Contacts of the strand formed by residues 761 - 769 (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 ARG 761 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A VAL* 4.7 0.2 - - - -
747A LEU* 3.6 2.8 - - - -
748A ARG* 2.8 45.2 + - + +
759A PRO* 3.6 4.6 + - + +
760A VAL* 1.3 77.9 - - - +
762A ALA* 1.3 63.2 + - - +
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Residues in contact with ALA 762 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A VAL* 4.1 8.8 - - + +
623A PHE* 3.6 37.9 - - + +
745A PHE* 4.6 4.6 - - + -
746A SER 3.2 5.8 - - - +
747A LEU* 3.6 19.3 - - + -
761A ARG* 1.3 78.2 - - - +
763A GLU* 1.3 61.3 + - - +
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Residues in contact with GLU 763 (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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724A LYS* 4.5 17.4 + - - +
745A PHE* 3.4 5.2 - - - -
746A SER* 2.9 37.2 + - - -
762A ALA* 1.3 75.8 - - - +
764A GLN* 1.3 72.6 + - + +
765A ALA* 3.0 4.6 + - - -
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Residues in contact with GLN 764 (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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625A LYS* 3.3 30.2 + - - +
743A TYR* 3.7 13.4 - - - -
744A ALA 3.6 2.7 - - - +
745A PHE* 3.5 28.8 - - + -
763A GLU* 1.3 79.6 - - - +
765A ALA* 1.3 60.3 + - - +
766A LYS 3.8 13.7 - - - +
767A GLU* 3.0 36.2 + - - +
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Residues in contact with ALA 765 (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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723A LEU* 3.7 34.8 - - + +
724A LYS* 3.9 31.1 - - + +
744A ALA 2.8 7.3 + - - +
746A SER* 4.1 7.4 - - - +
763A GLU* 3.0 5.0 + - - +
764A GLN* 1.3 73.6 - - - +
766A LYS* 1.3 68.0 + - + +
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Residues in contact with LYS 766 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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722A TYR 4.2 0.8 + - - -
723A LEU* 2.5 58.1 + - + +
734A TRP* 4.5 3.4 - - + -
742A ILE 4.3 0.2 - - - -
743A TYR* 3.6 3.3 - - - -
744A ALA* 3.0 39.3 + - + +
764A GLN* 3.6 11.1 - - - +
765A ALA* 1.3 81.5 - - - +
767A GLU* 1.3 62.4 + - - +
768A ILE* 4.2 13.9 - - + -
824A LEU* 4.3 2.0 - - - +
825A PRO* 2.7 32.1 + - - +
826A LYS 5.3 0.4 - - - -
827A VAL* 3.6 19.8 - - + +
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Residues in contact with GLU 767 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625A LYS* 5.2 1.6 + - - -
630A PRO 4.0 21.3 - - - -
741A THR* 3.9 12.1 - - + +
742A ILE 3.4 3.4 - - - -
743A TYR* 3.5 27.5 - - + +
764A GLN* 3.0 21.8 + - - +
766A LYS* 1.3 75.7 - - - +
768A ILE* 1.3 62.4 + - - +
769A GLN* 4.0 2.5 + - + +
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Residues in contact with ILE 768 (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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734A TRP* 3.9 27.8 - - + -
741A THR* 3.3 6.1 - - - +
742A ILE* 2.7 65.1 + - + +
766A LYS* 4.2 17.5 - - + -
767A GLU* 1.3 75.3 - - - +
769A GLN* 1.3 69.5 + - - +
770A LEU* 4.9 0.4 - - + -
811A LEU* 4.4 3.8 - - + -
813A VAL* 6.2 0.2 - - + -
822A PHE* 4.7 17.5 - - + -
827A VAL* 3.7 38.1 - - + -
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Residues in contact with GLN 769 (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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630A PRO* 5.0 7.3 - - - +
739A GLY 3.2 21.9 + - - +
740A GLY 3.5 4.3 + - - -
741A THR* 3.1 23.1 + - + +
767A GLU* 4.0 2.7 + - + +
768A ILE* 1.3 80.2 - - - +
770A LEU* 1.3 92.2 + - - +
771A MET* 3.8 20.8 + - + +
773A ARG* 3.5 33.5 + - - +
820A LYS* 5.6 0.3 + - - -
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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