Contacts of the helix formed by residues 724 - 737 (chain B) in PDB entry 1DQA
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717B VAL* 3.7 7.4 - - - -
718B ARG* 4.3 22.7 - - - +
723B THR* 1.3 89.7 + - - +
725B THR* 1.3 65.8 + - - +
726B GLU* 3.8 7.7 + - - +
727B ALA* 3.2 22.7 + - - +
728B MET* 3.1 21.3 + - - +
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Residues in contact with THR 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B VAL* 3.8 14.7 - - - +
718B ARG* 5.9 0.2 - - - +
724B THR* 1.3 73.2 - - - +
726B GLU* 1.3 63.2 + - - +
728B MET* 3.2 6.4 + - - +
729B ILE* 2.9 43.6 + - + +
783B ALA* 4.3 3.8 - - + -
788B ASN 4.6 3.6 - - - +
789B GLU* 2.7 32.4 + - - +
790B ASP 3.5 21.5 - - - +
791B LEU* 3.5 23.5 + - + +
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Residues in contact with GLU 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724B THR* 3.3 7.6 + - - +
725B THR* 1.3 79.1 - - - +
727B ALA* 1.3 63.6 + - - +
729B ILE* 3.3 8.1 + - - +
730B GLU* 3.0 40.5 + - + +
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Residues in contact with ALA 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LEU* 5.3 0.4 - - - +
723B THR* 3.6 18.2 - - - +
724B THR* 3.2 18.1 + - - +
726B GLU* 1.3 78.6 - - - +
728B MET* 1.3 63.4 + - - +
730B GLU* 3.3 7.0 + - - +
731B VAL* 3.0 28.2 + - - +
858B ALA* 4.0 13.9 - - + +
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Residues in contact with MET 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B VAL* 4.1 11.2 - - - -
721B LEU* 4.1 4.9 - - + -
723B THR* 3.6 31.9 - - + -
724B THR 3.1 10.7 + - - +
725B THR 3.7 3.8 - - - +
727B ALA* 1.3 78.0 - - - +
729B ILE* 1.3 56.8 + - - +
731B VAL* 3.4 4.6 + - - +
732B ASN* 2.8 29.3 + - - +
781B MET* 3.8 23.9 - - + +
791B LEU* 3.6 31.0 - - + -
851B LEU* 3.3 37.5 - - + +
854B MET* 4.1 7.2 - - + +
855B ALA* 3.9 17.5 - - + +
858B ALA* 4.4 4.5 - - + -
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Residues in contact with ILE 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725B THR* 2.9 36.4 + - + +
726B GLU* 3.8 6.7 - - - +
728B MET* 1.3 73.0 - - - +
730B GLU* 1.3 71.9 + - - +
732B ASN* 3.9 5.1 - - - +
733B ILE* 2.9 47.0 + - + +
781B MET* 4.2 11.2 - - + +
782B GLU* 3.6 9.0 - - - +
783B ALA* 3.3 36.1 - - + +
791B LEU* 4.0 14.6 - - + -
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Residues in contact with GLU 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A ARG* 2.9 33.8 + - - +
641A ARG* 5.3 0.2 + - - -
681A LEU* 4.0 20.3 - - + +
726B GLU* 3.0 34.0 + - + +
727B ALA* 3.8 6.1 - - - +
729B ILE* 1.3 85.0 - - - +
731B VAL* 1.3 62.5 + - - +
733B ILE* 4.7 7.8 - - - +
734B ASN* 2.9 36.3 + - - +
782D GLU* 5.0 4.2 - - - +
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Residues in contact with VAL 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A VAL* 6.2 0.9 - - + -
681A LEU* 3.6 34.3 - - + +
682A ALA* 4.0 19.5 - - + -
727B ALA* 3.0 17.2 + - + +
728B MET* 3.8 5.4 - - - +
