Contacts of the helix formed by residues 938 - 947 (chain B) in PDB entry 2X36
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 938 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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757A TYR* 4.8 9.4 - + - -
820B PHE* 4.1 14.4 - + - -
824B PHE* 5.8 0.9 - + - -
886B THR 3.0 25.5 + - - -
887B GLY 3.6 17.9 - - - -
888B LYS* 3.8 5.8 - - + -
889B ILE* 3.5 5.8 - - - -
936B VAL* 4.0 3.5 - - - +
937B GLU* 1.3 80.2 - - + +
939B TYR* 1.3 79.6 + - - +
940B ARG* 3.1 60.3 + - + +
941B GLU* 3.2 24.9 + - - +
942B ILE 4.0 1.0 + - - -
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Residues in contact with TYR 939 (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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820B PHE* 3.4 35.4 - + + -
824B PHE* 4.3 4.9 - + - -
858B CYS* 3.6 12.3 - - + -
861B VAL* 3.2 34.1 - - + -
862B THR* 2.8 31.5 + - - +
865B LEU* 3.3 21.9 - - + +
883B VAL* 4.6 2.2 - - + -
887B GLY 3.0 12.3 + - - +
889B ILE* 3.5 12.2 - - + +
938B HIS* 1.3 72.2 + - - +
940B ARG* 1.3 70.8 + - - +
941B GLU 2.5 2.6 + - - -
942B ILE* 2.6 47.5 + - + +
943B PHE* 3.0 30.1 + + + -
947B PHE* 4.4 4.3 - - - -
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Residues in contact with ARG 940 (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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824B PHE* 4.0 23.1 - - + -
938B HIS* 3.1 47.0 + - + +
939B TYR* 1.3 79.2 - - - +
941B GLU* 1.3 77.8 + - + +
943B PHE* 3.0 23.0 + - - +
944B ASP* 3.2 17.0 + - - +
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Residues in contact with GLU 941 (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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935B PHE 4.6 2.8 - - - +
936B VAL* 3.4 27.8 - - + +
937B GLU* 3.7 12.7 + - - +
938B HIS* 3.3 33.5 + - - +
939B TYR 2.5 3.6 + - - -
940B ARG* 1.3 89.2 + - + +
942B ILE* 1.3 65.8 + - - +
944B ASP* 3.6 11.3 + - - +
945B ILE* 3.5 23.1 + - + +
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Residues in contact with ILE 942 (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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858B CYS* 5.0 7.2 - - + -
862B THR* 3.0 32.1 - - + +
877B LEU* 5.6 0.2 - - - +
879B MET* 3.4 25.1 - - + -
889B ILE* 4.7 6.5 - - + -
911B VAL* 3.9 14.6 - - + -
936B VAL* 3.4 30.2 - - + +
939B TYR* 2.6 52.4 + - + +
941B GLU* 1.3 72.8 - - - +
943B PHE* 1.3 61.3 + - - +
945B ILE* 3.1 22.3 + - - +
946B ALA* 3.1 13.2 + - + -
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Residues in contact with PHE 943 (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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824B PHE* 3.4 31.4 - + + -
828B HIS* 3.3 40.2 - + - -
865B LEU* 4.0 16.8 - - + -
869B MET* 4.2 14.8 - - + -
939B TYR* 3.0 19.9 + - + -
940B ARG 3.0 13.2 + - - +
942B ILE* 1.3 79.6 - - - +
944B ASP* 1.3 75.2 + - - +
947B PHE* 3.2 64.9 + + + +
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Residues in contact with ASP 944 (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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940B ARG* 3.2 14.3 + - - +
941B GLU* 3.8 11.9 - - - +
943B PHE* 1.3 86.1 - - - +
945B ILE* 1.3 64.1 + - + +
947B PHE 2.9 27.6 + - - +
948B PRO* 3.5 4.5 - - - +
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Residues in contact with ILE 945 (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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874B ARG* 3.4 33.3 + - - +
877B LEU* 3.5 27.8 - - + -
909B CYS* 4.4 4.7 - - - -
911B VAL* 3.9 13.9 - - + -
934B HIS* 3.2 46.4 - - + +
936B VAL* 5.0 3.4 - - + -
941B GLU 3.5 15.0 + - - +
942B ILE* 3.1 11.0 + - - +
944B ASP* 1.3 79.0 - - + +
946B ALA* 1.3 61.3 + - - +
947B PHE 3.4 0.5 + - - -
948B PRO* 4.3 6.1 - - - +
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Residues in contact with ALA 946 (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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862B THR* 4.3 15.5 - - + -
871B ARG* 5.1 0.5 + - - -
872B PRO 4.7 0.7 - - - +
873B VAL* 4.1 5.8 - - + -
874B ARG* 3.4 22.6 + - - +
877B LEU* 3.8 21.1 - - + -
942B ILE* 3.1 17.2 + - + +
945B ILE* 1.3 79.3 - - - +
947B PHE* 1.3 88.3 + - + +
948B PRO* 3.8 4.1 - - - +
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Residues in contact with PHE 947 (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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862B THR* 4.0 13.9 - - + -
865B LEU* 4.5 2.9 - - + -
866B SER* 3.8 27.6 - - - -
869B MET* 3.6 19.1 - - + -
871B ARG* 3.7 39.7 - - + +
872B PRO 4.2 5.6 - - - -
873B VAL* 4.0 10.1 - - + -
939B TYR* 4.4 4.3 - - - -
943B PHE* 3.2 63.0 + + + +
944B ASP* 2.9 16.6 + - - +
945B ILE 3.2 0.6 - - - -
946B ALA* 1.3 97.7 - - + +
948B PRO* 1.4 67.4 - - - +
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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