Contacts of the strand formed by residues 776 - 782 (chain A) in PDB entry 6N8Q
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 776 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714A ARG* 3.7 16.3 - - - +
715A THR* 2.8 19.7 + - - +
736A GLY* 3.8 13.6 - - - +
737A THR 2.9 22.8 + - - +
740A GLY* 3.9 23.3 - - - -
742A ILE* 4.1 11.2 - - + -
770A LEU* 3.9 18.4 - - + -
775A PRO* 1.3 69.7 - - - +
777A VAL* 1.3 55.8 + - - +
778A GLY 4.0 3.8 - - - +
779A ILE* 3.6 31.6 - - + -
813A VAL* 4.3 6.1 - - + -
814A VAL 3.7 11.7 - - - +
815A SER* 4.2 0.9 - - - +
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Residues in contact with VAL 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A ARG* 3.5 34.4 - - - +
715A THR* 3.3 14.5 + - - +
775A PRO 3.3 12.3 + - - +
776A VAL* 1.3 72.6 - - - +
778A GLY* 1.3 59.7 + - - +
814A VAL* 2.9 22.8 + - + +
815A SER 4.1 3.1 - - - +
816A GLU* 3.7 13.9 - - + -
843A VAL* 3.6 33.4 - - + +
844A ARG 4.8 8.3 - - - +
845A ARG* 5.5 1.3 - - - -
846A VAL* 4.1 13.0 + - + +
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Residues in contact with GLY 778 (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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715A THR* 3.7 4.7 + - - -
776A VAL* 3.6 2.5 - - - +
777A VAL* 1.3 80.5 - - - +
779A ILE* 1.3 68.1 + - - +
780A LEU* 6.2 1.1 - - - -
812A LEU* 4.5 0.4 - - - -
813A VAL* 3.5 1.0 - - - -
814A VAL* 2.7 39.0 + - - +
846A VAL* 4.2 16.2 - - - -
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Residues in contact with ILE 779 (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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715A THR* 3.8 16.5 - - + +
717A TYR* 3.3 28.7 - - + +
734A TRP* 4.0 24.5 - - + +
735A ALA* 3.8 6.3 - - - +
736A GLY* 3.6 34.1 - - - +
742A ILE* 4.1 13.7 - - + -
776A VAL* 3.6 12.8 - - + -
778A GLY* 1.3 79.5 - - - +
780A LEU* 1.3 69.7 + - - +
811A LEU* 3.8 24.2 - - + -
812A LEU 3.4 5.2 - - - +
813A VAL* 4.7 7.2 - - + -
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Residues in contact with LEU 780 (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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717A TYR* 3.5 20.4 - - + +
779A ILE* 1.3 77.8 - - - +
781A VAL* 1.3 70.7 + - - +
782A LEU* 3.6 33.4 - - + -
788A PRO* 4.2 10.1 - - + -
811A LEU* 3.7 2.3 - - - +
812A LEU* 2.7 65.8 + - + +
814A VAL* 6.0 1.8 - - + -
848A VAL* 3.5 29.8 - - + -
864A LEU* 4.2 7.6 - - + -
878A LEU* 5.5 0.9 - - + -
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Residues in contact with VAL 781 (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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717A TYR* 3.3 19.3 + - + -
719A ALA* 3.9 12.1 - - + -
721A THR* 3.6 28.7 - - + +
734A TRP* 4.7 3.1 - - - +
780A LEU* 1.3 82.7 - - - +
782A LEU* 1.3 72.7 + - - +
788A PRO* 3.4 3.8 - - - +
789A LEU* 2.8 46.8 + - + +
809A HIS* 4.0 2.2 - - - +
810A GLN 3.3 12.1 - - - +
811A LEU* 4.0 17.3 - - + -
824A LEU* 3.8 7.2 - - + -
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Residues in contact with LEU 782 (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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780A LEU* 3.6 23.1 - - + -
781A VAL* 1.3 75.9 - - - +
783A ASP* 1.3 61.3 + - - +
786A SER* 3.8 17.5 - - - +
787A VAL 3.3 3.6 - - - -
788A PRO* 3.4 30.5 - - + -
789A LEU* 4.3 1.8 - - - -
809A HIS* 3.4 11.1 - - - +
810A GLN* 2.8 49.0 + - + +
812A LEU* 5.2 8.5 - - + -
821A VAL* 5.4 5.8 - - + -
878A LEU* 4.4 17.9 - - + -
879A PRO* 3.9 28.9 - - + +
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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