Contacts of the helix formed by residues 1040 - 1051 (chain A) in PDB entry 5JQE
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 ASP1040 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1012A GLU* 5.3 5.0 - - - +
1019A LEU* 3.7 15.4 - - - +
1038A ILE* 4.2 2.1 - - - +
1039A LYS* 1.3 98.4 + - + +
1041A ALA* 1.3 66.3 + - - +
1042A LEU* 3.8 18.6 + - - +
1043A MET* 3.1 32.1 + - - +
1044A LEU* 3.3 8.0 + - - +
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Residues in contact with ALA1041 (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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1011A GLY* 3.7 30.7 + - - +
1014A LEU* 3.9 29.1 + - + +
1019A LEU* 3.6 20.9 - - + +
1022A LEU* 5.3 0.7 - - + -
1040A ASP* 1.3 74.7 - - - +
1042A LEU* 1.3 62.9 + - - +
1044A LEU* 3.1 6.9 + - - +
1045A PHE* 3.0 27.9 + - + -
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Residues in contact with LEU1042 (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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1004A SER 5.1 1.6 - - - +
1007A LEU* 3.4 36.3 - - + +
1008A TYR* 3.5 33.4 - - + +
1011A GLY* 4.6 6.4 - - - -
1040A ASP* 3.2 16.5 + - - +
1041A ALA* 1.3 78.6 - - - +
1043A MET* 1.3 57.7 + - + +
1045A PHE* 3.0 12.1 + - + +
1046A GLN* 2.9 55.3 + - + +
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Residues in contact with MET1043 (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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1037A PRO* 3.2 40.8 - - + +
1038A ILE* 4.1 8.0 - - + +
1039A LYS* 3.6 30.3 - - + +
1040A ASP* 3.1 22.3 + - - +
1042A LEU* 1.3 78.4 - - + +
1044A LEU* 1.3 57.9 + - - +
1046A GLN* 3.7 15.8 - - - +
1047A ARG* 2.9 40.7 + - - +
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Residues in contact with LEU1044 (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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1019A LEU* 4.1 16.2 - - + -
1022A LEU* 3.6 44.2 - - + +
1023A LYS* 4.2 3.1 - - + +
1026A SER* 4.2 8.1 - - - +
1030A ILE* 3.4 32.1 - - + -
1035A GLN* 4.4 7.0 - - - +
1038A ILE* 4.0 21.6 - - + +
1040A ASP 3.3 6.2 + - - +
1041A ALA* 3.1 12.9 + - - +
1043A MET* 1.3 77.6 - - - +
1045A PHE* 1.3 67.3 + - + +
1047A ARG* 3.4 3.7 + - - +
1048A LEU* 3.1 35.1 + - + +
1065A LEU* 5.5 1.8 - - + -
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Residues in contact with PHE1045 (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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1007A LEU* 3.8 45.5 - - + -
1010A ILE* 3.6 23.6 - - + -
1011A GLY* 3.9 9.0 - - - -
1014A LEU* 3.7 25.4 - - + -
1022A LEU* 5.0 9.0 - - + -
1041A ALA* 3.0 14.7 + - + -
1042A LEU* 3.0 14.2 + - + +
1044A LEU* 1.3 83.8 - - + +
1046A GLN* 1.3 58.0 + - + +
1048A LEU* 3.3 18.5 + - + +
1049A GLN* 3.1 30.6 + - - +
1054A LEU* 4.0 6.8 - - + +
1062A LEU* 3.5 32.3 - - + -
1065A LEU* 5.4 3.1 - - + -
1066A LEU* 5.0 0.9 - - + -
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Residues in contact with GLN1046 (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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1007A LEU* 6.1 0.7 - - + -
1042A LEU* 2.9 46.7 + - + +
1043A MET* 3.2 16.2 + - - +
1045A PHE* 1.3 76.3 - - + +
1047A ARG* 1.3 64.3 + - - +
1049A GLN* 3.2 21.0 + - - +
1050A GLU* 3.1 21.1 + - - +
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Residues in contact with ARG1047 (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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1030A ILE* 3.6 39.5 - - + +
1034A LYS* 2.7 56.4 + - - +
1037A PRO* 4.1 14.6 - - - +
1038A ILE* 3.7 20.9 - - + +
1043A MET* 2.9 26.1 + - - +
1044A LEU* 3.6 8.7 - - - +
1046A GLN* 1.3 77.2 - - - +
1048A LEU* 1.3 60.4 + - - +
1050A GLU* 3.1 48.4 + - - +
1051A LYS* 3.3 13.6 + - + +
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Residues in contact with LEU1048 (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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1026A SER* 4.8 2.0 - - - -
1029A TYR* 5.6 0.2 - - + -
1030A ILE* 3.4 27.4 - - + -
1044A LEU* 3.1 24.2 + - + +
1045A PHE* 3.5 24.5 - - + +
1046A GLN 3.2 0.4 - - - -
1047A ARG* 1.3 74.4 - - - +
1049A GLN* 1.3 64.5 + - - +
1051A LYS* 3.3 4.8 + - - +
1052A ARG 3.0 16.6 + - - -
1053A MET* 3.1 25.5 + - + +
1054A LEU* 3.7 24.2 - - + +
1061A PHE* 4.0 25.4 - - + -
1062A LEU* 5.6 0.9 - - + -
1065A LEU* 4.3 19.7 - - + -
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Residues in contact with GLN1049 (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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379A HIS* 5.5 5.7 + - - -
1003A PHE* 3.7 26.5 - - - -
1004A SER* 5.6 2.5 + - - -
1007A LEU* 3.6 18.3 - - + +
1045A PHE 3.1 15.1 + - - +
1046A GLN* 3.2 21.7 + - - +
1048A LEU* 1.3 75.5 - - - +
1050A GLU* 1.3 64.5 + - - +
1052A ARG* 2.9 19.6 + - - +
1054A LEU* 3.2 27.1 + - + +
1055A GLU* 5.2 2.1 - - - +
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Residues in contact with GLU1050 (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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1034A LYS* 4.4 11.3 + - - +
1046A GLN 3.1 10.9 + - - +
1047A ARG* 3.1 41.2 + - - +
1049A GLN* 1.3 76.6 - - - +
1051A LYS* 1.3 77.7 + - + +
1052A ARG* 3.1 9.5 + - - +
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Residues in contact with LYS1051 (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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1029A TYR* 3.6 22.0 - - + +
1030A ILE* 4.5 9.2 - - + -
1031A PRO* 3.5 19.8 - - + +
1034A LYS* 3.4 29.2 - - - +
1047A ARG* 3.3 17.7 + - + +
1048A LEU* 3.3 4.0 + - - +
1050A GLU* 1.3 90.5 + - + +
1052A ARG* 1.3 68.8 + - - +
1053A MET* 2.9 19.0 + - + +
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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