Contacts of the helix formed by residues 737 - 749 (chain B) in PDB entry 4X52
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 HIS 737 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733B ILE* 3.4 17.6 - - + +
734B HIS* 3.1 26.4 + - + +
736B LEU* 1.3 78.5 - - - +
738B PRO* 1.4 81.7 - - + +
739B GLU* 3.1 54.1 + - + +
740B TYR* 2.9 14.0 + - - +
741B VAL* 3.1 10.6 + - - +
734C HIS* 4.4 10.6 - + - -
736C LEU* 4.1 37.0 - - + +
901C SO4 5.3 0.9 + - - -
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Residues in contact with PRO 738 (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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736B LEU 3.5 5.8 - - - +
737B HIS* 1.4 98.7 - - + +
739B GLU* 1.4 57.3 + - + +
741B VAL* 3.4 10.0 + - + +
742B ARG* 2.9 39.4 + - - +
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Residues in contact with GLU 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B ILE* 4.5 12.1 - - + -
737B HIS* 3.1 27.4 + - + +
738B PRO* 1.4 71.7 - - + +
740B TYR* 1.4 64.9 + - - +
742B ARG* 3.5 27.4 + - - +
743B VAL* 3.0 30.9 + - - +
761B LYS* 3.0 39.3 + - - +
889B TYR* 2.7 28.9 + - - +
734C HIS* 5.2 0.7 + - - -
901C SO4 3.6 10.9 + - - -
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Residues in contact with TYR 740 (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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733B ILE* 3.6 26.1 - - + +
734B HIS 3.2 26.9 - - - +
735B HIS* 3.3 39.0 - - + +
737B HIS 2.9 6.0 + - - +
739B GLU* 1.4 77.7 - - - +
741B VAL* 1.3 54.6 + - + +
743B VAL* 3.2 1.8 + - - -
744B SER* 2.8 50.4 + - - -
756B ILE* 3.4 25.2 + - + +
757B GLU 4.9 3.7 + - - -
758B LYS* 4.6 2.2 - - - -
759B ILE* 3.7 50.6 - - + +
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Residues in contact with VAL 741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B HIS 3.9 15.5 - - - +
736B LEU* 4.3 9.0 - - + +
737B HIS 3.1 16.2 + - - +
738B PRO* 3.6 11.2 - - + +
740B TYR* 1.3 75.7 - - - +
742B ARG* 1.3 55.9 + - - +
744B SER* 3.6 6.1 - - - -
745B GLU* 2.9 54.8 + - + +
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Residues in contact with ARG 742 (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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738B PRO* 2.9 27.6 + - - +
739B GLU* 3.5 36.1 + - - +
741B VAL* 1.3 76.8 - - - +
743B VAL* 1.3 64.9 + - + +
745B GLU* 3.4 13.2 + - - +
746B HIS* 3.0 48.8 + - + +
784B LEU* 5.6 5.4 - - + -
889B TYR* 4.7 6.7 + - - -
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Residues in contact with VAL 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739B GLU 3.0 17.9 + - - +
740B TYR 3.8 2.2 - - - +
742B ARG* 1.3 78.9 - - + +
744B SER* 1.3 62.3 - - - +
746B HIS* 3.2 10.0 + - + +
747B PHE* 3.0 21.7 + - - +
759B ILE* 3.9 19.1 - - + -
784B LEU* 5.5 4.9 - - + -
786B PHE* 5.3 0.3 - - - -
842B VAL* 4.0 14.6 - - + -
889B TYR* 3.4 40.6 - - + +
891B ILE* 3.7 29.4 - - + -
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Residues in contact with SER 744 (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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740B TYR* 2.8 35.0 + - - -
741B VAL* 3.6 6.3 - - - -
743B VAL* 1.3 72.2 - - - +
745B GLU* 1.4 56.3 + - - +
747B PHE* 3.4 1.9 + - - +
748B LYS* 2.8 41.7 + - - +
756B ILE* 3.4 28.8 - - - +
759B ILE* 3.9 5.8 - - - +
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Residues in contact with GLU 745 (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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741B VAL* 2.9 38.3 + - + +
742B ARG* 3.7 11.7 - - - +
743B VAL 3.3 0.2 - - - -
744B SER* 1.4 73.0 - - - +
746B HIS* 1.4 65.6 + - + +
748B LYS* 3.9 4.1 - - - +
749B ALA* 3.1 24.3 + - - +
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Residues in contact with HIS 746 (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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742B ARG* 3.0 44.4 + - + +
743B VAL* 3.2 9.6 + - - +
745B GLU* 1.4 74.7 - - + +
747B PHE* 1.3 62.8 + - - +
749B ALA* 3.6 14.8 - - - +
750B SER* 4.5 2.4 + - - -
784B LEU* 3.8 37.6 - - + +
786B PHE* 3.8 24.5 - + + -
824B ALA 5.5 0.2 + - - -
842B VAL* 6.3 0.2 - - + -
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Residues in contact with PHE 747 (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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743B VAL 3.0 11.6 + - - +
744B SER 3.5 7.4 - - - +
746B HIS* 1.3 78.0 - - - +
748B LYS* 1.3 65.8 + - + +
749B ALA 3.3 1.0 + - - -
750B SER* 3.4 5.2 + - - -
751B MET* 3.0 64.3 + - + +
754B PHE* 4.3 10.3 - - + -
756B ILE* 3.6 30.3 - - + -
786B PHE* 3.9 9.1 - + + -
824B ALA* 3.9 13.2 - - + -
840B MET* 4.1 15.0 - - + -
891B ILE* 3.7 27.6 - - + -
893B TYR* 3.6 37.9 - + + -
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Residues in contact with LYS 748 (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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744B SER* 2.8 35.7 + - - +
745B GLU* 4.1 5.4 - - - +
747B PHE* 1.3 82.2 - - + +
749B ALA* 1.4 60.7 + - - +
750B SER 3.1 3.4 + - - -
751B MET 2.8 23.8 + - - +
752B LYS* 2.9 47.0 + - - +
754B PHE 2.8 28.5 + - - +
756B ILE* 4.4 7.2 - - + +
896B ASP* 5.1 0.2 + - - -
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Residues in contact with ALA 749 (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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745B GLU 3.1 12.2 + - - +
746B HIS* 3.6 15.7 - - - +
747B PHE 3.2 0.6 - - - -
748B LYS* 1.4 75.3 - - - +
750B SER* 1.4 57.3 + - - +
752B LYS* 3.2 22.4 + - - +
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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