Contacts of the helix formed by residues 93 - 103 (chain R) 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 ILE 93 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R GLY* 5.3 0.4 - - - -
80R CYS* 4.1 29.2 - - + +
81R VAL 3.9 23.8 - - - +
82R PHE* 4.0 11.9 - - + -
89R SER 3.7 10.1 - - - +
90R PHE* 3.0 20.1 + - + +
92R ASP* 1.3 77.2 - - - +
94R HIS* 1.3 65.8 + - - +
96R TYR* 3.0 25.2 + - + +
97R ARG* 3.0 12.9 + - + +
113R LEU* 4.0 22.2 - - + -
133R LEU* 4.3 7.9 - - + -
137R TYR* 4.2 20.4 - - + -
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Residues in contact with HIS 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90R PHE 4.6 0.2 + - - -
91R GLU 3.9 10.1 + - - +
92R ASP 3.3 0.8 - - - -
93R ILE* 1.3 79.6 - - - +
95R GLN* 1.3 66.9 + - + +
97R ARG* 3.4 3.9 + - - +
98R GLU* 3.2 53.3 + - + +
133R LEU* 5.6 1.9 - - + +
137R TYR* 2.7 39.4 + + - +
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Residues in contact with GLN 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R ARG* 5.7 5.0 - - - +
91R GLU 4.9 1.2 + - - +
92R ASP* 3.3 10.5 + - - +
93R ILE 3.2 1.0 - - - -
94R HIS* 1.3 79.9 - - + +
96R TYR* 1.3 67.0 + - + +
98R GLU* 3.3 16.1 + - - +
99R GLN* 3.0 35.5 + - - +
102R ARG* 5.4 4.9 - - - +
1003S LYS* 3.4 49.0 + - + +
1006S THR* 6.0 4.0 - - - +
1007S ASP* 5.1 3.8 + - - -
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Residues in contact with TYR 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R VAL* 4.4 20.6 - - + -
10R GLY* 3.8 19.0 + - - -
11R ALA* 3.7 32.4 + - - -
62R GLU* 5.6 3.3 - - - +
68R ARG* 4.3 27.1 + - - -
72R MET* 4.3 11.8 - - + +
80R CYS* 5.0 2.9 - - - -
92R ASP* 3.1 43.7 + - + -
93R ILE* 3.0 15.7 + - + +
95R GLN* 1.3 76.0 - - + +
97R ARG* 1.3 58.8 + - - +
99R GLN* 2.9 20.3 + - - +
100R ILE* 2.9 32.4 + - + +
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Residues in contact with ARG 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R CYS* 5.0 4.0 - - - -
93R ILE* 3.0 12.6 + - + +
94R HIS* 3.7 9.0 - - - +
96R TYR* 1.3 76.5 - - - +
98R GLU* 1.3 65.5 + - - +
99R GLN 3.1 0.3 + - - -
100R ILE* 3.1 11.3 + - - +
101R LYS* 2.9 53.7 + - + +
107R ASP 4.0 15.0 + - - -
108R ASP* 6.0 0.4 - - - +
109R VAL 5.3 3.6 + - - +
111R MET* 3.8 38.5 - - + +
137R TYR* 3.3 73.5 + - + +
139R ILE* 4.3 3.6 - - - +
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Residues in contact with GLU 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R HIS* 3.2 46.8 + - + +
95R GLN* 3.3 22.4 + - - +
97R ARG* 1.3 78.8 + - - +
99R GLN* 1.3 57.4 + - - +
101R LYS* 3.0 33.6 + - - +
102R ARG* 3.2 31.4 + - - +
1003S LYS* 5.7 3.1 - - - +
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Residues in contact with GLN 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R SER 4.7 2.4 + - - -
68R ARG* 3.0 55.5 + - - +
69R ASP* 3.2 27.4 + - - +
72R MET* 4.0 14.7 - - + +
95R GLN* 3.0 23.1 + - - +
96R TYR* 2.9 15.5 + - - +
98R GLU* 1.3 75.6 - - - +
100R ILE* 1.3 65.4 + - - +
102R ARG* 3.3 7.2 + - + +
103R VAL* 3.0 29.6 + - - +
1006S THR* 6.1 5.7 - - + +
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Residues in contact with ILE 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R VAL* 3.9 14.8 - - + -
72R MET* 3.9 17.3 - - + -
78R PHE* 3.5 48.9 - - + -
80R CYS* 3.6 29.6 - - - -
96R TYR 2.9 20.3 + - - +
97R ARG 3.1 4.2 + - - +
99R GLN* 1.3 75.3 - - - +
101R LYS* 1.3 63.1 + - - +
103R VAL* 3.2 11.6 + - - +
104R LYS* 3.1 22.2 + - + +
109R VAL* 4.2 6.7 - - + -
111R MET* 3.7 21.1 - - + -
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Residues in contact with LYS 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R ARG* 2.9 59.1 + - + +
98R GLU* 3.0 34.3 + - - +
100R ILE* 1.3 77.7 - - - +
102R ARG* 1.3 60.7 + - - +
104R LYS 3.8 0.3 - - - -
105R ASP* 3.1 17.8 + - - -
106R SER 3.2 30.2 + - - +
107R ASP* 3.6 29.7 + - - +
109R VAL* 4.5 8.3 - - + +
111R MET* 5.1 2.5 - - + -
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Residues in contact with ARG 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95R GLN* 5.4 6.1 - - - +
98R GLU* 3.2 20.7 + - - +
99R GLN* 3.7 8.4 - - + +
100R ILE 3.2 0.4 - - - -
101R LYS* 1.3 80.2 - - - +
103R VAL* 1.3 61.4 + - + +
105R ASP* 3.3 14.0 + - - +
881S SER* 3.6 19.0 + - - +
1003S LYS* 5.4 0.4 - - - +
1006S THR* 4.4 13.3 - - - +
1007S ASP* 2.7 38.4 + - - +
1010S PHE* 3.4 61.9 - - + +
1011S ASN* 5.3 3.2 + - - -
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Residues in contact with VAL 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R ASP* 3.2 41.5 - - + +
72R MET* 3.9 29.6 - - + -
73R ARG* 3.4 33.0 + - - +
99R GLN* 3.0 16.3 + - + +
100R ILE* 3.3 12.6 - - + +
102R ARG* 1.3 76.3 - - + +
104R LYS* 1.3 75.2 + - + +
105R ASP* 3.2 2.5 + - - +
881S SER* 3.3 14.6 - - - +
884S TYR* 5.6 0.9 - - - -
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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