Contacts of the strand formed by residues 721 - 728 (chain A) in PDB entry 5J9H
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 721 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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718A SER* 5.6 1.1 - - - +
719A LYS 4.2 7.9 - - - +
720A GLN* 1.3 76.1 - - - +
722A ILE* 1.3 76.5 + - - +
723A HIS* 3.9 2.4 + - + +
810A ARG 3.7 0.9 - - - +
811A TYR* 3.4 4.7 - - - -
812A THR* 2.9 41.8 + - - +
949A GLU* 4.0 27.8 - - + +
950A TRP 3.6 9.4 - - - +
951A ILE* 4.2 17.9 - - + -
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Residues in contact with ILE 722 (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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720A GLN* 4.8 6.7 - - - +
721A VAL* 1.3 75.6 - - - +
723A HIS* 1.3 62.2 + - - +
809A LEU* 4.0 15.5 - - + -
810A ARG 3.6 2.9 - - - +
811A TYR* 3.7 34.1 - - + -
850A PHE* 4.1 12.1 - - + -
948A LEU 3.8 0.5 - - - +
949A GLU* 3.2 6.6 - - - -
950A TRP* 2.8 85.6 + - + +
952A ASP* 3.9 22.7 - - + +
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Residues in contact with HIS 723 (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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721A VAL* 5.2 1.8 - - + +
722A ILE* 1.3 74.8 - - - +
724A ALA* 1.3 66.2 + - - +
725A GLU* 2.9 29.0 + - + -
808A SER* 3.8 0.9 - - - +
809A LEU* 3.5 4.5 - - - -
810A ARG* 2.8 52.0 + - + +
812A THR* 6.3 0.4 - - + -
947A ALA* 3.6 19.6 - - + +
948A LEU 3.8 2.5 - - - -
949A GLU* 2.7 35.3 + - + +
1023A MET* 3.1 34.8 - - + -
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Residues in contact with ALA 724 (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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722A ILE 4.1 0.4 - - - -
723A HIS* 1.3 76.0 - - - +
725A GLU* 1.3 63.5 + - - +
726A ILE* 3.6 14.9 + - + +
806A ILE* 4.4 9.4 - - + -
808A SER 3.3 11.2 - - - +
809A LEU* 4.1 14.6 - - + -
856A LEU* 5.9 0.7 - - + -
947A ALA* 3.2 2.4 - - - +
948A LEU 2.8 41.9 + - - +
950A TRP* 4.2 15.0 - - + -
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Residues in contact with GLU 725 (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 HIS* 2.9 31.0 + - + +
724A ALA* 1.3 73.0 - - - +
726A ILE* 1.3 55.6 + - - +
806A ILE* 3.7 1.2 - - - -
807A VAL* 2.7 40.2 + - + -
808A SER* 3.3 30.4 + - - +
946A SER* 2.7 30.2 + - - +
947A ALA* 3.6 6.1 - - - +
1023A MET* 4.1 7.0 - - + +
1025A TYR* 3.6 21.8 + - + -
1044A LYS 3.9 10.5 - - - +
1045A GLY* 3.5 4.8 - - - -
1046A GLY 3.1 14.2 + - - -
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Residues in contact with ILE 726 (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 ALA* 3.7 20.4 - - + +
725A GLU* 1.3 80.1 - - - +
727A GLN* 1.3 65.0 - - - +
728A HIS* 3.8 21.3 + - + +
804A PHE* 3.6 44.4 - - + -
805A LYS 3.2 13.5 - - - +
806A ILE* 4.6 3.6 - - + -
807A VAL* 3.9 5.1 - - - +
856A LEU* 5.6 2.0 - - + -
943A ILE* 4.3 2.7 - - + -
946A SER* 2.8 36.6 + - - +
947A ALA* 3.7 17.0 - - - +
948A LEU* 4.2 13.2 - - + +
993A GLY* 5.0 6.4 - - - -
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Residues in contact with GLN 727 (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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726A ILE* 1.3 74.8 - - - +
728A HIS* 1.3 60.3 + - - +
729A LEU* 3.1 30.0 + - + +
804A PHE* 3.3 6.2 - - - -
805A LYS* 2.9 46.2 + - + +
807A VAL* 3.6 14.6 - - + +
993A GLY* 2.8 31.6 + - - +
994A SER* 3.9 9.5 - - - +
995A GLY 4.4 3.2 - - - +
1072A LEU* 3.7 36.0 - - + +
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Residues in contact with HIS 728 (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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726A ILE* 3.8 16.8 - - + +
727A GLN* 1.3 69.6 - - - +
729A LEU* 1.3 63.3 + - - +
730A GLY* 3.2 4.9 + - - +
802A LYS* 4.5 14.5 + - - +
803A VAL 4.1 4.7 - - - -
804A PHE* 3.7 26.0 - + - -
888A THR* 5.2 4.2 - - - +
889A PRO* 6.2 0.3 - - - +
943A ILE* 4.1 12.1 - - + -
944A SER 3.4 14.3 + - - -
945A THR* 3.1 29.1 + - - -
946A SER* 4.9 0.9 - - - -
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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