Contacts of the helix formed by residues 966 - 975 (chain A) in PDB entry 3AR2
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 GLN 966 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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854A TRP* 4.8 14.5 - - + -
855A TRP* 3.1 38.8 - - - -
862A GLY* 5.2 2.2 - - - -
863A PRO* 5.9 0.2 - - - +
895A GLU* 5.4 0.8 + - - -
899A MET* 3.8 8.9 - - - +
961A ALA 4.4 1.6 - - - +
962A LEU* 3.1 26.6 - - + +
963A ASP* 2.6 48.5 + - + +
965A THR* 1.3 77.1 - - - +
967A TRP* 1.3 60.7 + - - +
968A LEU 3.3 0.4 - - - -
969A MET* 3.1 11.3 - - - +
970A VAL* 3.0 28.6 + - - +
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Residues in contact with TRP 967 (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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902A SER* 3.6 19.7 - - - -
906A THR* 3.9 20.0 - - - -
941A MET* 5.0 1.8 - - + -
944A HIS* 4.3 6.7 - + - -
945A PHE* 3.5 40.5 - + - -
948A LEU* 3.4 26.7 - - + -
949A TYR* 3.2 20.4 + - - -
962A LEU* 3.9 19.3 - - + +
963A ASP 3.3 20.0 + - - -
964A LEU* 4.2 13.2 - - + +
966A GLN* 1.3 75.3 - - - +
968A LEU* 1.3 53.6 + - + +
969A MET 2.9 4.9 - - - -
970A VAL* 3.0 23.0 + - + -
971A LEU* 2.8 54.3 + - + +
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Residues in contact with LEU 968 (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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964A LEU 3.5 15.0 - - - +
965A THR* 3.4 34.1 - - + +
967A TRP* 1.3 78.7 - - + +
969A MET* 1.3 56.7 + - - +
971A LEU* 3.9 11.9 - - + +
972A LYS* 2.9 34.3 + - - +
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Residues in contact with MET 969 (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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850A GLY 4.6 6.3 - - - +
851A ALA* 5.0 3.6 - - - -
854A TRP* 3.7 56.8 - - + -
899A MET* 3.7 19.3 - - + -
965A THR 3.6 2.2 + - - +
966A GLN* 3.1 14.5 + - - +
967A TRP 2.9 0.2 - - - -
968A LEU* 1.3 77.1 - - - +
970A VAL* 1.3 65.8 + - - +
971A LEU 3.0 1.6 - - - -
972A LYS* 2.9 21.5 + - + +
973A ILE* 2.9 53.8 + - + +
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Residues in contact with VAL 970 (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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899A MET* 3.7 19.5 - - - -
902A SER* 3.6 29.8 - - - +
903A VAL* 3.6 23.8 - - + +
906A THR* 3.7 14.4 - - + +
962A LEU* 4.1 8.3 - - + -
966A GLN 3.0 15.7 + - - +
967A TRP* 3.0 30.2 + - + +
969A MET* 1.3 74.2 - - - +
971A LEU* 1.3 54.8 + - + +
973A ILE* 3.7 2.9 + - - +
974A SER* 2.7 35.2 + - - -
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Residues in contact with LEU 971 (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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906A THR* 4.5 14.6 - - + -
967A TRP* 2.8 46.2 + - + +
968A LEU* 4.0 10.8 - - + +
970A VAL* 1.3 76.0 - - + +
972A LYS* 1.3 56.9 + - - +
973A ILE 2.9 4.7 - - - -
974A SER* 2.8 25.4 + - - +
975A LEU* 2.9 26.8 + - + +
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Residues in contact with LYS 972 (chain A).
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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968A LEU* 2.9 29.8 + - - +
969A MET* 2.9 21.5 + - + +
971A LEU* 1.3 73.8 - - - +
973A ILE* 1.3 56.6 + - - +
975A LEU* 5.5 0.7 - - - -
976A PRO* 3.3 18.3 - - - +
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Residues in contact with ILE 973 (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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843A TYR* 2.8 43.1 + - + +
847A ALA* 3.6 28.9 - - + +
850A GLY* 5.8 3.8 - - - +
851A ALA* 4.8 3.4 - - + -
903A VAL* 3.4 36.3 - - + -
907A ILE* 3.9 1.6 - - - +
969A MET* 2.9 32.1 + - + +
970A VAL 3.7 5.6 - - - +
971A LEU 2.9 0.6 - - - -
972A LYS* 1.3 75.8 - - - +
974A SER* 1.3 63.5 + - - +
976A PRO* 3.5 4.4 - - + +
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Residues in contact with SER 974 (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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903A VAL* 3.5 14.7 + - - +
906A THR* 3.7 15.2 - - - +
907A ILE* 3.4 38.4 + - - +
910A CYS* 4.4 4.3 - - - -
970A VAL 2.7 21.2 + - - -
971A LEU* 2.8 3.7 + - - -
973A ILE* 1.3 76.1 - - - +
975A LEU* 1.3 54.3 + - - -
976A PRO* 3.1 2.5 - - - -
977A VAL* 2.8 41.4 + - - +
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Residues in contact with LEU 975 (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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910A CYS* 4.3 20.3 - - - -
971A LEU* 2.9 28.6 + - + +
972A LYS* 5.5 0.7 - - - -
974A SER* 1.3 72.9 - - - +
976A PRO* 1.3 62.9 - - + +
977A VAL 3.1 1.3 + - - -
978A ILE* 3.2 28.4 + - + +
979A GLY 4.2 0.5 + - - -
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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