Contacts of the strand formed by residues 461 - 467 (chain G) in PDB entry 1H1V
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 461 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412G MET* 4.7 1.6 - - - +
450G LEU* 3.6 14.4 - - + +
451G TYR 3.4 14.6 - - - +
452G ASN* 3.1 30.3 + - - +
453G TYR* 3.9 5.9 - - - -
460G GLY* 1.3 79.1 - - - +
462G ILE* 1.3 64.5 + - - +
490G LEU* 3.5 32.9 + - - +
493G THR* 4.3 7.4 + - - +
494G PRO* 3.2 32.9 - - + +
495G VAL* 3.0 22.0 + - - +
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Residues in contact with ILE 462 (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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449G ILE 3.6 1.2 - - - +
450G LEU* 3.8 0.5 - - - +
451G TYR* 3.1 47.3 + - + +
453G TYR* 3.4 37.9 - - + +
461G GLN* 1.3 78.4 - - - +
463G ILE* 1.3 75.6 + - - +
464G TYR* 3.4 40.3 + - + +
495G VAL* 3.1 25.8 - - + +
497G SER* 4.2 8.1 - - - -
507G HIS* 5.2 0.7 - - - +
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Residues in contact with ILE 463 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448G ILE* 3.7 22.7 - - + -
449G ILE 3.2 10.8 - - - +
450G LEU* 4.5 9.0 - - + -
462G ILE* 1.3 78.9 - - - +
464G TYR* 1.3 65.0 + - - +
465G ASN 4.0 0.2 + - - -
483G THR* 3.6 28.2 - - + +
486G LEU* 4.2 17.9 - - + -
487G ASP* 4.1 26.0 - - + +
490G LEU* 5.4 2.0 - - + -
494G PRO* 3.8 33.0 - - + -
495G VAL 2.7 9.9 + - - +
496G GLN* 3.5 3.9 - - + +
497G SER* 2.9 29.3 + - - -
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Residues in contact with TYR 464 (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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448G ILE* 3.5 4.3 - - - -
449G ILE* 3.0 48.6 + - + +
451G TYR* 5.3 1.3 - - + -
453G TYR* 5.0 0.2 + - - -
462G ILE* 3.4 34.1 - - + +
463G ILE* 1.3 76.2 - - - +
465G ASN* 1.3 59.6 + - - +
466G TRP 3.5 2.8 + - - +
497G SER* 3.2 30.1 - - - -
499G VAL* 3.8 9.6 - - + -
505G PRO* 4.4 11.5 - - + +
507G HIS* 3.3 30.3 - + - +
508G LEU* 3.4 51.6 + - + -
511G LEU* 4.0 13.0 - - + -
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Residues in contact with ASN 465 (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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146A GLY 4.1 1.0 - - - +
447G TYR 3.0 17.6 + - - -
463G ILE* 4.0 1.4 + - - +
464G TYR* 1.3 71.2 - - - +
466G TRP* 1.3 60.4 + - - +
467G GLN* 2.5 29.6 + - - +
479G SER* 2.9 31.9 + - - +
480G ALA* 3.7 9.0 - - - +
483G THR* 3.4 27.5 + - + +
497G SER 2.9 9.8 + - - +
498G ARG* 3.7 12.2 - - + +
499G VAL* 3.1 23.6 + - - +
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Residues in contact with TRP 466 (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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441G PHE* 4.1 28.9 - + + -
442G TYR 4.1 8.7 - - - -
443G GLY* 4.2 7.9 - - - -
445G ASP 3.9 5.8 - - - -
446G SER* 3.5 1.0 - - - -
447G TYR* 2.8 60.2 + + + +
449G ILE* 5.2 6.1 - - + -
464G TYR 3.5 4.3 + - - +
465G ASN* 1.3 70.4 - - - +
467G GLN* 1.3 59.5 + - - +
468G GLY* 3.4 26.5 - - - -
499G VAL* 3.3 35.2 - - + -
501G GLN* 3.5 35.8 - - + +
504G GLU* 3.2 26.6 + - + +
508G LEU* 4.2 8.3 - - + -
517G MET* 3.3 24.8 - - + +
519G ILE* 4.1 3.4 - - + -
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Residues in contact with GLN 467 (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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145A SER 5.0 0.9 - - - +
146A GLY* 3.2 20.2 + - - +
446G SER* 4.0 9.2 - - - +
465G ASN* 2.5 31.8 + - - +
466G TRP* 1.3 75.3 - - - +
468G GLY* 1.3 69.9 + - - +
469G ALA* 4.4 0.5 - - - -
476G VAL* 3.0 34.4 - - + +
479G SER* 3.7 13.0 + - - +
498G ARG* 3.7 28.1 + - - +
499G VAL 3.1 11.7 + - - +
500G VAL* 3.8 9.2 - - + +
501G GLN 3.3 18.1 + - - -
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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
------------------------------------------------------------
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