Contacts of the helix formed by residues 938 - 947 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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918A LYS* 5.3 7.7 + - + +
921A TYR* 3.6 53.6 + - + +
922A ASP* 4.7 6.7 - - + -
820F PHE* 4.8 7.2 - + - -
824F PHE* 5.5 2.8 - - - -
886F THR 3.2 26.5 + - - -
887F GLY* 3.2 14.1 + - - -
888F LYS* 4.3 2.6 + - - -
889F ILE* 3.8 6.5 - - - +
936F VAL* 3.7 0.4 - - - +
937F GLU* 1.3 82.6 + - + +
939F TYR* 1.3 84.9 - - + +
940F ARG* 2.9 27.2 + - + +
941F GLU* 3.0 22.7 + - - +
942F ILE* 3.6 2.4 + - - +
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Residues in contact with TYR 939 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820F PHE* 3.6 35.7 - + + -
824F PHE* 4.0 12.3 - + - -
858F CYS* 3.8 6.5 - - - -
861F VAL* 3.4 24.0 - - + -
862F THR* 2.8 44.8 + - - +
865F LEU* 3.6 26.5 - - + +
883F VAL* 4.5 2.5 - - + -
887F GLY 2.8 14.2 + - - +
889F ILE* 3.7 13.2 - - + +
938F HIS* 1.3 73.3 - - + +
940F ARG* 1.3 57.3 + - - +
942F ILE* 2.8 46.6 + - + +
943F PHE* 2.9 25.7 + + + -
947F PHE* 4.5 0.2 - - - -
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Residues in contact with ARG 940 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921A TYR* 3.6 38.6 - - + +
928A THR* 6.2 3.8 - - - -
824F PHE* 3.3 33.4 - - + -
828F HIS* 3.5 29.0 + - - +
938F HIS* 2.9 16.6 + - + +
939F TYR* 1.3 77.1 - - - +
941F GLU* 1.3 62.2 + - - +
943F PHE* 3.4 22.1 + - - +
944F ASP* 2.8 62.3 + - - +
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Residues in contact with GLU 941 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917A LYS* 3.3 26.9 + - - -
921A TYR* 3.5 35.0 - - + +
935F PHE 4.3 3.8 - - - +
936F VAL* 3.8 19.8 - - + +
937F GLU* 3.1 21.4 + - - +
938F HIS* 3.0 30.3 + - - +
940F ARG* 1.3 74.4 - - - +
942F ILE* 1.3 65.1 + - - +
944F ASP* 3.4 8.0 + - - +
945F ILE* 3.4 27.8 + - + +
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Residues in contact with ILE 942 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858F CYS* 3.5 31.2 - - + -
862F THR* 4.3 0.9 - - - +
879F MET* 3.6 28.0 - - + -
880F THR 5.6 0.4 - - - +
889F ILE* 4.0 18.8 - - + -
911F VAL* 3.7 24.9 - - + -
936F VAL* 3.8 14.6 - - + -
938F HIS 4.5 0.2 - - - +
939F TYR* 2.8 43.0 + - + +
941F GLU* 1.3 72.1 - - - +
943F PHE* 1.3 55.7 + - - +
945F ILE* 3.2 10.8 + - - +
946F ALA* 2.9 28.3 + - + +
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Residues in contact with PHE 943 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824F PHE* 3.7 15.3 - + + -
825F LEU* 6.3 0.9 - - + -
828F HIS* 5.2 8.5 - - + -
865F LEU* 3.4 35.2 - - + -
869F MET* 3.8 24.9 - - + -
939F TYR* 2.9 20.9 + + + +
940F ARG* 3.5 41.1 - - - +
942F ILE* 1.3 78.2 - - - +
944F ASP* 1.3 57.8 + - - +
946F ALA* 4.5 1.3 - - - +
947F PHE* 3.0 59.5 + + + +
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Residues in contact with ASP 944 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921A TYR* 5.9 0.5 - - - -
940F ARG* 2.8 54.6 + - - +
941F GLU* 4.0 7.3 - - - +
942F ILE 3.2 0.4 - - - -
943F PHE* 1.3 80.8 - - - +
945F ILE* 1.3 62.0 + - + +
947F PHE 4.9 2.9 - - - -
948F PRO* 3.5 23.7 - - - +
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Residues in contact with ILE 945 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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874F ARG* 3.4 26.7 + - - +
877F LEU* 4.0 20.9 - - + -
909F CYS* 4.8 1.3 - - - -
911F VAL* 4.2 14.6 - - + -
934F HIS* 3.7 47.1 - - + +
936F VAL* 4.2 14.4 - - + -
941F GLU* 3.4 18.1 + - + +
942F ILE* 3.2 6.6 + - - +
944F ASP* 1.3 79.1 - - + +
946F ALA* 1.3 63.4 + - - +
947F PHE 3.5 0.3 + - - -
948F PRO* 3.6 9.8 - - - +
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Residues in contact with ALA 946 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862F THR* 4.1 11.7 - - + -
871F ARG* 5.1 0.3 + - - -
872F PRO 4.8 0.2 - - - +
873F VAL* 3.6 17.4 - - + +
874F ARG* 3.3 29.1 + - - +
877F LEU* 4.4 1.6 - - - -
879F MET* 4.5 11.4 - - + -
942F ILE 2.9 18.3 + - - +
945F ILE* 1.3 80.3 - - + +
947F PHE* 1.3 80.5 - - + +
948F PRO* 3.5 5.2 - - - +
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Residues in contact with PHE 947 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862F THR* 3.8 22.2 - - + -
865F LEU* 4.5 2.5 - - + -
866F SER* 3.8 26.2 - - - -
869F MET* 3.8 14.6 - - + -
871F ARG* 3.3 54.5 + - - +
872F PRO 3.9 11.0 - - - -
873F VAL* 3.6 24.0 - - + -
943F PHE* 3.0 48.1 + + + +
944F ASP* 3.8 5.8 - - - +
946F ALA* 1.3 84.0 - - + +
948F PRO* 1.3 66.1 - - - +
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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