Contacts of the helix formed by residues 1012 - 1021 (chain A) in PDB entry 4Z02
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 ASP1012 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010A GLY 3.5 1.4 - - - -
1011A ILE* 1.4 83.4 - - - +
1013A GLU* 1.3 62.1 + - - +
1014A THR* 3.0 27.7 + - - -
1015A ILE* 3.0 23.6 + - + +
1016A ASP* 3.0 33.9 + - - +
1006B MET 4.0 13.0 - - - +
1007B VAL* 3.4 7.6 - - - +
1008B PRO* 3.4 32.5 - - + +
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Residues in contact with GLU1013 (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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1012A ASP* 1.3 75.0 + - - +
1014A THR* 1.4 57.4 + - - +
1016A ASP* 4.0 5.7 - - - +
1017A LYS* 2.9 43.6 + - + +
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Residues in contact with THR1014 (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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1012A ASP* 3.0 11.8 + - - -
1013A GLU* 1.4 73.9 - - - +
1015A ILE* 1.3 60.2 + - - +
1017A LYS* 3.5 5.0 + - - +
1018A LEU* 3.0 30.5 + - + +
1004B SER 5.2 4.5 + - - -
1006B MET 4.5 4.2 + - - -
1007B VAL* 3.8 32.1 - - + +
1015B ILE* 5.2 6.7 - - + -
1019B LYS* 5.7 2.5 - - - +
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Residues in contact with ILE1015 (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 TRP* 4.8 0.4 - - + -
1007A VAL* 3.8 16.8 - - + -
1008A PRO 4.5 8.5 - - - +
1011A ILE* 4.7 2.7 - - + -
1012A ASP* 3.0 24.5 + - + +
1014A THR* 1.3 75.1 - - - +
1016A ASP* 1.4 65.4 + - - +
1018A LEU* 3.3 3.1 + - - +
1019A LYS* 3.1 32.6 + - + +
1007B VAL* 4.0 5.4 - - + -
1008B PRO* 3.8 27.6 - - + +
1011B ILE* 3.4 31.2 - - + -
1012B ASP* 3.3 23.6 - - + +
1015B ILE* 3.4 23.3 - - + +
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Residues in contact with ASP1016 (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 TRP* 2.8 26.3 + - - +
1008A PRO 4.5 1.7 - - - +
1009A LEU* 3.8 1.2 - - - -
1010A GLY* 3.1 39.1 + - - -
1011A ILE 4.6 0.4 + - - -
1012A ASP 3.0 23.1 + - - +
1013A GLU* 4.0 5.6 + - - +
1015A ILE* 1.4 75.2 - - - +
1017A LYS* 1.4 57.6 + - - +
1019A LYS* 3.4 3.3 + - - +
1020A MET* 3.0 36.5 + - + +
1036A PHE* 3.5 29.7 - - + -
1040A MET* 5.2 0.5 - - - +
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Residues in contact with LYS1017 (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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1013A GLU* 2.9 32.2 + - + +
1014A THR* 3.9 5.4 - - - +
1016A ASP* 1.4 76.2 - - - +
1018A LEU* 1.4 61.7 + - - +
1020A MET* 3.2 17.3 + - + +
1021A MET* 3.1 30.8 + - + +
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Residues in contact with LEU1018 (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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1014A THR* 3.0 19.5 + - + +
1015A ILE 3.7 3.1 - - - +
1017A LYS* 1.4 71.0 - - - +
1019A LYS* 1.3 73.9 + - - +
1021A MET* 3.1 17.5 + - + +
1022A GLU* 3.4 13.1 + - + +
1012B ASP* 4.5 0.2 - - - +
1014B THR* 3.8 28.9 - - + -
1015B ILE* 3.7 31.2 - - + +
1018B LEU* 3.8 22.2 - - + -
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Residues in contact with LYS1019 (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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934A TRP* 3.5 49.4 - - + -
941A PRO* 5.7 0.2 - - - +
942A SER* 3.5 21.2 + - - +
1007A VAL* 3.8 24.3 - - - +
1015A ILE* 3.1 19.7 + - + +
1018A LEU* 1.3 81.9 - - - +
1020A MET* 1.4 60.8 + - - +
1022A GLU* 3.3 42.2 + - - +
1023A GLY 4.8 0.5 + - - -
1032A VAL* 4.5 4.2 - - - +
1012B ASP* 2.8 36.5 + - - +
1014B THR* 4.1 15.0 + - - +
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Residues in contact with MET1020 (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 TRP* 3.6 16.6 - - + -
1016A ASP* 3.0 31.1 + - + +
1017A LYS* 3.2 17.7 + - + +
1019A LYS* 1.4 75.7 - - - +
1021A MET* 1.3 71.4 + - + +
1022A GLU 3.5 0.4 + - - -
1023A GLY 4.6 0.7 + - - -
1029A ARG* 3.7 24.9 - - - +
1032A VAL* 4.3 14.8 - - + +
1033A ARG* 4.2 24.9 - - + -
1036A PHE* 3.7 45.5 - - + -
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Residues in contact with MET1021 (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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1017A LYS* 3.1 17.7 + - + +
1018A LEU* 3.1 10.2 + - + +
1020A MET* 1.3 101.8 - - + +
1022A GLU* 1.4 61.2 + - - +
1023A GLY 3.4 7.7 + - - +
1029A ARG* 3.8 27.4 + - + +
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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