730B GLU* 1.3 76.7 - - - +
732B ASN* 1.3 57.4 + - - +
735B LYS* 2.8 45.3 + - + +
854B MET* 3.4 20.2 - - + +
857B LEU* 4.4 9.2 - - + -
858B ALA* 3.8 20.9 - - + -
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Residues in contact with ASN 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728B MET 2.8 21.7 + - - +
729B ILE 3.2 3.3 + - - +
731B VAL* 1.3 73.8 - - - +
733B ILE* 1.3 62.7 + - + +
736B ASN* 2.8 51.4 + - - +
737B LEU* 3.4 9.4 + - - +
779B THR* 2.9 34.2 + - - +
780B LEU* 3.7 4.4 - - - +
781B MET* 3.6 38.7 + - + +
854B MET* 3.4 11.3 - - + +
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Residues in contact with ILE 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729B ILE* 2.9 40.5 + - + +
730B GLU* 4.2 9.6 - - - +
732B ASN* 1.3 78.2 - - + +
734B ASN* 1.3 73.8 + - - +
737B LEU* 3.3 20.3 - - + +
738B VAL* 2.9 27.7 + - + +
781B MET 5.2 5.8 - - - +
733D ILE* 4.1 26.9 - - + -
737D LEU* 4.4 20.9 - - + -
780D LEU* 6.3 0.4 - - + -
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Residues in contact with ASN 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A VAL* 4.6 5.4 - - + -
595A ARG* 3.7 21.8 + - - +
642A ASN* 2.8 30.2 + - - +
644A TYR* 2.6 30.2 + - - +
681A LEU* 3.7 19.0 - - + +
730B GLU* 2.9 31.6 + - - +
731B VAL 4.5 0.4 - - - +
733B ILE* 1.3 88.9 - - - +
735B LYS* 1.3 57.5 + - - +
738B VAL* 4.1 10.9 - - - +
739B GLY 3.0 8.5 + - - -
780D LEU* 5.6 1.4 - - - +
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Residues in contact with LYS 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A VAL* 5.0 3.4 - - + -
684A SER* 3.0 31.8 + - - +
685A GLY* 3.8 14.6 - - - -
686A ASN* 2.7 36.2 + - - +
202B MAH 2.7 29.9 + - - -
731B VAL* 2.8 26.2 + - + +
734B ASN* 1.3 73.7 - - - +
736B ASN* 1.3 69.4 + - - +
737B LEU 3.4 0.9 - - - -
739B GLY* 3.2 3.8 - - - -
740B SER 3.1 25.6 + - - -
751B ALA* 3.6 20.2 - - - -
854B MET* 3.8 16.8 - - + -
857B LEU* 3.6 16.5 - - + +
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Residues in contact with ASN 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A ASN* 3.0 12.8 + - - +
732B ASN* 2.8 40.4 + - - +
735B LYS* 1.3 88.7 - - - +
737B LEU* 1.3 60.2 + - + +
740B SER* 3.4 3.0 + - - -
749B TYR* 3.0 42.1 - - - +
750B ASN* 3.0 27.1 - - - +
751B ALA* 3.2 11.1 + - - +
779B THR* 4.1 5.0 - - - +
850B GLU* 3.9 5.9 + - - -
854B MET* 3.5 18.5 - - - -
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Residues in contact with LEU 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732B ASN* 3.4 9.6 + - - +
733B ILE* 3.3 23.6 + - + +
736B ASN* 1.3 85.1 - - - +
738B VAL* 1.3 67.5 + - - +
739B GLY 3.4 0.2 - - - -
740B SER 3.5 0.9 + - - -
741B ALA* 3.0 24.9 + - - +
749B TYR* 3.7 11.7 - - + -
778B ILE* 3.9 30.1 - - + -
779B THR 4.7 2.9 - - - +
780B LEU* 4.0 15.7 - - + -
733D ILE* 4.1 17.9 - - + -
737D LEU* 4.2 24.5 - - + +
738D VAL* 3.9 24.7 - - + -
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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