Contacts of the helix formed by residues 894 - 908 (chain A) in PDB entry 4ZTZ
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 894 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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853A ARG* 3.8 5.5 + - - -
891A VAL* 3.7 22.3 - - + +
893A SER* 1.3 73.5 - - - +
895A GLU* 1.3 69.2 + - - +
896A LEU 3.2 2.4 + - - -
897A TRP* 3.2 6.8 + - - +
898A ILE* 2.9 38.6 + - + +
1105A ALA* 3.5 35.8 + - - +
1108A TYR* 4.7 12.7 - - + -
1109A LEU* 6.1 0.2 - - - +
1134A HIS 4.5 4.1 + - - -
1135A ASP* 3.3 39.3 + - - +
1161A ARG* 5.3 1.3 - - - +
4003A DCP 3.2 29.9 + - - +
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Residues in contact with GLU 895 (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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853A ARG* 3.4 11.4 + - - -
894A GLN* 1.3 77.8 - - - +
896A LEU* 1.3 56.9 + - - +
898A ILE* 3.2 9.2 - - - +
899A ALA* 2.9 27.2 + - - +
951A TYR* 3.9 7.2 - - + -
954A ILE* 5.4 1.1 - - - +
955A TYR* 2.3 34.9 + - - +
1098A ASN* 4.7 0.7 + - - -
1101A VAL* 3.3 21.6 - - + +
1102A GLN* 3.3 33.5 + - - +
1105A ALA* 3.8 17.4 - - + +
4003A DCP 2.8 45.1 + - + +
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Residues in contact with LEU 896 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A SER* 3.5 16.6 - - - +
894A GLN 3.2 0.8 + - - -
895A GLU* 1.3 77.5 - - - +
897A TRP* 1.3 57.3 + - - +
898A ILE 3.2 0.2 + - - -
899A ALA* 3.3 6.4 + - - +
900A ALA* 2.9 27.5 + - - +
916A PHE* 3.6 27.5 - - + -
920A THR* 3.9 15.5 - - + +
931A LEU* 3.6 28.5 - - + -
932A HIS* 3.3 32.1 - - + +
950A ASN* 5.1 7.4 - - + -
951A TYR* 3.4 19.0 + - + +
953A ARG* 6.1 0.4 - - - +
954A ILE* 4.0 16.4 - - + -
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Residues in contact with TRP 897 (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 SER* 3.6 19.2 + - - +
894A GLN* 3.2 5.8 + - - -
896A LEU* 1.3 79.4 - - - +
898A ILE* 1.3 64.2 + - + +
900A ALA* 3.4 7.0 - - + +
901A VAL* 2.9 54.0 + - + +
911A HIS* 5.1 6.7 + - - -
920A THR* 4.5 12.8 - - - +
921A LEU* 4.2 25.3 - - + +
1108A TYR* 4.8 4.3 - + - -
1161A ARG* 3.6 50.7 - - + -
1164A PHE* 3.7 29.4 - + + -
1165A ALA* 4.6 6.1 - - + -
1173A LEU* 5.6 1.8 - - + -
1174A PRO* 4.9 4.2 - - + +
1177A VAL* 3.4 41.6 - - + +
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Residues in contact with ILE 898 (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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894A GLN* 2.9 27.9 + - + +
895A GLU* 3.2 11.4 - - - +
896A LEU 3.1 0.2 - - - -
897A TRP* 1.3 85.5 - - + +
899A ALA* 1.3 60.8 + - - +
901A VAL* 3.2 5.1 + - - +
902A LEU* 2.9 44.6 + - + +
1101A VAL* 3.8 17.3 - - + +
1104A SER* 3.5 29.4 - - - +
1105A ALA* 3.4 35.2 - - - +
1108A TYR* 5.3 4.0 - - + -
1164A PHE* 4.4 13.9 - - + -
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Residues in contact with ALA 899 (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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895A GLU 2.9 17.2 + - - +
896A LEU 3.7 4.0 - - - +
898A ILE* 1.3 77.8 - - - +
900A ALA* 1.3 63.5 + - - +
902A LEU* 3.3 10.3 + - - +
903A GLY 2.9 17.5 + - - -
916A PHE* 4.1 8.3 - - + -
954A ILE* 4.8 15.3 - - + -
1057A MET* 3.6 32.6 - - + +
1061A LEU* 5.0 7.4 - - + +
1101A VAL* 5.1 6.1 - - + -
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Residues in contact with ALA 900 (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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896A LEU 2.9 14.1 + - - +
897A TRP* 3.4 13.2 - - + +
899A ALA* 1.3 76.2 - - - +
901A VAL* 1.3 53.1 - - + +
903A GLY* 2.9 4.3 + - - -
904A ASP* 2.8 36.4 + - - +
914A THR* 4.3 3.5 + - - -
916A PHE* 3.5 16.1 - - + -
917A GLY* 3.6 15.3 - - - +
920A THR* 3.5 24.0 - - + +
921A LEU* 5.6 1.1 - - + -
