Contacts of the strand formed by residues 251 - 256 (chain A) in PDB entry 3BWB
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 GLY 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A TYR* 5.0 1.4 - - - -
209A GLN* 3.8 1.9 - - - +
210A GLY* 2.7 31.9 + - - +
211A GLU 3.6 3.2 + - - -
237A TYR* 3.3 20.2 + - - -
238A ALA 3.2 12.6 - - - -
240A MSE 3.7 9.5 - - - +
250A ILE* 1.3 81.9 - - - +
252A THR* 1.3 57.3 + - - -
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Residues in contact with THR 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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84A VAL* 4.0 11.7 - - + +
85A LEU* 3.8 15.4 - - + +
88A THR* 5.7 0.4 - - - -
207A CYS* 3.3 23.9 - - - -
208A ASN 3.0 17.8 + - - -
209A GLN* 4.6 0.2 - - - -
210A GLY 3.7 1.1 - - - +
236A GLN 3.6 0.7 - - - +
237A TYR* 3.4 5.3 - - - -
238A ALA* 2.8 54.2 + - + +
240A MSE 3.6 15.5 - - + -
251A GLY* 1.3 75.0 - - - -
253A LEU* 1.3 62.1 + - - +
254A VAL* 3.6 9.0 + - + +
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Residues in contact with LEU 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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206A CYS 3.5 2.8 - - - +
207A CYS* 3.5 2.6 - - - -
208A ASN* 2.7 48.1 + - + +
210A GLY* 4.5 6.9 - - - +
220A ILE* 4.6 7.0 - - + +
223A MSE 4.2 27.8 - - + -
224A SER* 4.3 17.7 - - - +
227A ILE* 3.7 25.8 - - + -
235A VAL* 3.9 22.0 - - + -
236A GLN 3.5 1.3 - - - -
237A TYR* 3.8 33.4 - - + -
252A THR* 1.3 69.9 - - - +
254A VAL* 1.3 61.7 + - - +
255A CYS* 3.9 5.9 - - - -
300A ILE* 5.2 0.9 - - + -
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Residues in contact with VAL 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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88A THR* 3.9 28.9 - - + +
89A SER* 4.8 4.5 - - - +
92A SER* 4.5 7.4 - - - +
205A ILE* 4.3 17.0 - - + -
206A CYS 3.7 2.7 - - - -
207A CYS* 4.6 9.2 - - + +
234A SER* 4.3 0.3 + - - +
235A VAL* 3.7 0.7 - - - -
236A GLN* 2.8 36.5 + - - +
252A THR* 4.5 17.7 - - + +
253A LEU* 1.3 72.4 - - - +
255A CYS* 1.3 61.4 + - - +
263A VAL* 3.8 36.8 - - + +
291A PHE* 4.4 8.3 - - + -
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Residues in contact with CYS 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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204A GLY 4.1 0.2 - - - +
205A ILE* 3.3 10.4 - - - +
206A CYS* 2.8 52.9 + - + +
208A ASN* 5.3 1.6 - - - -
227A ILE* 3.8 21.8 - - + -
232A PHE* 3.7 20.6 - - + -
234A SER 3.3 10.5 - - - +
235A VAL* 3.7 23.1 - - - -
253A LEU* 3.9 12.1 - - - -
254A VAL* 1.3 78.9 - - - +
256A SER* 1.3 59.9 + - - +
263A VAL* 5.1 0.4 - - - -
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Residues in contact with SER 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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203A ASP 5.6 0.5 + - - -
204A GLY 3.8 5.1 + - - -
205A ILE* 3.9 7.9 - - - +
232A PHE* 3.5 8.1 - - - -
233A ALA 2.9 23.2 + - - -
234A SER* 2.9 24.2 + - - +
254A VAL 4.4 0.2 + - - -
255A CYS* 1.3 74.2 - - - +
257A LYS* 1.3 60.7 + - - +
258A LYS* 2.7 28.8 + - - +
261A VAL* 2.9 29.3 - - - +
263A VAL* 4.4 3.8 - - - +
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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