Contacts of the strand formed by residues 111 - 117 (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 MET 111 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78R PHE* 3.1 19.1 - - + +
80R CYS* 3.9 19.5 - - - -
97R ARG* 3.8 41.5 - - + +
100R ILE* 3.7 35.9 - - + -
101R LYS* 5.1 2.2 - - + -
109R VAL* 2.9 24.0 + - + +
110R PRO* 1.3 75.0 - - - +
112R VAL* 1.3 64.0 + - - +
139R ILE* 3.5 38.4 - - + +
140R PRO* 3.9 6.4 - - - +
159R LEU* 3.7 4.9 - - - +
162R GLU* 4.4 7.3 + - - +
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Residues in contact with VAL 112 (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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78R PHE 2.9 11.5 + - - +
79R LEU* 4.1 12.3 - - + -
80R CYS* 2.9 26.5 + - - +
111R MET* 1.3 75.2 - - - +
113R LEU* 1.3 58.3 + - - +
114R VAL* 3.7 20.9 - - + -
139R ILE* 4.0 5.8 - - - -
140R PRO* 3.4 32.3 - - + +
142R ILE* 3.4 27.4 - - + -
155R ALA 4.2 11.0 - - - +
158R THR* 4.0 7.6 - - + -
159R LEU* 4.3 12.3 - - + -
162R GLU* 5.5 0.7 - - + -
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Residues in contact with LEU 113 (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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80R CYS* 3.6 17.7 - - + +
82R PHE* 3.7 25.8 - - + -
93R ILE* 4.0 27.1 - - + -
112R VAL* 1.3 72.0 - - - +
114R VAL* 1.3 58.4 + - - +
130R ALA* 3.5 25.8 - - + +
133R LEU* 4.3 12.3 - - + -
134R ALA* 4.0 13.7 - - + +
137R TYR* 5.8 1.3 - - + -
139R ILE* 3.7 14.2 - - + +
140R PRO 3.0 13.6 + - - +
141R TYR* 3.3 20.6 - - + -
142R ILE* 2.9 24.9 + - - +
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Residues in contact with VAL 114 (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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19R LEU* 4.1 15.5 - - + -
79R LEU* 3.8 22.9 - - + -
80R CYS 2.9 10.8 + - - +
81R VAL* 3.3 13.5 - - + +
82R PHE* 3.1 29.1 + - - +
112R VAL* 3.7 23.6 - - + +
113R LEU* 1.3 76.3 - - - +
115R GLY* 1.3 62.7 + - - +
116R ASN 4.7 0.9 - - - +
142R ILE* 3.3 13.2 - - + +
144R THR* 3.7 27.4 - - + +
155R ALA* 4.2 11.7 - - + -
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Residues in contact with GLY 115 (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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82R PHE* 3.6 28.5 - - - -
84R ILE* 3.6 8.9 - - - +
114R VAL* 1.3 70.8 - - - +
116R ASN* 1.3 62.5 + - - -
141R TYR* 3.9 10.9 - - - -
142R ILE 3.0 10.3 + - - -
143R GLU* 3.3 4.9 - - - -
144R THR* 2.9 26.6 + - - +
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Residues in contact with ASN 116 (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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14R VAL 4.3 10.1 + - - -
15R GLY 3.6 22.2 + - - -
16R LYS* 4.9 3.0 - - - +
18R ALA* 4.7 3.3 - - - +
19R LEU* 5.6 7.9 + - + -
22R GLN* 5.0 1.2 - - - +
81R VAL* 4.3 14.1 - - + -
82R PHE 3.0 13.7 + - - +
83R ALA* 3.6 7.9 - - - +
84R ILE* 3.0 24.5 + - - -
85R ASN* 4.3 1.0 - - - +
114R VAL* 3.8 2.3 + - + -
115R GLY* 1.3 72.9 - - - +
117R LYS* 1.3 68.0 + - - +
118R CYS* 4.3 2.9 + - - +
144R THR* 3.5 17.5 + - - +
145R SER 4.1 0.2 - - - -
146R ALA* 3.6 30.0 + - - +
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Residues in contact with LYS 117 (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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84R ILE* 4.4 24.7 - - + -
85R ASN* 4.9 0.9 - - - +
116R ASN* 1.3 77.7 + - - +
118R CYS* 1.3 64.5 + - - +
119R ASP* 3.2 38.9 + - - +
121R ALA 5.8 2.0 - - - -
123R ARG* 5.0 9.2 - - - +
143R GLU* 5.8 0.4 - - - +
144R THR 2.8 18.9 + - - +
145R SER* 3.9 16.7 + - - +
146R ALA* 3.0 28.8 + - - +
147R LYS 4.5 0.5 + - - -
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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