Contacts of the strand formed by residues 287 - 293 (chain A) in PDB entry 5BNQ
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 GLU 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A ILE* 3.6 1.9 - - - -
208A VAL* 2.9 35.9 + - + +
244A LYS* 3.1 38.8 + - + -
245A THR 3.4 10.2 - - - +
246A SER* 4.3 10.6 - - - +
282A LYS 4.0 2.8 - - - +
283A LEU* 3.4 12.6 - - + +
284A ARG* 2.7 52.7 + - + +
285A SER 3.3 1.3 - - - +
286A GLY* 1.3 78.7 - - - +
288A GLU* 1.3 58.6 + - - +
289A ILE* 5.5 0.4 - - - -
84R GLU* 5.5 3.3 - - - +
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Residues in contact with GLU 288 (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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205A LYS* 3.9 33.1 - - + +
206A LEU 3.4 4.9 - - - +
207A ILE* 3.5 24.6 - - + +
243A THR 3.8 0.5 - - - +
244A LYS* 3.4 3.7 - - - +
245A THR* 2.6 53.2 + - + +
246A SER 3.2 21.3 - - - +
247A ILE* 3.2 26.7 + - - +
286A GLY 3.5 7.9 - - - +
287A GLU* 1.3 78.2 - - - +
289A ILE* 1.3 65.6 + - - +
290A SER* 4.0 0.7 + - - -
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Residues in contact with ILE 289 (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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199A MET* 6.2 0.2 - - + -
205A LYS* 3.9 3.3 - - - -
206A LEU* 2.9 49.6 + - + +
208A VAL* 4.9 5.6 - - + -
216A LEU* 4.1 22.7 - - + -
242A VAL* 3.8 24.5 - - + -
243A THR 3.4 6.5 - - - +
244A LYS* 4.3 8.3 - - + -
255A LEU* 4.2 10.1 - - + -
283A LEU* 4.0 33.4 - - + -
288A GLU* 1.3 81.1 - - - +
290A SER* 1.3 66.6 + - - +
308A PHE* 4.3 19.6 - - + -
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Residues in contact with SER 290 (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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183A SER* 4.2 16.5 + - - -
184A LEU 5.1 2.7 - - - -
204A GLY 4.6 7.6 - - - -
205A LYS* 3.4 29.2 + - - +
241A TYR 3.6 0.7 - - - +
242A VAL* 3.7 3.6 - - - +
243A THR* 2.9 46.5 + - - +
245A THR* 4.9 2.8 - - - +
288A GLU 4.4 3.1 + - - -
289A ILE* 1.3 76.7 - - - +
291A ILE* 1.3 67.6 + - - +
308A PHE* 5.3 2.5 - - - -
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Residues in contact with ILE 291 (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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183A SER* 3.6 3.0 + - - -
184A LEU* 2.7 38.2 + - + +
187A TRP* 3.8 16.8 - - + +
218A ALA* 4.3 3.1 - - + -
220A ILE* 4.2 11.9 - - + -
240A VAL* 3.8 21.8 - - + -
241A TYR 3.6 1.1 - - - -
242A VAL* 3.8 30.1 - - + -
290A SER* 1.3 79.6 - - - +
292A GLU* 1.3 60.2 + - - +
293A VAL* 4.1 14.1 - - + -
308A PHE* 3.6 53.8 - - + -
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Residues in contact with GLU 292 (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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181A LYS* 3.9 26.5 + - + +
182A VAL 3.2 10.8 - - - +
183A SER* 3.8 22.4 + - - +
240A VAL* 3.4 5.0 - - - +
241A TYR* 2.7 55.0 + - + +
243A THR* 3.7 28.7 + - + +
252A SER* 4.4 7.4 + - - -
291A ILE* 1.3 76.5 - - - +
293A VAL* 1.3 64.9 + - - +
126R GLU* 5.5 0.5 - - - +
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Residues in contact with VAL 293 (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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181A LYS* 3.2 7.0 - - - +
182A VAL* 3.0 32.2 + - + +
184A LEU* 4.0 30.3 - - + -
220A ILE* 4.0 25.1 - - + -
222A PHE* 4.3 6.5 - - + -
239A MET 3.4 13.0 - - - +
240A VAL* 4.4 3.1 - - + -
241A TYR* 5.1 0.9 - - - -
291A ILE* 4.1 16.2 - - + -
292A GLU* 1.3 80.5 - - - +
294A SER* 1.3 60.8 + - - +
295A ASN 4.7 0.9 - - - +
296A PRO* 4.4 14.7 - - + +
299A LEU* 4.1 14.6 - - + -
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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