Contacts of the helix formed by residues 724 - 739 (chain A) in PDB entry 3THY
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 THR 724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711A ARG* 5.8 0.2 + - - -
723A SER* 1.3 72.7 - - - +
725A PHE* 1.3 66.1 + - + +
727A ALA* 3.4 8.2 + - - +
728A GLU* 3.4 18.7 + - - +
753A GLY* 6.4 1.1 - - - -
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Residues in contact with PHE 725 (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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723A SER* 3.3 2.6 - - - -
724A THR* 1.3 80.8 + - + +
726A MET* 1.3 78.9 + - + +
727A ALA 3.0 1.6 - - - -
728A GLU* 3.0 23.9 + - - +
729A MET* 3.2 42.8 + - + +
751A GLY* 5.8 0.7 - - - -
753A GLY* 3.8 37.2 - - - +
754A THR* 3.9 28.9 - - + -
762A LEU* 4.3 14.8 - - + -
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Residues in contact with MET 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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723A SER* 3.4 27.8 + - - +
725A PHE* 1.3 95.7 - - + +
727A ALA* 1.3 61.1 + - - +
729A MET* 3.4 12.0 + - + -
730A LEU* 3.2 39.4 + - + +
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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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723A SER 3.0 13.7 + - - +
724A THR* 3.5 13.7 - - - +
725A PHE 3.0 0.4 - - - -
726A MET* 1.3 76.0 - - - +
728A GLU* 1.3 59.9 + - - +
730A LEU* 3.2 12.1 + - - +
731A GLU* 2.9 35.2 + - - +
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Residues in contact with GLU 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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711A ARG* 3.2 43.4 + - - +
724A THR 3.4 7.8 + - - +
725A PHE* 3.0 15.3 + - - +
727A ALA* 1.3 79.2 - - - +
729A MET* 1.3 64.2 + - + +
731A GLU* 3.3 3.4 + - - +
732A THR* 2.8 35.7 + - - +
749A GLU 4.3 3.1 - - - +
750A LEU* 3.0 18.1 - - + +
751A GLY* 2.7 35.2 + - - -
752A ARG* 4.4 6.3 + - - +
753A GLY* 4.7 6.5 + - - -
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Residues in contact with MET 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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725A PHE* 3.2 41.4 + - + +
726A MET* 3.6 17.7 - - + +
727A ALA 3.2 0.4 - - - -
728A GLU* 1.3 105.1 - - + +
730A LEU* 1.3 53.1 + - + +
732A THR* 2.7 28.5 + - - +
733A ALA* 2.7 25.1 + - - +
750A LEU* 4.7 6.1 - - + -
762A LEU* 4.2 28.7 - - + -
766A ILE* 5.4 4.0 - - + -
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Residues in contact with LEU 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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183A GLN* 5.2 6.4 + - - +
726A MET* 3.2 32.5 + - + +
727A ALA* 3.2 10.6 + - - +
729A MET* 1.3 76.7 - - + +
731A GLU* 1.3 61.8 + - - +
733A ALA* 3.3 10.0 + - + +
734A SER* 2.9 32.2 + - - -
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Residues in contact with GLU 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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219A ARG* 3.6 26.9 + - - +
303A ASP* 5.8 1.6 - - - +
305A ALA* 3.3 27.5 - - + +
710A ALA 4.4 7.4 - - - +
711A ARG* 3.6 31.0 + - - +
713A GLY* 4.7 7.9 - - - -
727A ALA* 2.9 21.3 + - - +
728A GLU* 3.6 5.8 - - - +
730A LEU* 1.3 78.6 - - - +
732A THR* 1.3 56.2 + - - +
734A SER* 3.3 8.8 - - - -
735A ILE* 3.2 31.9 + - + +
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Residues in contact with THR 732 (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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711A ARG* 4.3 16.4 - - + -
728A GLU 2.8 16.6 + - - +
729A MET* 2.7 30.3 + - - +
731A GLU* 1.3 72.6 - - - +
