Contacts of the helix formed by residues 724 - 739 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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725B ILE* 1.3 73.9 + - + +
726B SER* 2.9 16.7 - - - +
727B THR* 3.0 13.9 + - - +
728B GLY 2.9 21.0 + - - -
965B MET* 3.2 39.7 - - - +
966B ALA* 4.1 13.7 - - - +
968B GLY* 5.7 3.9 - - - -
1009B ILE* 4.2 13.2 - - - +
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Residues in contact with ILE 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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724B ASP* 1.3 81.8 - - + +
726B SER* 1.3 59.6 + - - +
728B GLY 3.6 0.2 + - - -
729B HIS* 3.3 37.1 + - + +
965B MET* 5.2 0.4 - - - -
1009B ILE* 5.5 4.5 - - + +
1010B LEU* 3.4 29.7 - - + +
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Residues in contact with SER 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B ASP 2.9 11.1 - - - +
725B ILE* 1.3 77.2 - - - +
727B THR* 1.3 60.3 + - - -
729B HIS* 3.2 9.9 + - - +
730B MET* 2.8 25.7 + - - +
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Residues in contact with THR 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B ASP* 3.0 12.7 + - - -
726B SER* 1.3 75.4 - - - +
728B GLY* 1.3 54.7 + - - +
730B MET* 3.0 12.8 + - + +
731B ILE* 2.6 34.6 + - + +
964B LYS 4.5 2.2 - - - +
965B MET* 3.5 37.5 - - + -
968B GLY* 3.2 34.5 + - - +
970B LYS* 4.9 2.7 + - - +
972B ILE* 5.0 13.7 - - + -
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Residues in contact with GLY 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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724B ASP 2.9 11.0 + - - -
725B ILE 3.9 3.1 - - - -
726B SER 3.2 0.2 - - - -
727B THR* 1.3 76.9 - - - +
729B HIS* 1.3 55.7 + - - +
731B ILE* 3.2 2.3 + - - +
732B LEU* 2.9 24.1 + - - +
965B MET* 3.6 16.9 - - - +
1006B VAL* 3.1 33.9 - - - +
1010B LEU* 4.0 5.8 - - - -
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Residues in contact with HIS 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B ILE* 3.3 31.0 + - + +
726B SER* 3.2 10.8 + - - +
728B GLY* 1.3 73.7 - - - +
730B MET* 1.3 64.5 + - - +
732B LEU* 3.2 10.8 + - + +
733B SER* 3.1 24.6 + - - -
1010B LEU* 3.4 24.1 - - + +
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Residues in contact with MET 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B SER 2.8 13.7 + - - +
727B THR* 3.0 19.5 + - + +
729B HIS* 1.3 76.4 - - - +
731B ILE* 1.3 57.0 + - - +
733B SER* 3.8 6.3 + - - -
734B TYR* 3.5 18.0 + - - +
970B LYS* 3.8 25.6 - - - +
971B GLU* 5.0 2.5 - - - -
972B ILE* 4.6 15.5 - - + +
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Residues in contact with ILE 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B THR* 2.6 17.2 + - + +
728B GLY* 3.4 9.2 - - - +
729B HIS 3.1 0.2 - - - -
730B MET* 1.3 72.9 - - - +
732B LEU* 1.3 62.6 + - + +
734B TYR* 3.1 9.7 + - - +
735B MET* 2.8 34.2 + - + +
965B MET* 5.7 2.0 - - + -
972B ILE* 5.2 14.4 - - + -
1002B VAL* 4.9 12.1 - - + -
1006B VAL* 4.2 18.6 - - + -
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Residues in contact with LEU 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 GLY 2.9 18.2 + - - +
729B HIS* 3.2 11.6 + - + +
731B ILE* 1.3 74.5 - - + +
733B SER* 1.3 65.7 + - - +
735B MET* 3.1 5.9 + - + +
736B GLU* 3.0 29.3 + - + +
1003B ALA* 4.2 22.7 - - + +
1006B VAL* 3.8 15.3 - - + -
1007B ASN* 3.3 28.3 - - - +
1010B LEU* 4.0 20.4 - - + -
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Residues in contact with SER 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B HIS 3.1 12.2 + - - -
730B MET* 3.8 10.7 + - - -
732B LEU* 1.3 76.5 - - - +
734B TYR* 1.3 66.4 + - - +
736B GLU* 3.4 9.2 + - - +
737B ASP* 3.3 23.3 + - - +
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Residues in contact with TYR 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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730B MET 3.5 9.9 + - - +
731B ILE* 3.1 12.5 + - - +
733B SER* 1.3 81.9 + - - +
735B MET* 1.3 71.1 + - + +
737B ASP* 3.0 5.7 + - - -
738B HIS* 2.9 88.2 + + + +
748B GLU* 4.1 6.4 + - - -
972B ILE* 3.3 39.0 - - + -
973B ASP* 4.0 8.9 + - + -
974B ILE* 3.3 27.6 + - + +
975B ALA* 3.7 9.5 + - - +
995B PHE* 5.6 1.0 - - - -
999B LEU* 4.0 18.4 - - + +
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Residues in contact with MET 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B ILE* 2.8 26.0 + - + +
732B LEU* 3.1 11.4 + - + +
734B TYR* 1.3 79.9 - - + +
736B GLU* 1.3 61.7 + - - +
739B LEU* 2.6 45.2 + - + +
740B LYS* 3.0 7.4 + - - -
972B ILE* 6.5 0.2 - - + -
974B ILE* 4.1 11.2 - - + -
999B LEU* 3.4 43.5 - - - +
1002B VAL* 3.4 34.5 - - + -
1003B ALA* 3.6 26.0 - - + +
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Residues in contact with GLU 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B LEU* 3.0 14.5 + - + +
733B SER* 3.4 12.8 - - - +
735B MET* 1.3 76.5 - - - +
737B ASP* 1.3 65.9 + - - +
740B LYS* 3.3 24.4 - - - +
741B ASN* 3.3 22.7 + - - +
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Residues in contact with ASP 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B SER* 3.3 11.8 + - - +
734B TYR* 3.0 10.3 + - - +
736B GLU* 1.3 84.4 - - - +
738B HIS* 1.3 70.9 + - + +
741B ASN* 3.4 19.0 - - - +
744B ARG* 3.0 35.6 + - - +
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Residues in contact with HIS 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B TYR* 2.9 72.5 + + + +
737B ASP* 1.3 91.5 - - + +
739B LEU* 1.3 60.3 + - - +
741B ASN 4.3 4.0 - - - -
744B ARG* 3.7 27.9 + - - -
745B LEU* 3.6 25.5 - - - +
748B GLU* 3.2 38.6 + - - +
995B PHE* 5.7 0.5 - - - -
999B LEU* 4.0 13.3 - - + +
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Residues in contact with LEU 739 (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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735B MET* 2.6 40.5 + - + +
738B HIS* 1.3 73.8 - - - +
740B LYS* 1.3 65.0 + - - +
741B ASN 3.3 3.3 + - - +
742B LYS* 3.2 40.6 + - - +
745B LEU* 4.5 5.1 - - + +
996B GLU* 3.9 19.1 - - + +
999B LEU* 3.8 13.5 - - + +
1000B THR* 3.3 45.8 - - - +
1003B ALA* 4.5 4.5 - - + -
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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