Contacts of the strand formed by residues 257 - 263 (chain B) in PDB entry 4BOS
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 LYS 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B TYR 3.8 13.5 + - - -
233B GLN* 3.3 24.3 + - - +
234B CYS* 3.4 18.6 - - + +
235B GLU* 2.8 25.6 + - - +
255B TYR* 4.0 2.8 - - - +
256B THR* 1.3 97.3 - - + +
258B ARG* 1.3 64.8 + - - +
285B ILE* 3.7 29.2 - - + -
286B PHE 3.4 9.9 - - - +
288B SER* 4.3 2.8 - - - +
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Residues in contact with ARG 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B CYS* 4.6 0.4 - - - -
235B GLU* 2.7 49.3 + - + +
237B CYS* 3.9 8.7 - - - -
248B ARG* 3.9 15.4 - - - +
257B LYS* 1.3 79.2 - - - +
259B VAL* 1.3 68.3 + - - +
260B LEU* 4.0 12.6 - - + -
285B ILE* 3.6 4.4 - - - -
286B PHE* 2.9 36.4 + - + +
287B SER 3.7 8.4 + - - +
288B SER* 3.1 31.2 + - - -
289B ASN 4.5 0.2 - - - -
290B ASP 3.1 28.9 + - - -
291B ASP* 5.2 1.0 + - - -
293B VAL* 4.0 16.4 - - - -
294B LEU* 3.7 25.5 - - - +
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Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B VAL* 6.1 0.7 - - + -
168B VAL* 3.7 39.0 - - + +
169B VAL* 4.3 5.6 - - + -
234B CYS* 4.1 16.6 - - - -
235B GLU 2.9 16.8 + - - +
236B ILE* 3.7 26.9 - - + +
237B CYS* 2.9 26.7 + - - +
258B ARG* 1.3 77.1 - - - +
260B LEU* 1.3 68.0 + - - +
261B LEU* 5.6 0.4 - - + -
284B THR 3.6 18.6 - - - +
285B ILE* 4.3 10.5 - - + -
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LEU* 4.3 2.0 - - + -
168B VAL* 3.8 3.7 - - - +
237B CYS* 3.3 20.6 - - + +
239B VAL* 4.8 4.7 - - + -
246B ILE* 5.7 1.1 - - + -
258B ARG* 4.0 12.3 - - + -
259B VAL* 1.3 81.9 - - - +
261B LEU* 1.3 69.0 + - - +
271B LEU* 3.1 43.4 + - + +
284B THR 4.7 3.2 + - - -
286B PHE* 3.7 28.3 - - + -
293B VAL* 3.8 21.8 - - + +
294B LEU* 4.4 10.5 - - + -
297B ALA* 3.5 30.7 - - + -
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Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 4.1 17.7 - - + -
164B SER* 3.7 37.2 - - - +
165B VAL* 3.9 18.2 - - + +
168B VAL* 4.1 11.7 - - + -
225B ILE* 5.1 1.3 - - + -
236B ILE* 3.9 27.1 - - + -
237B CYS 2.8 8.1 + - - +
238B VAL* 3.5 14.9 - - + -
239B VAL* 2.8 30.2 + - - +
259B VAL* 5.6 0.4 - - + -
260B LEU* 1.3 83.1 - - - +
262B ILE* 1.3 60.4 + - - +
268B TYR* 4.3 11.9 - - + -
269B ASP 3.5 6.5 - - - +
270B PRO* 4.3 3.4 - - + -
271B LEU* 4.1 4.0 - - - -
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ARG* 3.4 43.9 + - - +
239B VAL* 3.4 14.1 - - + +
241B THR* 3.5 27.6 - - + -
261B LEU* 1.3 74.6 - - - +
263B TYR* 1.3 64.2 + - - +
267B HIS 3.6 0.9 - - - +
268B TYR* 3.3 6.1 - - - +
269B ASP* 2.9 45.9 + - + +
271B LEU* 3.7 19.9 - - + +
300B LEU* 3.9 35.4 - - + -
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Residues in contact with TYR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ARG* 6.3 0.2 - - - -
238B VAL* 3.6 22.9 - - + -
239B VAL 2.7 8.5 + - - +
240B ASP* 3.4 25.4 - - + +
241B THR* 2.8 32.5 + - - -
247B ASP* 5.9 1.3 - - - -
262B ILE* 1.3 77.1 - - - +
264B ASP* 1.3 56.3 + - - +
265B GLY* 2.8 45.9 + - - -
266B ILE* 3.6 8.7 - - - -
267B HIS 3.4 12.3 - - - -
268B TYR* 3.3 48.4 + + + -
1311B NO3 3.4 14.4 + - - -
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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
------------------------------------------------------------
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