Contacts of the helix formed by residues 901 - 915 (chain A) in PDB entry 3IAY
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 901 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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891A LYS* 5.7 2.4 + - - -
897A TYR* 3.5 28.0 - - + -
899A ASN* 3.2 28.7 + - - +
900A PRO* 1.3 78.3 + - - +
902A PRO* 1.3 78.0 - - + +
903A HIS* 3.7 20.8 - - + -
904A ALA* 3.1 9.6 + - + +
905A VAL* 2.9 23.0 + - - +
936A TYR* 4.0 3.1 - - - -
6P C 5.4 1.0 + - - -
7P C 3.2 34.0 + - - +
8P C 4.3 2.8 - - - +
11T G 5.0 8.9 + - - +
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Residues in contact with PRO 902 (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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891A LYS* 6.2 1.6 - - - +
900A PRO 4.3 0.7 - - - +
901A GLN* 1.3 94.2 - - + +
903A HIS* 1.3 58.9 + - - +
905A VAL* 3.5 2.1 + - - +
906A LEU* 3.0 28.2 + - - +
909A ARG* 5.6 0.2 + - - -
926A TYR* 4.6 14.4 - - + +
928A ILE* 4.7 4.9 - - + -
935A LEU* 4.1 14.8 - - + +
936A TYR* 3.5 37.1 - - + +
939A ALA* 3.5 25.3 - - + +
12T A 6.2 2.0 - - - -
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Residues in contact with HIS 903 (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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891A LYS* 3.3 45.4 - - + +
892A THR 3.0 25.3 + - - -
893A LEU* 4.1 5.2 - - - -
897A TYR* 3.4 6.7 + - - -
901A GLN* 3.7 20.0 - - + +
902A PRO* 1.3 81.8 - - - +
904A ALA* 1.3 58.1 + - - +
906A LEU* 3.8 4.7 - - - +
907A ALA* 2.9 27.2 + - - +
924A VAL* 3.7 20.3 - - + +
926A TYR* 3.6 30.3 - - + -
8P C 3.0 27.2 + - - -
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Residues in contact with ALA 904 (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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893A LEU* 3.6 14.6 - - + +
897A TYR* 3.4 44.6 - - + +
900A PRO* 5.9 0.7 - - + -
901A GLN* 3.1 13.6 + - + +
903A HIS* 1.3 78.7 - - - +
905A VAL* 1.3 65.7 + - + +
907A ALA* 3.4 2.8 + - - +
908A GLU* 3.3 21.7 + - - +
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Residues in contact with VAL 905 (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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900A PRO* 4.2 13.7 - - + -
901A GLN 2.9 17.7 + - - +
902A PRO 3.7 0.4 - - - +
904A ALA* 1.3 76.8 - - + +
906A LEU* 1.3 61.9 + - - +
908A GLU* 3.4 7.8 + - - +
909A ARG* 3.2 44.6 + - + +
936A TYR* 3.4 38.4 - - + +
937A ASN* 3.7 11.0 - - - +
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Residues in contact with LEU 906 (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 PRO 3.0 17.5 + - - +
903A HIS* 3.8 4.0 - - - +
905A VAL* 1.3 76.8 - - - +
907A ALA* 1.3 67.2 + - - +
909A ARG* 3.1 20.5 + - + +
910A MET* 2.9 41.4 + - + +
913A ARG* 4.3 1.8 - - - +
924A VAL* 4.1 9.9 - - + -
925A ASP 3.7 10.3 - - - +
926A TYR* 3.6 27.6 - - + -
939A ALA 3.7 8.7 - - - +
940A GLU* 3.3 26.9 - - - +
941A ASP* 3.5 19.7 - - - +
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Residues in contact with ALA 907 (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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893A LEU* 3.9 29.6 - - + -
903A HIS 2.9 19.5 + - - +
904A ALA 3.7 5.8 - - - +
905A VAL 3.4 0.2 - - - -
906A LEU* 1.3 76.3 - - - +
