Contacts of the strand formed by residues 250 - 256 (chain A) in PDB entry 2BKE
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 ALA 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ILE* 4.1 5.4 - - + -
104A ILE* 3.6 23.6 - - + -
105A GLU 3.4 20.2 - - - +
106A THR* 3.4 14.0 - - + +
108A THR 3.8 0.2 - - - -
205A LYS 3.1 15.9 + - - +
206A LEU* 3.3 10.4 - - + +
207A ILE 2.9 25.5 + - - -
249A ILE* 1.3 74.6 - - - +
251A VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 251 (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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104A ILE* 5.4 0.2 - - - +
108A THR 3.1 7.7 + - - +
109A MSE 3.2 28.7 - - + -
110A THR* 2.8 27.4 + - - -
207A ILE* 3.2 24.5 - - + +
240A LEU* 3.8 42.0 - - + +
243A LEU* 5.0 1.3 - - + -
244A ALA* 3.9 14.8 - - + +
249A ILE* 3.8 1.8 + - + +
250A ALA* 1.3 77.1 - - - +
252A ILE* 1.3 69.4 + - - +
253A ILE* 4.0 13.7 - - + -
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Residues in contact with ILE 252 (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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104A ILE* 4.2 21.8 - - + -
110A THR* 3.3 12.8 - - - +
112A PHE* 3.8 17.5 - - + -
124A CYS* 4.6 10.3 - - - +
127A LEU* 3.2 35.9 - - + -
206A LEU* 4.0 20.9 - - + -
207A ILE 2.8 7.1 + - - +
208A VAL* 3.2 14.8 - - + -
209A VAL* 2.7 32.2 + - - +
251A VAL* 1.3 78.9 - - - +
253A ILE* 1.3 73.8 + - - +
254A THR* 4.6 7.9 - - + -
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Residues in contact with ILE 253 (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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109A MSE 3.8 33.9 - - + -
110A THR 3.1 5.4 + - - +
111A GLU* 3.4 34.6 - - + +
112A PHE 3.1 21.7 + - - -
209A VAL* 3.4 11.9 - - + -
212A VAL* 3.4 26.2 - - + -
237A LEU* 4.8 12.8 - - + -
240A LEU* 4.9 6.1 - - + -
251A VAL* 4.0 17.9 - - + -
252A ILE* 1.3 82.7 - - - +
254A THR* 1.3 67.7 + - - +
255A ASN* 6.2 1.1 - - - +
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Residues in contact with THR 254 (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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111A GLU* 5.2 0.7 - - - -
112A PHE* 3.1 15.3 - - + +
120A LYS* 3.6 22.0 - - + +
124A CYS* 3.6 30.5 - - - -
209A VAL 3.3 5.3 + - - -
210A ASP* 2.6 27.9 + - + +
211A SER* 3.0 13.4 - - - -
212A VAL* 3.1 17.2 + - - +
252A ILE* 4.6 4.3 - - + -
253A ILE* 1.3 81.1 - - - +
255A ASN* 1.3 76.4 + - - +
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Residues in contact with ASN 255 (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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111A GLU* 3.8 14.3 - - - +
112A PHE 3.1 4.0 + - - -
113A PHE* 3.1 21.2 - - + +
114A GLY 3.0 26.0 + - - +
120A LYS* 3.6 7.7 - - - +
211A SER* 4.3 3.9 - - - -
212A VAL* 3.9 3.6 - - - +
213A THR* 2.7 49.1 + - - +
217A ARG* 3.4 12.0 + - - -
253A ILE* 6.2 0.8 - - - +
254A THR* 1.3 87.1 + - - +
256A GLN* 1.3 62.7 + - - +
257A VAL* 5.3 2.3 - - + +
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Residues in contact with GLN 256 (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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114A GLY 3.3 10.5 - - - +
115A GLU* 4.4 0.7 - - - -
116A PHE* 3.7 40.0 - - - +
120A LYS* 3.3 21.4 + - - +
150A GLU* 5.0 13.1 - - - +
211A SER* 4.9 8.3 + - - +
213A THR* 5.2 0.6 + - - -
217A ARG* 3.4 26.4 + - - +
255A ASN* 1.3 76.6 - - - +
257A VAL* 1.3 80.0 + - - +
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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