Contacts of the strand formed by residues 767 - 772 (chain A) in PDB entry 6EJ9
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 767 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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742A VAL* 3.2 5.2 - - - -
743A GLY 2.8 37.9 + - - +
744A THR* 4.7 7.2 - - - -
745A ASP 5.4 2.0 - - - +
746A TRP* 4.9 6.1 - - + +
753A PHE* 3.6 16.2 - - + -
765A GLU 3.9 3.6 - - - +
766A PRO* 1.3 77.6 - - - +
768A GLY* 1.3 69.0 + - - +
784A TRP* 4.1 3.1 - - - -
807A HIS* 4.2 21.3 - - + -
808A TYR 3.6 17.9 - - - +
809A LYS* 3.6 26.9 - - + +
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Residues in contact with GLY 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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741A GLU 3.7 4.3 - - - -
742A VAL* 4.4 4.7 - - - -
767A VAL* 1.3 72.8 - - - +
769A MET* 1.3 59.7 + - - -
770A GLN* 3.7 13.3 + - - -
784A TRP* 3.8 20.3 - - - -
795A TYR* 5.5 1.5 + - - -
807A HIS* 3.1 5.9 - - - +
808A TYR* 3.0 36.3 + - - +
823A VAL* 6.1 1.6 - - - -
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Residues in contact with MET 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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739A PHE* 4.4 11.4 - - + +
740A SER* 3.3 8.8 + - - -
741A GLU* 2.8 65.3 + - + +
746A TRP* 3.7 36.1 - - + -
751A ARG 5.6 0.9 - - - +
752A LEU* 5.9 1.1 - - - -
753A PHE* 4.0 17.0 - - + -
767A VAL 4.0 0.2 + - - -
768A GLY* 1.3 74.1 - - - -
770A GLN* 1.3 82.6 + - - +
771A LYS* 3.9 5.8 - - + -
805A PHE* 4.1 16.6 - - + -
806A THR 3.3 10.3 - - - +
807A HIS* 4.2 4.7 - - + -
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Residues in contact with GLN 770 (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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737A LEU* 4.2 2.2 - - + -
739A PHE 3.5 7.0 - - - +
740A SER* 4.3 4.8 + - - +
768A GLY* 3.7 17.1 + - - +
769A MET* 1.3 91.8 + - - +
771A LYS* 1.3 61.0 + - - +
772A TRP* 3.6 20.4 + - + +
780A VAL* 6.4 0.2 - - + -
782A VAL* 4.7 17.9 - - - +
795A TYR* 5.1 3.6 + - - -
797A ILE* 3.8 17.1 - - + +
805A PHE* 3.4 3.8 - - - -
806A THR* 2.8 65.8 + - - +
807A HIS* 4.3 1.7 + - - -
823A VAL* 5.7 3.4 - - - +
825A ILE* 3.8 26.5 - - + +
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Residues in contact with LYS 771 (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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737A LEU* 3.6 5.9 - - - +
738A GLN* 2.9 52.2 + - + +
739A PHE* 2.9 33.7 + - + +
769A MET* 3.9 3.8 - - + -
770A GLN* 1.3 73.2 - - - +
772A TRP* 1.3 65.5 + - - +
804A GLU 3.5 6.1 - - - +
805A PHE* 3.7 40.2 - - + -
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Residues in contact with TRP 772 (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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736A ARG* 3.6 12.1 - - + +
737A LEU* 3.6 44.9 - - + -
738A GLN* 3.7 10.7 + - - +
770A GLN* 3.6 31.4 - - + +
771A LYS* 1.3 77.8 - - - +
773A GLY* 1.3 64.5 + - - +
778A VAL* 5.0 3.8 - - + -
780A VAL* 4.0 26.9 - - + -
797A ILE* 5.0 0.4 - - + -
799A ILE* 3.4 51.5 - - + +
803A ALA* 3.9 15.6 - - + +
804A GLU* 2.9 31.1 + - - +
805A PHE 4.5 0.2 - - - -
806A THR* 2.9 31.9 + - + -
825A ILE* 4.9 6.5 - - + -
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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