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Residues in contact with VAL 901 (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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897A TRP* 2.9 61.5 + - + +
898A ILE* 3.7 4.9 - - - +
900A ALA* 1.3 70.7 - - + +
902A LEU* 1.3 57.9 + - + +
903A GLY 3.0 5.2 - - - -
904A ASP* 3.0 16.0 - - - +
905A ALA* 2.9 34.1 + - + +
911A HIS* 4.5 13.2 - - + +
921A LEU* 6.0 0.4 - - + -
1164A PHE* 4.3 15.9 - - + +
1165A ALA* 5.4 2.2 - - - -
1168A LEU* 3.7 22.9 - - + -
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Residues in contact with LEU 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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898A ILE* 2.9 36.5 + - + +
899A ALA* 3.6 7.0 - - - +
901A VAL* 1.3 76.2 - - + +
903A GLY* 1.3 56.6 + - - +
906A HIS* 3.3 10.5 + - - +
1057A MET* 4.8 0.9 - - + -
1060A LYS* 3.2 46.7 + - + +
1061A LEU* 3.8 28.5 - - + -
1064A ILE* 5.8 0.7 - - + -
1073A PRO* 5.2 14.8 - - + +
1074A VAL* 5.4 2.2 - - + -
1100A VAL* 4.0 17.3 - - + -
1101A VAL* 5.2 0.4 - - - -
1104A SER* 4.6 7.2 - - - +
1168A LEU* 3.7 25.6 - - + -
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Residues in contact with GLY 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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899A ALA 2.9 9.5 + - - -
900A ALA 2.9 5.8 + - - -
902A LEU* 1.3 77.1 - - - +
904A ASP* 1.3 59.2 + - - -
906A HIS* 3.1 7.4 + - - +
907A PHE* 2.9 27.0 + - - +
914A THR* 3.7 8.2 - - - +
1057A MET* 3.6 30.5 - - - +
1060A LYS* 5.2 0.7 - - - -
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Residues in contact with ASP 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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900A ALA* 2.8 29.6 + - - +
901A VAL* 3.0 21.3 - - - +
903A GLY* 1.3 71.7 - - - +
905A ALA* 1.3 72.3 + - - +
908A ALA 2.8 34.5 + - - +
909A GLY 5.3 0.2 - - - +
910A MET 3.4 14.4 - - - +
911A HIS* 2.8 41.7 + - - +
913A CYS* 3.2 13.9 - - - -
914A THR* 3.4 21.5 + - - +
917A GLY* 4.8 0.3 - - - +
921A LEU* 5.2 1.4 - - - +
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Residues in contact with ALA 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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901A VAL* 2.9 17.1 + - + +
902A LEU 5.0 0.2 - - - +
904A ASP* 1.3 87.3 + - - +
906A HIS* 1.3 59.7 + - - +
908A ALA 2.9 17.0 - - - +
910A MET 4.8 0.9 - - - -
1060A LYS* 5.2 2.0 - - - +
1168A LEU* 3.6 41.7 - - + +
1169A GLY 4.2 11.9 - - - +
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Residues in contact with HIS 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 LEU 3.3 20.3 + - - +
903A GLY* 3.1 6.4 + - - +
904A ASP 3.1 0.6 - - - -
905A ALA* 1.3 80.5 - - - +
907A PHE* 1.3 69.6 + - - +
908A ALA* 4.7 0.2 - - - -
1059A ASN* 5.5 7.8 + - + -
1060A LYS* 3.5 43.4 - - + +
1063A SER* 5.4 7.4 + - - -
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Residues in contact with PHE 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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99A ALA* 3.9 12.2 - - - +
102A ARG* 4.2 14.1 - - + -
103A SER* 3.6 37.2 - - - -
106A HIS* 5.0 12.6 - + + -
903A GLY 2.9 15.4 + - - +
904A ASP 3.9 2.9 - - - +
906A HIS* 1.3 85.5 + - - +
908A ALA* 1.3 67.7 + - + +
913A CYS 3.5 22.2 - - - +
914A THR* 4.3 7.0 - - + -
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Residues in contact with ALA 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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99A ALA* 3.9 28.9 - - + +
100A VAL* 5.1 6.1 - - + +
103A SER* 5.3 0.2 - - - -
904A ASP 2.8 22.8 + - - +
905A ALA* 2.9 19.5 - - - +
906A HIS 4.7 0.2 - - - -
907A PHE* 1.3 83.3 - - + +
909A GLY* 1.3 61.2 + - - +
910A MET 4.5 0.9 - - - +
913A CYS* 3.6 19.1 - - + -
1169A GLY 5.1 0.2 - - - +
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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