733A ALA* 1.3 56.8 + - - -
734A SER 3.1 1.8 - - - -
735A ILE* 3.3 8.5 + - + +
736A LEU* 2.9 44.7 + - + +
747A ILE* 5.7 2.9 - - + -
750A LEU* 3.8 30.3 - - + -
766A ILE* 4.6 16.9 - - + +
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Residues in contact with ALA 733 (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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183A GLN* 3.8 16.2 - - - +
729A MET 2.7 22.0 + - - +
730A LEU* 3.6 12.8 - - + +
732A THR* 1.3 72.3 - - - +
734A SER* 1.3 63.7 + - - +
736A LEU* 4.7 5.8 - - - -
737A ARG* 3.3 36.8 + - - +
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Residues in contact with SER 734 (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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183A GLN* 3.9 27.3 + - - +
185A SER* 4.3 1.0 + - - -
188A GLU* 4.9 11.6 + - - -
216A ILE* 5.5 3.6 - - - +
219A ARG* 5.7 2.8 + - - -
303A ASP* 6.2 3.4 - - - -
730A LEU 2.9 15.3 + - - -
731A GLU* 3.3 14.0 - - - -
732A THR 3.1 0.2 - - - -
733A ALA* 1.3 75.1 - - - +
735A ILE* 1.3 60.3 + - - +
737A ARG* 3.0 4.7 + - - +
738A SER* 2.7 39.1 + - - -
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Residues in contact with ILE 735 (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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303A ASP* 4.1 15.3 - - - +
709A LEU* 3.8 20.9 - - + -
710A ALA 3.6 26.7 - - - +
711A ARG* 3.8 20.2 - - + -
731A GLU* 3.2 17.8 + - + +
732A THR* 3.3 12.8 + - + +
734A SER* 1.3 75.1 - - - +
736A LEU* 1.3 64.5 + - + +
738A SER* 4.3 0.4 - - - -
739A ALA* 3.0 30.7 + - - +
745A ILE* 3.7 36.6 - - + -
747A ILE* 5.3 3.1 - - + -
770A ILE* 5.5 0.7 - - + -
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Residues in contact with LEU 736 (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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732A THR* 2.9 30.1 + - - +
733A ALA* 4.3 6.5 - - - +
735A ILE* 1.3 79.1 - - + +
737A ARG* 1.3 64.5 + - + +
738A SER 3.5 0.2 - - - -
739A ALA 4.7 3.6 - - - +
766A ILE* 4.2 28.5 - - + -
769A TYR* 4.3 29.0 + - + -
770A ILE* 3.8 33.7 - - + -
773A LYS* 5.0 3.5 + - - -
774A ILE* 4.1 24.2 - - + +
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Residues in contact with ARG 737 (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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181A ASN* 3.4 22.4 + - + +
182A ASP* 5.9 1.4 + - - -
183A GLN* 3.4 32.3 + - + -
185A SER* 4.3 0.9 - - - -
733A ALA* 3.3 26.0 + - - +
734A SER 3.0 3.4 + - - -
736A LEU* 1.3 84.7 - - + +
738A SER* 1.3 60.7 + - - +
739A ALA 4.9 1.1 - - - -
769A TYR* 6.2 0.2 - - - -
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Residues in contact with SER 738 (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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181A ASN* 4.9 0.2 - - - +
185A SER* 2.7 34.3 + - - -
188A GLU* 5.3 2.6 + - - -
706A ASP* 4.8 0.3 - - - +
707A CYS* 4.6 6.8 - - - -
709A LEU* 3.7 20.6 - - - -
734A SER* 2.7 23.7 + - - -
737A ARG* 1.3 80.4 - - - +
739A ALA* 1.3 68.3 + - - +
740A THR* 3.8 9.2 + - - +
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Residues in contact with ALA 739 (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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707A CYS* 4.5 0.7 - - - -
709A LEU* 3.4 16.2 - - + -
735A ILE 3.0 18.1 + - - +
736A LEU 4.8 5.5 - - - +
737A ARG 3.9 1.2 - - - -
738A SER* 1.3 83.6 + - - +
740A THR* 1.3 63.4 + - - +
743A SER* 3.4 14.8 - - - +
745A ILE* 3.6 25.4 - - + -
774A ILE* 4.6 13.7 - - + +
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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