Contacts of the helix formed by residues 1002 - 1016 (chain S) in PDB entry 1BKD
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 GLU1002 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65R SER* 4.0 23.4 + - - +
68R ARG* 2.8 35.0 + - - -
833S LEU* 6.3 2.5 - - + -
997S MET* 3.6 21.2 - - + +
1001S MET* 1.3 75.2 - - - +
1003S LYS* 1.3 59.2 + - - +
1005S PHE* 3.0 2.8 + - - +
1006S THR* 2.8 39.5 + - - +
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Residues in contact with LYS1003 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95R GLN* 3.4 40.9 + - + +
98R GLU* 5.7 3.8 - - - +
102R ARG* 5.4 0.4 - - - +
1001S MET* 3.4 2.5 - - + +
1002S GLU* 1.3 77.2 - - - +
1004S GLU* 1.3 67.6 + - - +
1006S THR* 4.3 6.7 - - - -
1007S ASP* 2.8 55.2 + - - +
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Residues in contact with GLU1004 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000S SER* 4.0 20.5 + - - -
1001S MET* 3.3 30.6 + - + +
1003S LYS* 1.3 80.8 - - - +
1005S PHE* 1.3 57.0 + - - +
1007S ASP* 3.5 5.4 + - - +
1008S TYR* 3.1 26.2 + - - +
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Residues in contact with PHE1005 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833S LEU* 4.3 22.0 - - + -
837S LYS* 3.8 22.4 - - + -
996S PRO* 3.1 31.0 - - + -
997S MET* 3.5 38.8 - - + -
1000S SER* 4.2 12.3 - - - -
1001S MET 3.1 10.4 + - - +
1002S GLU 3.0 8.4 + - - +
1004S GLU* 1.3 74.5 - - - +
1006S THR* 1.3 68.1 + - - +
1008S TYR* 3.0 31.5 + + + +
1009S LEU* 3.0 44.9 + - + +
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Residues in contact with THR1006 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69R ASP* 5.7 4.7 - - - +
99R GLN* 6.1 6.3 - - + +
102R ARG* 4.4 15.5 - - - +
833S LEU* 5.7 4.9 - - - +
882S PRO* 4.7 6.5 - - + +
1002S GLU* 2.8 35.2 + - - +
1003S LYS* 3.9 7.6 - - - -
1005S PHE* 1.3 76.8 - - - +
1007S ASP* 1.3 64.7 + - - +
1009S LEU* 3.3 11.5 + - + +
1010S PHE* 3.1 21.7 + - + +
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Residues in contact with ASP1007 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95R GLN* 5.1 2.1 + - - -
102R ARG* 2.7 36.3 + - - +
1003S LYS* 2.8 57.4 + - - +
1004S GLU* 3.8 5.9 - - - +
1006S THR* 1.3 79.0 - - - +
1008S TYR* 1.3 57.9 + - - +
1010S PHE* 3.4 1.7 + - - +
1011S ASN* 2.9 45.4 + - - +
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Residues in contact with TYR1008 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837S LYS* 5.1 0.7 - - - -
841S GLU* 2.7 41.6 + - + +
1004S GLU 3.1 14.3 + - - +
1005S PHE* 3.0 27.7 + + + +
1007S ASP* 1.3 74.6 - - - +
1009S LEU* 1.3 81.9 + - + +
1011S ASN* 3.4 6.9 + - + +
1012S LYS* 3.0 50.7 + - + +
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Residues in contact with LEU1009 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833S LEU* 4.6 6.1 - - + +
836S GLU* 3.2 34.5 - - + +
837S LYS* 3.9 27.4 - - + +
840S VAL* 3.4 16.0 - - + +
882S PRO* 3.8 16.3 - - + +
1005S PHE* 3.0 48.8 + - + +
1006S THR* 3.3 11.2 + - + +
1008S TYR* 1.3 87.5 - - + +
