Contacts of the helix formed by residues 1031 - 1048 (chain A) in PDB entry 2RD0
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 THR1031 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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992A ARG* 4.3 2.5 - - - -
1030A LYS* 1.3 76.3 - - - +
1032A GLU* 1.3 85.2 + - - +
1033A GLN* 3.5 11.2 - - + +
1034A GLU* 3.2 26.8 - - - +
1035A ALA* 2.8 32.6 + - - +
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Residues in contact with GLU1032 (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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989A LEU* 4.4 23.4 - - + +
992A ARG* 4.3 23.5 - - - +
1031A THR* 1.3 92.8 - - - +
1033A GLN* 1.3 67.2 + - - +
1034A GLU 2.9 1.9 + - - -
1035A ALA* 3.0 1.4 + - - +
1036A LEU* 2.9 30.3 + - - +
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Residues in contact with GLN1033 (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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989A LEU* 5.3 0.4 - - - +
1031A THR* 4.6 11.3 - - - +
1032A GLU* 1.3 87.8 + - - +
1034A GLU* 1.3 62.3 + - + +
1036A LEU* 3.9 20.2 - - + +
1037A GLU* 2.9 25.3 - - - +
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Residues in contact with GLU1034 (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 LYS* 3.6 24.4 - - + +
1031A THR* 3.1 39.6 + - - +
1032A GLU 2.9 0.8 + - - -
1033A GLN* 1.3 79.9 - - + +
1035A ALA* 1.3 60.9 + - - +
1037A GLU* 3.0 30.6 + - - +
1038A TYR* 3.4 3.8 + - - +
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Residues in contact with ALA1035 (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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988A TYR* 4.2 11.8 + - + +
992A ARG* 3.1 13.7 - - - +
1027A ALA* 3.0 37.5 - - + -
1030A LYS* 4.4 4.0 - - + -
1031A THR 2.8 14.0 + - - +
1032A GLU 3.8 1.8 - - - +
1034A GLU* 1.3 69.3 - - - +
1036A LEU* 1.3 67.6 + - - +
1037A GLU 3.0 2.0 - - - -
1038A TYR* 2.8 21.7 + - + +
1039A PHE* 2.9 14.2 + - - +
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Residues in contact with LEU1036 (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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985A TYR* 3.8 46.0 - - + +
988A TYR* 4.9 9.3 - - + -
989A LEU* 4.0 25.6 - - + -
1032A GLU 2.9 14.9 + - - +
1033A GLN* 3.9 16.6 - - + +
1035A ALA* 1.3 77.5 - - - +
1037A GLU* 1.3 63.8 + - - +
1039A PHE* 3.3 9.7 + - + +
1040A MET* 3.3 23.3 + - + +
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Residues in contact with GLU1037 (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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1033A GLN 2.9 24.0 - - - +
1034A GLU* 3.0 12.9 + - - +
1036A LEU* 1.3 78.6 - - - +
1038A TYR* 1.3 65.0 + - - +
1040A MET* 3.0 17.0 + - - +
1041A LYS* 2.9 30.7 + - + +
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Residues in contact with TYR1038 (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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909A PHE* 4.3 13.7 - + - -
951A ARG* 4.5 10.6 + - - -
988A TYR* 4.1 13.7 - - - -
1024A LYS* 4.0 34.6 - - + +
1025A THR* 3.8 22.9 + - - -
1027A ALA* 5.0 3.1 - - - -
1028A LEU* 5.9 2.5 - - + -
1030A LYS* 4.3 23.6 - - - -
1034A GLU 3.4 3.4 + - - +
1035A ALA* 2.8 20.5 + - - +
1037A GLU* 1.3 73.3 - - - +
1039A PHE* 1.3 66.0 + - - +
1041A LYS* 3.0 40.0 + - - +
1042A GLN* 3.1 35.9 + - + +
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Residues in contact with PHE1039 (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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905A CYS* 5.4 3.6 - - + -
906A VAL* 4.5 20.6 - - + -
909A PHE* 3.7 39.9 - + + -
984A CYS* 4.3 14.6 - - + -
985A TYR* 3.6 40.6 - + - -
988A TYR* 3.7 33.7 - + + -
1035A ALA 2.9 9.8 + - - +
1036A LEU* 3.5 9.6 - - + +
1038A TYR* 1.3 82.6 - - - +
1040A MET* 1.3 49.8 + - - +
1042A GLN* 3.0 8.8 + - + +
1043A MET* 2.8 42.5 + - + +