908A GLU* 1.3 61.5 + - - +
910A MET* 3.4 5.3 + - - +
911A LYS* 3.2 31.4 + - - +
918A PRO* 4.1 27.3 - - + +
924A VAL* 4.3 1.6 - - + -
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Residues in contact with GLU 908 (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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904A ALA 3.3 10.1 + - - +
905A VAL* 3.8 9.2 - - - +
906A LEU 3.2 0.4 - - - -
907A ALA* 1.3 75.6 - - - +
909A ARG* 1.3 66.8 + - - +
911A LYS* 3.1 21.1 + - + +
912A ARG* 3.0 49.2 + - - +
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Residues in contact with ARG 909 (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 PRO 5.6 0.2 + - - -
905A VAL* 3.2 36.7 + - - +
906A LEU* 3.1 18.8 + - + +
908A GLU* 1.3 79.9 - - - +
910A MET* 1.3 61.6 + - - +
912A ARG* 3.2 33.2 + - - +
913A ARG* 3.0 54.7 + - + +
936A TYR 4.7 0.6 + - - -
937A ASN* 3.6 24.6 + - - +
939A ALA 2.8 27.7 + - - -
940A GLU* 2.8 26.1 + - - +
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Residues in contact with MET 910 (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 LEU* 2.9 46.9 + - + +
907A ALA* 3.6 5.6 - - - +
908A GLU 3.2 0.2 - - - -
909A ARG* 1.3 77.6 - - - +
911A LYS* 1.3 57.8 + - - +
913A ARG* 3.3 17.4 + - - +
914A GLU* 2.9 32.6 + - + +
916A VAL 3.4 7.8 - - - +
917A GLY* 4.5 4.9 - - - -
918A PRO* 4.0 32.8 - - + -
924A VAL* 5.1 2.5 - - - -
925A ASP 5.5 1.1 - - - +
941A ASP* 4.1 24.0 - - + +
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Residues in contact with LYS 911 (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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893A LEU* 4.3 9.7 - - - +
907A ALA* 3.2 20.2 + - - +
908A GLU* 3.1 20.6 + - - +
910A MET* 1.3 75.3 - - - +
912A ARG* 1.3 60.5 + - - +
915A GLY* 2.7 32.9 + - - +
916A VAL* 3.7 10.8 - - - +
917A GLY 3.4 26.2 - - - +
918A PRO 2.6 30.8 + - - -
919A ASN* 4.3 11.7 - - - +
920A VAL* 5.2 1.0 - - - +
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Residues in contact with ARG 912 (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 GLU* 3.0 45.1 + - - +
909A ARG* 3.2 36.4 + - - +
911A LYS* 1.3 76.8 - - - +
913A ARG* 1.3 62.5 + - + +
915A GLY 4.5 1.0 + - - -
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Residues in contact with ARG 913 (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 LEU* 4.3 1.2 - - - +
909A ARG* 3.0 42.8 + - + +
910A MET* 3.8 18.0 - - - +
911A LYS 3.2 0.2 - - - -
912A ARG* 1.3 78.1 - - + +
914A GLU* 1.3 73.2 + - + +
915A GLY 3.8 0.2 - - - -
940A GLU* 2.7 40.4 + - - -
941A ASP* 4.0 9.1 + - - +
944A PHE* 3.5 46.7 - - - +
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Residues in contact with GLU 914 (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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329A GLY 5.0 9.6 - - - +
910A MET* 2.9 18.5 + - + +
913A ARG* 1.3 90.3 - - + +
915A GLY* 1.3 59.5 + - - +
916A VAL* 3.0 26.1 + - + +
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Residues in contact with GLY 915 (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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911A LYS* 2.7 28.6 + - - +
912A ARG 4.5 1.0 + - - -
913A ARG 3.8 0.8 - - - -
914A GLU* 1.3 71.1 - - - +
916A VAL* 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