Contacts of the helix formed by residues 724 - 739 (chain A) in PDB entry 2QEP
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 ASP 724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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725A ILE* 1.3 69.0 + - - +
726A SER* 3.1 11.7 - - - -
727A THR* 2.7 23.3 + - - +
728A GLY 2.7 31.4 + - - -
965A MET* 2.6 51.1 - - - +
966A ALA* 3.8 11.8 - - - +
968A GLY* 4.5 11.7 - - - +
1009A ILE* 5.1 3.6 - - - +
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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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724A ASP* 1.3 85.3 + - - +
726A SER* 1.3 64.8 + - - +
728A GLY* 2.8 12.1 + - - +
729A HIS* 2.9 32.9 + - + +
965A MET* 4.5 5.4 - - + -
1009A ILE* 5.1 13.0 - - + +
1010A LEU* 5.5 13.7 - - + -
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Residues in contact with SER 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A ASP 3.8 11.9 - - - -
725A ILE* 1.3 80.4 - - - +
727A THR* 1.3 61.9 + - - -
729A HIS* 3.3 8.6 + - - +
730A MET* 3.1 19.5 + - - +
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Residues in contact with THR 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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724A ASP* 2.7 19.8 + - - -
726A SER* 1.3 72.7 - - - +
728A GLY* 1.3 59.0 + - - -
730A MET* 3.5 10.2 - - + +
731A ILE* 2.9 43.8 + - + +
964A LYS* 4.6 1.6 - - + +
965A MET* 4.0 17.3 - - - +
968A GLY* 3.0 35.4 + - - +
970A LYS* 4.2 10.2 + - - +
972A ILE* 4.4 14.1 - - + -
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Residues in contact with GLY 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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724A ASP 2.7 16.1 + - - -
725A ILE* 2.8 7.1 + - - -
727A THR* 1.3 73.8 - - - +
729A HIS* 1.3 56.4 + - - -
731A ILE* 3.0 5.9 + - - +
732A LEU* 2.9 26.1 + - - +
965A MET* 4.0 14.3 - - - +
1006A VAL* 3.6 27.1 - - - +
1010A LEU* 6.2 3.4 - - - -
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Residues in contact with HIS 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A ILE* 2.9 31.5 + - + +
726A SER* 3.7 9.5 + - - +
728A GLY* 1.3 74.9 - - - +
730A MET* 1.3 57.3 + - - +
732A LEU* 3.4 20.6 + - + +
733A SER* 2.9 28.4 + - - -
1010A LEU* 5.2 13.0 - - + +
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Residues in contact with MET 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A SER 3.1 14.0 + - - +
727A THR* 3.5 16.4 - - + +
728A GLY 3.1 0.2 - - - -
729A HIS* 1.3 75.6 - - - +
731A ILE* 1.3 64.8 + - - +
733A SER* 3.4 23.6 + - - +
734A TYR* 3.1 21.3 + - - +
970A LYS 3.6 22.9 - - - +
971A GLU* 5.4 1.1 - - - -
972A ILE* 3.9 12.3 - - + +
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Residues in contact with ILE 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A THR* 2.9 27.4 + - + +
728A GLY 3.5 4.3 - - - +
730A MET* 1.3 73.5 - - - +
732A LEU* 1.3 61.2 + - + +
734A TYR* 2.9 10.5 + - + +
735A MET* 2.8 41.1 + - + +
961A VAL* 4.9 11.0 - - + +
962A LEU* 5.7 0.4 - - + -
964A LYS* 6.4 0.2 - - + -
965A MET* 3.7 38.4 - - + +
972A ILE* 3.8 22.4 - - + -
974A ILE* 5.4 3.4 - - + -
1002A VAL* 3.8 28.0 - - + -
1006A VAL* 4.3 13.0 - - + -
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Residues in contact with LEU 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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728A GLY 2.9 15.8 + - - +
729A HIS* 3.7 25.4 - - + +
730A MET 3.4 0.2 - - - -
731A ILE* 1.3 76.6 - - - +
733A SER* 1.3 63.1 + - - +
735A MET* 3.1 7.5 + - + +
736A GLU* 3.0 26.8 + - - +
1003A ALA* 4.2 20.6 - - + +
1006A VAL* 4.1 22.9 - - + +
1007A ASN* 3.6 28.5 - - - +
1010A LEU* 5.5 6.1 - - + -
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Residues in contact with SER 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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729A HIS 2.9 15.0 + - - -
730A MET* 3.6 26.9 - - - +
732A LEU* 1.3 76.4 - - - +
734A TYR* 1.3 64.5 + - - +
736A GLU* 3.3 15.1 + - - +
737A ASP* 3.4 17.7 + - - +
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Residues in contact with TYR 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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730A MET 3.1 13.2 + - - +
731A ILE* 2.9 10.0 + - + +
733A SER* 1.3 76.4 - - - +
735A MET* 1.3 63.0 + - + +
737A ASP* 3.1 4.8 + - - -
738A HIS* 2.8 77.8 + + + +
748A GLU* 3.7 14.6 + - - -
972A ILE* 3.3 36.8 - - + -
973A ASP* 3.5 12.7 + - - -
974A ILE* 3.1 51.1 + - + +
975A ALA 3.3 12.3 + - - -
995A PHE* 5.4 0.5 - - - -
999A LEU* 4.5 5.1 - - + +
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Residues in contact with MET 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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731A ILE* 2.8 27.2 + - + +
732A LEU* 3.1 13.0 + - + +
734A TYR* 1.3 75.8 - - - +
736A GLU* 1.3 60.2 + - - +
739A LEU* 2.6 42.5 + - + +
740A LYS* 2.9 12.7 + - + -
974A ILE* 3.5 28.0 - - + -
999A LEU* 3.2 42.2 - - - +
1002A VAL* 3.5 22.4 - - + -
1003A ALA* 3.8 22.4 - - + +
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Residues in contact with GLU 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 LEU* 3.0 15.1 + - + +
733A SER* 3.5 12.3 - - - +
735A MET* 1.3 77.3 - - - +
737A ASP* 1.3 65.5 + - - +
740A LYS* 3.4 36.2 - - - +
741A ASN* 3.4 19.8 + - - +
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Residues in contact with ASP 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A SER* 3.4 14.1 + - - +
734A TYR* 3.1 8.6 + - - +
736A GLU* 1.3 83.0 - - - +
738A HIS* 1.3 73.5 + - + +
741A ASN* 3.7 10.8 + - - +
744A ARG* 3.2 26.8 - - + +
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Residues in contact with HIS 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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734A TYR* 2.8 74.5 + + + +
737A ASP* 1.3 87.5 - - + +
739A LEU* 1.3 58.8 + - - +
741A ASN 4.4 3.1 - - - -
744A ARG* 4.0 19.4 - - + +
745A LEU* 3.6 27.9 - - - +
748A GLU* 3.1 41.0 + - - +
999A LEU* 3.8 10.2 - - + +
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Residues in contact with LEU 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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735A MET* 2.6 32.7 + - + +
738A HIS* 1.3 73.9 - - - +
740A LYS* 1.3 79.7 + - + +
741A ASN 4.1 2.5 - - - -
742A LYS* 4.4 0.9 + - - +
745A LEU* 3.7 19.1 - - + +
996A GLU* 3.9 26.2 - - + +
999A LEU* 3.9 14.3 - - + +
1000A THR* 3.7 44.2 - - + +
1003A ALA* 4.3 12.8 - - + -
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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