Contacts of the helix formed by residues 944 - 954 (chain A) in PDB entry 3O37
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 944 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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924A PHE* 3.4 14.6 - - - +
925A GLN 2.8 12.3 - - - +
926A ASP* 3.3 15.5 - - - +
927A PRO* 3.4 25.3 - - + +
928A VAL* 5.4 0.4 - - + +
943A MET* 1.3 79.8 - - - +
945A LEU* 1.3 64.1 + - - +
946A SER* 2.3 30.9 + - - -
947A THR* 2.5 34.7 + - - -
948A ILE* 3.3 14.4 + - - +
972A ILE* 3.5 10.5 - - - -
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Residues in contact with LEU 945 (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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912A LEU* 3.7 11.1 - - + +
915A LEU* 3.9 30.7 - - + -
916A TYR* 3.3 27.3 + - + +
921A SER* 4.2 12.8 - - - +
924A PHE* 2.8 28.1 + - + +
925A GLN* 3.8 20.2 - - + +
944A ASP* 1.3 72.3 - - - +
946A SER* 1.3 57.6 + - - +
948A ILE* 3.3 2.1 + - - +
949A LYS* 3.0 27.4 + - - +
969A PHE* 3.9 24.5 - - + -
972A ILE* 3.6 18.6 - - + +
973A PHE* 6.3 0.7 - - + -
993A LEU* 4.9 4.3 - - + -
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Residues in contact with SER 946 (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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916A TYR* 3.0 13.2 + - - -
925A GLN 2.9 17.3 + - - -
926A ASP* 3.9 10.9 + - - -
927A PRO* 3.6 13.3 - - - +
944A ASP* 2.3 24.0 + - - -
945A LEU* 1.3 73.4 - - - +
947A THR* 1.3 58.2 + - - +
949A LYS* 3.5 7.5 - - - +
950A LYS* 2.9 39.1 + - - +
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Residues in contact with THR 947 (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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927A PRO* 4.5 4.5 - - - +
943A MET* 3.7 21.0 - - + -
944A ASP* 2.5 31.9 + - - -
946A SER* 1.3 79.6 + - - +
948A ILE* 1.3 59.7 + - - +
950A LYS* 3.3 14.8 + - + +
951A ARG* 2.8 54.1 + - + +
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Residues in contact with ILE 948 (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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908A CYS* 4.3 4.9 - - - -
912A LEU* 4.0 16.6 - - + -
943A MET* 3.8 13.0 - - - -
944A ASP 3.3 8.0 + - - +
945A LEU* 3.3 7.7 + - + +
947A THR* 1.3 76.7 - - - +
949A LYS* 1.3 58.4 + - - +
951A ARG* 3.7 0.9 - - - +
952A LEU* 2.8 29.6 + - - +
959A TYR* 3.5 24.9 - - + +
965A PHE* 4.6 1.8 - - + -
968A ASP* 3.8 7.9 - - + -
969A PHE* 3.6 60.8 - - + +
972A ILE* 3.8 18.4 - - + -
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Residues in contact with LYS 949 (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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851A SER 2.8 28.7 + - - -
852A CYS 4.0 6.1 + - - -
853A HIS 3.0 22.2 + - - -
854A VAL* 4.1 18.0 - - + +
855A PRO* 5.5 1.6 - - + -
856A THR* 3.0 26.5 + - - +
912A LEU* 3.6 15.7 - - + +
916A TYR* 4.0 24.8 + - + +
945A LEU 3.0 17.3 + - - +
946A SER* 3.5 8.3 - - - +
948A ILE* 1.3 77.2 - - - +
950A LYS* 1.3 60.7 + - - +
952A LEU* 3.4 3.7 + - - +
953A GLN* 3.2 23.7 + - + +
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Residues in contact with LYS 950 (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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946A SER* 2.9 30.1 + - - +
947A THR* 3.6 14.1 + - - +
949A LYS* 1.3 75.6 - - - +
951A ARG* 1.3 62.1 + - + +
953A GLN* 3.2 4.5 + - - +
954A GLU* 2.8 51.7 + - - +
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Residues in contact with ARG 951 (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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943A MET* 3.4 24.5 - - - +
947A THR* 2.8 33.5 + - + +
948A ILE 3.7 3.6 - - - +
950A LYS* 1.3 78.8 - - + +
952A LEU* 1.3 64.3 + - - +
953A GLN 3.4 0.3 + - - -
954A GLU* 3.5 12.8 + - - +
957A SER* 3.6 18.5 - - - -
958A MET* 3.4 47.2 + - + +
959A TYR* 3.5 26.4 - - + -
968A ASP* 2.8 23.6 + - - -
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Residues in contact with LEU 952 (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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854A VAL* 5.2 0.7 - - + -
900A LEU* 3.7 30.3 - - + -
905A LYS* 3.3 34.4 + - + +
908A CYS* 3.6 34.5 - - + -
909A GLU* 3.5 33.4 - - + +
912A LEU* 3.9 11.2 - - + -
948A ILE 2.8 17.4 + - - +
949A LYS 3.6 6.1 - - - +
951A ARG* 1.3 79.5 - - - +
953A GLN* 1.3 59.6 + - - +
957A SER* 3.7 12.8 + - - -
959A TYR* 3.9 11.6 - - + -
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Residues in contact with GLN 953 (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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855A PRO* 3.4 29.4 - - + +
856A THR 6.0 1.6 - - - +
882A CYS* 3.5 40.3 + - + +
905A LYS* 3.6 20.7 + - - +
909A GLU* 4.3 3.5 - - - +
949A LYS* 3.2 13.8 + - + +
950A LYS* 3.2 4.5 + - - +
952A LEU* 1.3 79.1 - - - +
954A GLU* 1.3 68.6 + - - +
955A ASP* 3.1 4.7 + - - -
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Residues in contact with GLU 954 (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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950A LYS* 2.8 39.9 + - - +
951A ARG* 3.7 12.1 - - - +
952A LEU 3.5 0.4 - - - -
953A GLN* 1.3 76.2 - - - +
955A ASP* 1.3 65.4 + - - +
956A TYR* 4.5 7.2 - - + +
957A SER* 2.6 41.8 + - - +
958A MET 5.3 0.7 - - - +
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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