82.6 - - - +
672H VAL* 1.3 67.0 + - - +
673H GLN* 3.7 19.4 + - + +
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Residues in contact with VAL 672 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H LEU* 3.7 37.9 - - + -
173H VAL 2.8 15.6 + - - +
174H PHE* 4.0 19.5 - - + -
175H THR* 3.1 25.8 + - - +
646H GLY 5.9 0.7 - - - -
670H VAL* 4.3 1.8 - - + +
671H THR* 1.3 71.7 - - - +
673H GLN* 1.3 69.9 + - - +
676H VAL* 4.3 12.8 - - + -
677H ILE* 4.3 10.5 - - + +
680H CYS* 5.5 2.5 - - - -
681H PHE* 4.1 21.3 - - + -
694H PHE* 5.7 4.9 - - + -
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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