Contacts of the strand formed by residues 722 - 727 (chain C) in PDB entry 6RIN
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 GLY 722 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720C ARG 3.5 1.8 + - - -
721C GLY* 1.3 75.8 - - - -
723C VAL* 1.3 64.3 + - - +
734C ILE* 4.7 1.3 - - - +
735C LYS 3.4 12.3 - - - -
737C ASN* 3.3 19.3 - - - -
776C PRO* 3.5 4.7 - - - +
777C VAL* 2.9 39.0 + - - +
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Residues in contact with VAL 723 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722C GLY* 1.3 78.1 - - - +
724C VAL* 1.3 76.3 + - - +
725C GLN* 3.3 0.8 + - + -
734C ILE* 3.9 2.3 - - - -
735C LYS* 3.0 43.2 + - + +
736C VAL 5.2 0.4 - - - -
737C ASN* 4.3 9.1 + - - +
774C GLY* 4.9 4.9 - - - -
775C GLU 4.4 12.8 - - - +
776C PRO* 4.5 11.4 - - + -
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Residues in contact with VAL 724 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722C GLY 4.2 0.2 - - - -
723C VAL* 1.3 81.5 - - - +
725C GLN* 1.3 61.4 + - - +
726C TYR 4.1 7.4 - - - +
727C VAL* 3.7 30.5 - - + -
732C ILE* 5.0 1.8 - - + -
734C ILE* 3.5 25.1 - - + -
771C VAL* 4.2 17.7 - - + -
772C SER 4.1 13.9 - - - +
773C LEU* 4.6 2.1 - - - +
774C GLY* 3.5 17.3 + - - -
775C GLU* 3.3 23.9 + - + +
777C VAL* 3.9 15.9 - - + -
783C LEU* 5.0 1.1 - - + -
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Residues in contact with GLN 725 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723C VAL* 3.3 6.1 + - + +
724C VAL* 1.3 77.5 - - - +
726C TYR* 1.3 65.9 + - + +
733C VAL* 3.0 24.0 + - + +
735C LYS* 3.8 38.6 + - + +
748C ILE* 4.8 9.3 - - - +
773C LEU* 3.9 21.6 - - - +
966C ILE* 6.5 0.7 - - - -
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Residues in contact with TYR 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLU* 4.4 7.1 + - - -
73A GLY* 4.5 4.5 - - - -
134A THR* 3.9 28.5 - - + +
135A ASP* 5.7 3.4 - - + +
724C VAL* 3.8 1.0 - - - +
725C GLN* 1.3 84.0 - - + +
727C VAL* 1.3 85.8 + - - +
728C ASP* 3.3 30.7 + - + +
731C ARG* 4.1 21.9 + - + -
732C ILE* 3.6 5.5 - - - +
733C VAL* 2.9 58.0 + - + +
773C LEU* 5.3 2.7 - - + -
966C ILE* 5.9 4.9 - - + -
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Residues in contact with VAL 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLN* 3.8 28.5 - - + +
134A THR* 3.5 18.9 + - - +
724C VAL* 3.7 22.7 - - + -
726C TYR* 1.3 94.3 - - - +
728C ASP* 1.3 71.6 + - - +
731C ARG 3.9 3.6 - - - +
732C ILE* 4.9 6.7 - - + +
769C PRO* 4.2 15.5 - - + -
771C VAL* 4.1 24.2 - - + +
772C SER 4.2 0.4 - - - -
773C LEU* 4.2 17.8 - - + +
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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