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Residues in contact with MET1040 (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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981A GLN* 5.2 0.7 - - - +
985A TYR* 3.4 41.7 - - + +
1036A LEU* 3.3 12.5 + - + +
1037A GLU* 3.0 20.3 + - - +
1039A PHE* 1.3 75.3 - - - +
1041A LYS* 1.3 58.3 + - + +
1043A MET* 3.0 9.3 + - - +
1044A ASN* 2.8 36.8 + - + +
1050A GLY* 4.4 17.7 - - - +
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Residues in contact with LYS1041 (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 GLU* 2.9 18.9 + - + +
1038A TYR* 3.0 43.6 + - - +
1040A MET* 1.3 76.6 - - - +
1042A GLN* 1.3 66.4 + - - +
1044A ASN* 4.1 4.7 - - - +
1045A ASP* 3.1 37.8 + - - +
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Residues in contact with GLN1042 (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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909A PHE* 4.0 27.4 - - + -
951A ARG* 3.4 30.6 - - - +
952A VAL* 4.6 10.0 - - + +
1038A TYR* 3.1 40.9 + - + +
1039A PHE* 3.0 9.4 + - + +
1041A LYS* 1.3 86.4 - - - +
1043A MET* 1.3 66.3 + - - +
1045A ASP* 3.7 22.2 + - - +
1046A ALA* 3.5 22.2 + - - +
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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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952A VAL* 5.8 2.2 - - - -
956A LEU* 5.1 6.7 - - + -
977A PHE* 3.7 24.9 - - + -
980A PHE* 5.1 5.2 - - + -
981A GLN* 3.2 34.3 - - + +
985A TYR* 4.1 7.6 - - - +
1039A PHE* 2.8 30.9 + - + +
1040A MET* 3.4 13.2 - - - +
1042A GLN* 1.3 73.9 - - - +
1044A ASN* 1.3 61.3 + - - +
1046A ALA* 5.3 0.4 - - - -
1047A HIS* 2.8 57.7 + - + +
1049A GLY 4.9 4.9 - - - +
1050A GLY* 3.4 17.0 - - - +
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Residues in contact with ASN1044 (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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1040A MET* 2.8 19.7 + - + +
1041A LYS* 4.2 4.7 - - - +
1043A MET* 1.3 74.2 - - - +
1045A ASP* 1.3 64.7 + - - +
1046A ALA 3.1 0.2 + - - -
1047A HIS 4.6 0.2 - - - +
1048A HIS* 3.0 25.6 + - - -
1049A GLY* 3.0 11.0 + - - -
1050A GLY* 2.8 41.7 + - - +
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Residues in contact with ASP1045 (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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1041A LYS* 3.1 27.9 + - - +
1042A GLN* 3.7 22.8 + - - +
1043A MET 3.5 0.2 - - - -
1044A ASN* 1.3 78.0 - - - +
1046A ALA* 1.3 58.6 + - - +
1048A HIS* 4.4 12.0 + - - -
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Residues in contact with ALA1046 (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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952A VAL* 3.3 42.0 - - + -
955A VAL* 3.9 26.0 - - + +
1042A GLN 3.5 10.9 + - - +
1043A MET 4.1 2.9 - - - +
1044A ASN 3.2 0.6 - - - -
1045A ASP* 1.3 79.6 - - - +
1047A HIS* 1.3 64.2 + - - +
1048A HIS* 3.6 10.1 + - - -
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Residues in contact with HIS1047 (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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905A CYS* 5.5 2.2 - - - -
952A VAL* 5.4 4.3 - - + -
954A PHE 4.8 3.6 - - - -
955A VAL* 4.8 9.9 - - + -
956A LEU* 3.2 64.3 + - + +
958A GLN* 5.8 1.9 + - - -
961A LEU* 5.7 5.6 - - + -
977A PHE* 6.5 0.2 - + - -
1043A MET* 2.8 47.3 + - + +
1044A ASN 3.2 2.5 + - - +
1046A ALA* 1.3 82.6 - - + +
1048A HIS* 1.3 75.1 + - - +
1049A GLY* 4.2 15.9 - - - +
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Residues in contact with HIS1048 (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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1044A ASN* 3.0 11.1 + - - -
1045A ASP 4.4 9.6 + - - -
1046A ALA 3.7 13.8 + - - -
1047A HIS* 1.3 84.2 - - - +
1049A GLY* 1.3 57.9 + - - +
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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