Contacts of the strand formed by residues 680 - 684 (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 VAL 680 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673G LEU* 3.7 30.5 - - + -
674G LEU 3.6 6.7 - - - +
675G ASP* 3.6 26.5 - - + +
679G GLN* 1.3 86.1 - - - +
681G PHE* 1.3 64.5 + - - +
682G VAL* 3.7 1.2 + - + +
700G ALA* 4.0 14.1 - - + +
703G TYR* 5.7 3.1 - - + -
704G ILE* 4.4 22.4 - - + -
711G ARG* 4.5 6.3 - - - +
715G THR* 5.1 0.2 - - + -
716G PRO 3.0 8.0 + - - +
717G ILE* 3.4 11.8 - - + +
718G THR 2.9 24.9 + - - +
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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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672G MET 3.5 0.7 - - - +
673G LEU* 3.4 6.8 - - - +
674G LEU* 2.8 49.7 + - + +
676G THR* 4.4 12.6 - - + -
679G GLN* 3.2 38.4 - - + -
680G VAL* 1.3 73.4 - - - +
682G VAL* 1.3 60.5 + - - +
683G TRP 3.8 0.6 + - - -
718G THR* 3.4 16.6 - - + -
720G VAL* 3.6 21.8 - - + -
726G PRO* 4.3 8.7 - - + -
728G SER* 3.0 43.3 - - - -
729G PHE* 3.4 38.8 - + + -
732G TRP* 4.9 0.2 - - - -
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Residues in contact with VAL 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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671G VAL* 4.1 16.6 - - + -
672G MET 3.3 4.7 - - - +
673G LEU* 4.0 16.8 - - + -
680G VAL 4.2 0.4 - - - +
681G PHE* 1.3 75.2 - - - +
683G TRP* 1.3 56.8 + - - +
684G VAL* 3.7 10.0 + - + -
693G LYS* 4.6 7.9 - - + -
696G ALA* 5.0 4.0 - - + -
697G LEU* 3.9 17.0 - - + -
700G ALA* 5.1 0.7 - - + -
717G ILE* 3.6 26.7 - - + -
718G THR 2.8 18.1 + - - +
719G VAL* 3.5 14.8 - - + +
720G VAL* 3.0 24.7 + - - +
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Residues in contact with TRP 683 (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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666G LEU* 3.6 42.3 - - + +
667G ALA 3.5 23.8 - - - -
668G THR* 4.3 0.9 - - - -
671G VAL* 3.2 3.0 - - - -
672G MET* 2.5 66.2 + - + +
681G PHE 3.8 0.6 - - - +
682G VAL* 1.3 70.1 - - - +
684G VAL* 1.3 59.8 + - - +
685G GLY* 3.6 19.3 - - - -
720G VAL* 3.2 31.1 - - + +
722G GLN* 3.7 34.2 - - + +
725G GLU* 2.9 19.6 + - - -
729G PHE* 3.6 30.3 - + + -
741G TRP* 3.9 9.4 - + - -
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Residues in contact with VAL 684 (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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670G ASP 4.1 2.2 - - - -
671G VAL* 4.2 5.8 - - + -
682G VAL* 4.2 12.1 - - + +
683G TRP* 1.3 74.4 - - - +
685G GLY* 1.3 66.6 + - - +
686G LYS* 6.1 0.2 - - - -
688G SER* 4.3 10.5 - - - +
693G LYS* 3.5 43.5 - - + +
719G VAL* 4.4 3.1 - - + -
720G VAL 3.0 17.4 + - - +
721G LYS* 3.6 25.1 - - + -
722G GLN* 3.2 19.2 + - - +
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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