Contacts of the helix formed by residues 723 - 731 (chain A) in PDB entry 1SIW
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 GLY 723 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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617A GLN* 3.7 8.2 + - - -
721A GLY 3.4 0.2 + - - -
722A LYS* 1.3 75.7 - - - +
724A HIS* 1.3 66.4 + - - +
725A GLU 3.3 2.9 - - - -
726A PHE* 3.0 30.1 + - - +
727A MET* 3.1 13.0 + - - +
1185A ASN 3.8 0.2 - - - -
1188A THR* 3.3 32.2 + - - -
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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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717A LEU* 3.3 33.2 + - - -
718A GLY* 4.5 4.0 - - - -
719A SER 5.6 0.7 - - - -
721A GLY 3.5 8.9 + - - +
723A GLY* 1.3 74.2 - - - +
725A GLU* 1.3 71.1 + - - +
727A MET* 3.1 9.6 + - + +
728A LEU* 3.1 52.4 + - + +
781A TYR* 5.5 3.9 - + - -
1167A ARG* 2.8 41.6 + - + -
1183A ILE* 3.0 31.9 - - + +
1185A ASN* 2.9 23.5 + - + +
1186A SER* 4.0 0.9 - - - +
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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 GLY 3.3 1.2 - - - -
724A HIS* 1.3 85.1 + - - +
726A PHE* 1.3 60.7 + - + +
728A LEU* 3.6 10.3 + - - +
729A LYS* 3.2 23.2 + - - +
736A HIS* 3.5 11.4 - - - +
737A GLY* 2.6 36.7 + - - +
738A ILE* 3.6 18.0 - - + +
1141A ASN 3.4 26.2 + - - +
1142A GLY* 4.1 3.6 - - - -
1143A ALA 4.7 2.0 - - - +
1167A ARG* 3.8 15.7 + - - -
1179A GLN* 4.9 1.2 - - - +
1182A GLY* 4.5 1.4 - - - -
1185A ASN 4.6 0.4 + - - -
1186A SER* 2.9 32.6 + - - +
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Residues in contact with PHE 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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615A SER 3.6 8.3 - - - +
617A GLN* 3.6 28.0 - - + +
620A TYR* 3.4 43.1 - + + -
723A GLY* 3.0 23.6 + - - +
725A GLU* 1.3 75.6 - - - +
727A MET* 1.3 61.6 + - - +
730A TYR* 2.9 40.0 + + - +
738A ILE* 3.3 28.3 - - + -
1140A SER 5.2 0.2 - - - -
1141A ASN* 3.7 39.9 - - + -
1188A THR 4.2 0.9 - - - -
1189A ARG* 3.6 26.9 - - + -
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Residues in contact with MET 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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219A TRP* 3.8 22.4 - - + -
611A PHE* 3.4 43.5 - - + -
615A SER* 4.1 17.5 - - - +
617A GLN* 4.6 0.2 - - - +
716A LEU* 4.7 3.1 - - + -
717A LEU* 3.9 30.7 - - + -
721A GLY* 4.2 15.5 - - - +
722A LYS 4.0 7.2 - - - +
723A GLY 3.1 13.6 + - - +
724A HIS* 3.1 10.0 + - + +
726A PHE* 1.3 76.6 - - - +
728A LEU* 1.3 60.8 + - + +
731A LEU* 2.9 37.9 + - + +
732A LEU* 3.1 10.1 + - - +
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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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717A LEU* 5.2 4.7 - - + +
724A HIS* 3.1 42.3 + - + +
725A GLU* 3.8 19.1 - - - +
727A MET* 1.3 80.3 - - + +
729A LYS* 1.3 57.2 + - - +
732A LEU* 3.3 19.6 - - + +
733A GLY 2.9 25.1 + - - -
734A THR* 3.1 23.3 + - + -
735A GLU 4.0 15.5 - - - +
736A HIS* 4.6 0.9 - - + -
781A TYR* 4.1 22.2 - - + +
1167A ARG* 3.6 26.7 - - - +
1179A GLN* 6.1 0.4 - - - +
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Residues in contact with LYS 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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620A TYR* 3.1 11.1 + - - -
725A GLU 3.2 15.6 + - - +
726A PHE 3.8 2.9 - - - +
728A LEU* 1.3 80.6 - - - +
730A TYR* 1.3 99.3 + - + +
733A GLY* 3.2 23.0 + - - -
734A THR 4.0 8.7 - - - +
736A HIS* 3.5 39.9 + - + +
738A ILE* 4.0 7.6 - - + -
742A ASP* 5.5 2.0 + - - -
762A GLU* 3.7 34.3 - - - +
763A GLY 3.5 3.6 + - - -
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Residues in contact with TYR 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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614A HIS 4.0 4.5 - - - +
615A SER* 3.1 34.8 - - - +
616A SER* 3.7 19.5 - - - +
619A ARG* 4.2 9.0 + - - -
620A TYR* 2.7 40.9 + + - -
726A PHE* 2.9 26.1 + + - +
729A LYS* 1.3 108.8 + - + +
731A LEU* 1.3 61.0 + - - +
742A ASP* 4.9 2.1 + - - -
760A GLY* 4.4 17.2 + - - -
761A LEU 3.3 22.9 - - - +
762A GLU* 3.7 7.7 - - + -
763A GLY 3.1 4.4 + - - -
764A LYS* 3.0 30.6 + - - +
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Residues in contact with LEU 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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152A ARG* 3.9 0.5 + - - -
610A TYR* 6.5 0.7 - - + -
611A PHE* 4.0 30.5 - - + -
614A HIS* 3.5 37.0 - - + +
615A SER* 4.0 12.1 - - - -
706A PRO* 5.1 2.9 - - + -
709A LEU* 5.6 1.1 - - + -
717A LEU* 5.0 6.3 - - + -
727A MET* 2.9 33.5 + - + +
730A TYR* 1.3 74.4 - - - +
732A LEU* 1.3 71.4 + - + +
763A GLY 3.6 0.3 - - - -
764A LYS* 3.3 10.5 + - + +
765A LEU* 3.0 56.5 + - + +
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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