1010S PHE* 1.3 58.2 + - - +
1012S LYS* 3.0 6.1 + - - +
1013S SER* 2.9 25.8 + - - -
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Residues in contact with PHE1010 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102R ARG* 3.4 59.5 - - + +
105R ASP* 6.1 1.3 - - - -
881S SER* 3.8 30.1 - - - -
882S PRO* 3.7 16.5 - - + +
885S ARG* 4.3 21.3 - - + -
1006S THR* 3.1 13.9 + - + +
1007S ASP 3.9 3.6 - - - +
1009S LEU* 1.3 80.1 - - - +
1011S ASN* 1.3 63.2 + - - +
1013S SER* 3.3 3.3 + - - -
1014S LEU* 3.1 46.8 + - + +
1019S ARG* 4.5 11.9 - - - -
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Residues in contact with ASN1011 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102R ARG* 5.3 2.9 + - - -
1007S ASP* 2.9 35.9 + - - +
1008S TYR* 4.0 6.1 - - + +
1010S PHE* 1.3 81.4 - - - +
1012S LYS* 1.3 58.8 + - - +
1014S LEU* 3.6 17.3 + - - +
1015S GLU* 3.1 26.3 + - - +
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Residues in contact with LYS1012 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840S VAL* 3.1 38.4 - - + +
841S GLU* 4.9 4.5 - - + -
843S GLU* 2.8 38.8 + - - +
1008S TYR* 3.0 47.3 + - + +
1009S LEU* 3.0 4.0 + - - +
1011S ASN* 1.3 77.0 - - - +
1013S SER* 1.3 62.7 + - - +
1015S GLU* 3.1 30.1 + - - +
1016S ILE* 3.0 31.2 + - + +
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Residues in contact with SER1013 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840S VAL* 4.0 4.0 - - - +
882S PRO* 2.8 38.5 + - - -
885S ARG* 2.8 36.3 + - - -
886S LEU* 3.4 5.8 - - - +
1009S LEU 2.9 11.9 + - - -
1010S PHE* 3.5 9.6 - - - -
1012S LYS* 1.3 76.9 - - - +
1014S LEU* 1.3 52.6 + - - +
1016S ILE* 3.3 14.2 + - - +
1017S GLU* 3.0 21.5 + - - +
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Residues in contact with LEU1014 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885S ARG* 3.3 29.6 - - - +
1010S PHE* 3.1 40.7 + - + +
1011S ASN* 3.8 16.8 - - - +
1012S LYS 3.3 0.2 - - - -
1013S SER* 1.3 76.6 - - - +
1015S GLU* 1.3 56.8 + - - +
1017S GLU 5.0 0.7 - - - +
1018S PRO* 3.0 32.7 - - + +
1019S ARG* 3.8 41.3 - - + +
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Residues in contact with GLU1015 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843S GLU* 4.1 7.2 - - - +
1011S ASN 3.1 16.8 + - - +
1012S LYS* 3.1 43.8 + - - +
1013S SER 3.2 0.2 - - - -
1014S LEU* 1.3 77.7 - - - +
1016S ILE* 1.3 60.6 + - + +
1018S PRO* 4.0 7.2 - - - +
1025S PRO* 4.2 3.3 - - - +
1027S PHE* 3.1 29.0 - - + -
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Residues in contact with ILE1016 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840S VAL* 3.4 31.6 - - - +
842S THR 4.6 0.2 - - - +
843S GLU* 3.6 36.1 - - + +
848S ARG* 3.4 41.0 + - - +
886S LEU* 4.1 11.4 - - + -
1012S LYS* 3.0 15.8 + - + +
1013S SER* 3.3 18.2 - - - +
1015S GLU* 1.3 81.1 - - + +
1017S GLU* 1.3 66.3 + - - +
1018S PRO* 3.8 2.0 - - - -
1024S LEU* 3.2 14.7 - - - +
1027S PHE* 3.9 14.2 - - + -
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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