Contacts of the helix formed by residues 935 - 943 (chain A) in PDB entry 2WXL
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 THR 935 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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899A ILE* 5.5 2.3 - - - +
933A ILE* 4.0 14.4 + - + +
934A LEU* 1.3 75.4 - - - +
936A TYR* 1.3 69.3 + - + +
937A ASP* 4.4 7.4 - - + +
938A PHE* 3.2 43.2 + - + +
939A VAL* 3.0 22.7 + - - +
1026A SER* 3.9 1.8 - - - -
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Residues in contact with TYR 936 (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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852A LYS* 4.3 30.9 - - + +
934A LEU 4.1 0.2 + - - -
935A THR* 1.3 75.4 - - + +
937A ASP* 1.3 71.0 + - - +
939A VAL* 3.2 8.6 + - + +
940A HIS* 2.8 36.2 + - + +
1026A SER* 3.6 37.1 + - - +
1027A TRP* 4.1 26.5 - + + -
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Residues in contact with ASP 937 (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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838A GLN* 2.5 33.9 + - - +
851A ASN* 4.2 9.8 + - - +
852A LYS* 3.3 37.7 - - - +
855A LEU* 4.3 8.5 - - + +
935A THR* 3.4 6.6 - - + +
936A TYR* 1.3 86.7 - - - +
938A PHE* 1.3 70.5 + - + +
940A HIS* 3.5 5.7 - - - +
941A VAL* 3.3 27.0 + - - +
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Residues in contact with PHE 938 (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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834A ILE* 4.1 25.1 - - + -
855A LEU* 4.1 12.3 - - + -
875A PHE* 3.4 27.9 - + + -
879A CYS* 4.1 19.1 - - - -
883A CYS* 5.8 2.5 - - - -
896A SER* 6.2 0.7 - - - -
899A ILE* 4.0 32.1 - - + -
907A LEU* 3.7 25.8 - - + -
909A HIS* 6.0 0.4 - - - -
935A THR* 3.2 38.5 + - + +
936A TYR 3.1 0.6 - - - -
937A ASP* 1.3 81.6 - - + +
939A VAL* 1.3 61.5 + - + +
940A HIS 3.1 0.9 - - - -
941A VAL 3.0 2.3 + - - -
942A ILE* 2.9 33.6 + - + +
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Residues in contact with VAL 939 (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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934A LEU* 4.3 25.6 - - + -
935A THR 3.0 22.3 + - - +
936A TYR* 3.7 12.8 - - + +
938A PHE* 1.3 75.0 - - + +
940A HIS* 1.3 58.0 + - - +
942A ILE* 3.3 11.7 + - + +
943A GLN* 2.9 52.5 + - - +
953A PHE* 3.9 21.5 - - + -
1023A LEU* 5.0 8.3 - - + -
1026A SER* 4.3 10.3 - - - +
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Residues in contact with HIS 940 (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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852A LYS* 3.2 53.9 - - + +
853A ASP* 3.1 24.2 + - - -
856A LEU* 4.8 7.4 - - + -
936A TYR* 2.8 26.4 + - + +
937A ASP* 3.5 12.6 - - - +
938A PHE 3.1 0.2 - - - -
939A VAL* 1.3 76.9 - - - +
941A VAL* 1.3 60.0 + - + +
943A GLN* 3.4 6.8 + - - +
944A GLN 3.4 2.9 + - - -
945A GLY* 2.9 60.6 + - - -
946A LYS 4.7 5.5 + - - -
947A THR* 5.5 2.2 - - - -
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Residues in contact with VAL 941 (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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852A LYS 5.6 0.7 - - - +
855A LEU* 4.0 31.4 - - + -
856A LEU* 4.0 25.1 - - + +
859A LEU* 3.8 18.8 - - + -
872A ILE* 3.5 15.7 - - + +
875A PHE* 3.3 35.0 - - + -
937A ASP 3.3 13.7 + - - +
938A PHE 3.0 7.4 + - - +
940A HIS* 1.3 77.4 - - + +
942A ILE* 1.3 60.8 + - - +
944A GLN* 2.8 22.0 + - - -
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Residues in contact with ILE 942 (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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872A ILE* 4.3 4.9 - - - +
875A PHE* 4.2 9.6 - - + -
876A THR* 3.7 27.5 + - + +
879A CYS* 4.2 12.1 - - + -
934A LEU* 5.7 0.2 - - + -
938A PHE* 2.9 24.8 + - + +
939A VAL* 3.5 14.4 - - + +
941A VAL* 1.3 75.8 - - - +
943A GLN* 1.3 58.3 + - + +
944A GLN* 3.2 5.9 + - - +
952A LYS* 3.3 29.4 - - - +
953A PHE* 4.2 12.6 - - + -
956A PHE* 3.7 58.3 - - + -
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Residues in contact with GLN 943 (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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939A VAL* 2.9 37.2 + - + +
940A HIS* 3.9 4.3 - - - +
941A VAL 3.1 0.4 - - - -
942A ILE* 1.3 76.5 - - + +
944A GLN* 1.3 60.5 + - - +
945A GLY 3.1 1.6 - - - -
946A LYS* 2.9 42.0 + - - +
947A THR 3.0 18.7 + - - +
948A ASN* 5.4 0.2 - - - +
949A ASN* 3.1 46.0 + - + +
952A LYS* 4.4 0.4 - - - -
953A PHE* 3.7 27.5 - - + +
1023A LEU* 6.2 0.8 - - - +
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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