Contacts of the strand formed by residues 722 - 731 (chain A) in PDB entry 2G56
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 722 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579A PHE 3.9 3.5 - - - +
580A SER* 4.0 6.2 + - - -
581A PRO* 5.2 0.3 - - - +
718A GLN 4.4 0.6 + - - +
719A LEU 3.7 5.3 + - - +
721A SER* 1.3 91.8 + - - +
723A LEU* 1.3 75.0 + - - +
756A LYS* 3.4 32.0 - - - +
757A PRO* 3.4 19.6 + - - +
758A LEU* 3.5 27.5 - - + +
759A LEU* 5.1 10.9 - - - +
762A GLN* 5.1 6.0 + - - +
586B ASP* 5.6 4.9 - - - -
588B LEU* 6.0 8.8 - - - +
702B GLU* 5.6 7.5 + - - +
703B ALA* 5.8 5.0 - - - +
706B ASP* 3.0 37.8 + - - +
711B ARG* 5.8 2.6 - - - +
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Residues in contact with LEU 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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555A ALA 4.6 0.3 - - - +
556A MET* 4.2 9.8 - - - +
578A PHE* 4.5 19.5 - - + -
579A PHE 3.3 25.4 - - - +
580A SER* 3.5 9.6 - - - -
627A MET* 4.9 0.4 - - + -
719A LEU* 3.3 26.7 - - + +
720A LEU* 3.6 34.5 - - + +
722A ARG* 1.3 78.9 - - - +
724A HIS* 1.3 64.3 + - - +
725A ILE* 5.0 6.1 - - + -
749A LEU* 4.6 15.3 - - + -
755A THR* 3.8 16.0 - - + +
756A LYS 3.2 9.9 + - - +
757A PRO* 3.8 4.2 - - - +
758A LEU* 3.4 22.3 + - - +
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Residues in contact with HIS 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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554A THR 3.9 13.7 - - - -
555A ALA* 2.8 26.0 + - - +
556A MET 3.5 3.5 + - - -
557A SER* 3.9 13.7 - - - -
558A LYS* 3.9 32.2 - - - +
577A GLU 3.5 0.7 - - - +
578A PHE* 3.7 2.4 - - - -
579A PHE* 2.9 56.0 + + + -
723A LEU* 1.3 76.1 - - - +
725A ILE* 1.3 65.5 + - - +
726A GLU* 4.7 3.6 + - - +
758A LEU* 4.4 6.5 - - + +
763A LEU* 3.8 43.5 - - + +
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Residues in contact with ILE 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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556A MET* 2.8 22.1 + - - +
557A SER* 2.9 14.9 - - - -
558A LYS 2.7 32.8 + - - +
576A PHE* 4.1 18.4 - - + -
577A GLU 3.5 7.9 - - - +
578A PHE* 3.9 20.6 - - + -
723A LEU* 5.0 5.4 - - + -
724A HIS* 1.3 83.9 - - - +
726A GLU* 1.3 59.2 + - - +
742A MET* 3.7 32.5 - - + +
745A VAL* 4.2 3.4 - - + -
746A GLU* 4.7 9.9 - - + -
749A LEU* 3.9 28.3 - - + -
755A THR* 6.3 0.4 - - + -
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Residues in contact with GLU 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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558A LYS* 3.2 27.3 - - + +
560A TRP* 3.1 22.6 + - + +
577A GLU* 2.9 36.3 + - + +
579A PHE* 3.8 28.7 - - + -
724A HIS* 4.1 4.4 + - - +
725A ILE* 1.3 73.9 - - - +
727A ALA* 1.3 61.3 + - - +
765A ARG* 5.5 0.2 + - - -
908A TRP* 3.7 5.0 - - - -
911A ILE* 3.3 23.4 - - + +
914A GLN* 4.4 6.4 - - - +
916A TYR* 2.7 32.7 + - - -
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Residues in contact with ALA 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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558A LYS 2.8 7.3 + - - -
559A LEU* 3.9 18.4 - - + -
560A TRP* 2.9 34.9 + - - -
575A ASN 3.1 12.3 - - - +
576A PHE* 3.7 26.5 - - + -
725A ILE* 4.0 1.0 - - + -
726A GLU* 1.3 75.3 - - - +
728A LEU* 1.3 62.8 + - - +
729A LEU* 4.5 2.2 - - + -
742A MET* 4.1 8.5 - - - -
908A TRP* 4.2 2.7 - - - -
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Residues in contact with LEU 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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548A PRO* 4.2 19.5 - - + -
560A TRP* 3.3 25.4 - - + +
561A PHE* 4.8 0.9 - - - -
562A LYS 5.2 0.2 - - - +
573A CYS 3.4 2.8 - - - +
575A ASN* 2.9 32.4 + - - +
727A ALA* 1.3 76.4 - - - +
729A LEU* 1.3 66.9 + - - +
730A HIS* 4.0 11.9 - - + -
904A CYS* 3.2 40.8 - - - +
907A TYR* 4.7 7.2 - - + -
908A TRP* 3.4 25.6 - - + +
911A ILE* 3.7 15.3 - - + -
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Residues in contact with LEU 729 (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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559A LEU* 3.6 18.8 - - + -
560A TRP 3.0 7.3 + - - +
561A PHE* 3.5 9.3 - - + -
562A LYS 3.2 22.0 + - - -
573A CYS 3.5 3.1 - - - -
574A LEU* 3.8 23.8 - - + -
575A ASN 4.3 0.7 - - - +
576A PHE* 3.8 28.7 - - + -
727A ALA* 4.5 3.4 - - + -
728A LEU* 1.3 80.7 - - - +
730A HIS* 1.3 60.2 + - - +
733A ILE* 4.8 6.1 - - + -
738A ALA* 3.5 46.9 - - + +
741A ILE* 4.1 18.2 - - + -
742A MET* 4.8 2.5 - - + +
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Residues in contact with HIS 730 (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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562A LYS* 3.0 49.2 + - + +
564A ASP* 3.9 13.9 - - - -
572A ALA* 3.5 0.6 - - - -
573A CYS* 2.7 42.1 + - - +
574A LEU* 5.1 0.4 - - - +
728A LEU* 3.9 20.4 - - + -
729A LEU* 1.3 74.8 - - - +
731A GLY* 1.3 59.8 + - - +
733A ILE* 4.5 3.8 - - - +
900A LEU* 3.4 29.4 - - + +
903A GLU* 3.5 23.1 + - - -
904A CYS* 3.8 31.0 - - + -
907A TYR* 3.9 10.0 - + - -
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Residues in contact with GLY 731 (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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562A LYS 3.3 2.4 + - - -
563A GLN* 3.5 6.1 - - - +
564A ASP* 2.8 35.2 + - - -
571A LYS 3.6 9.2 - - - -
572A ALA* 4.0 2.0 - - - -
730A HIS* 1.3 82.7 + - - +
732A ASN* 1.3 61.3 + - - -
733A ILE* 2.8 12.7 + - - +
900A LEU* 3.8 8.3 - - - -
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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