Contacts of the strand formed by residues 832 - 835 (chain A) in PDB entry 6Q6Q
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 832 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610A LEU* 3.2 13.9 - - + +
612A LEU* 3.7 25.6 - - + -
679A LEU* 3.8 21.8 - - + -
759A LEU* 3.6 3.3 - - - +
760A VAL* 2.9 36.3 + - - +
821A THR* 3.6 27.2 - - + +
824A ALA* 4.3 3.6 - - + +
825A ALA* 3.6 31.2 - - + +
828A HIS* 6.4 0.4 - - + -
830A ARG* 3.8 2.9 + - + +
831A ALA* 1.3 79.0 - - - +
833A ARG* 1.3 62.5 + - - +
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Residues in contact with ARG 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LYS* 6.4 2.7 - - - +
600A CYS 4.1 3.6 + - - -
601A ASP* 3.0 51.1 + - - +
603A MET* 3.1 21.8 + - - +
604A PRO 3.6 9.7 + - - -
605A LEU* 3.7 6.1 - - - +
609A GLU* 2.7 41.5 + - - +
610A LEU 2.8 9.5 + - - +
611A PHE* 3.4 22.8 - - + -
612A LEU 3.1 23.3 + - - -
758A MET 3.4 13.9 - - - +
759A LEU* 3.7 22.4 - - + +
832A VAL* 1.3 74.6 - - - +
834A CYS* 1.3 62.2 + - - +
835A VAL* 4.1 11.4 - - + -
3005A MLI 4.4 8.1 + - - -
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Residues in contact with CYS 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A LEU* 3.4 25.4 - - + +
614A PHE* 3.4 30.3 - - - -
756A GLN 3.7 2.3 - - - +
757A SER* 3.5 3.1 - - - -
758A MET* 2.9 42.6 + - + +
817A ILE* 3.7 12.3 - - - -
821A THR* 4.0 19.1 - - + +
832A VAL 4.4 0.2 + - - -
833A ARG* 1.3 74.5 - - - +
835A VAL* 1.3 60.8 + - - +
836A LEU* 4.2 12.3 - - - -
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Residues in contact with VAL 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 5.6 6.5 - - + -
601A ASP* 3.2 37.0 - - + +
611A PHE* 3.4 29.3 - - + -
612A LEU 5.3 0.2 - - - +
683A GLU* 4.7 2.5 - - - +
687A LYS* 4.7 5.5 + - - -
755A THR* 4.1 4.0 - - - +
756A GLN 3.3 2.9 - - - +
757A SER* 3.8 26.5 - - - +
758A MET 4.4 1.6 - - - +
833A ARG* 4.1 13.0 - - + -
834A CYS* 1.3 79.4 - - - +
836A LEU* 1.3 75.4 + - - +
837A GLU* 4.0 1.2 + - - +
840A GLU* 4.8 0.7 - - - +
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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