Contacts of the strand formed by residues 247 - 256 (chain B) in PDB entry 1W5A
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 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B LYS* 5.3 9.0 - - - -
184B THR* 5.3 0.9 + - - -
185B ASP 3.3 8.3 + - - -
186B THR* 3.5 1.9 - - - +
187B LEU* 2.8 30.7 + - - +
245B ASN* 3.1 5.8 - - - +
246B GLY* 1.3 77.4 - - - +
248B LEU* 1.3 56.2 + - - -
341B GLN* 3.8 19.1 - - - -
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 5.5 0.2 - - + -
181B LYS* 4.8 9.1 - - + +
187B LEU* 3.1 28.7 - - + +
189B VAL* 3.4 25.6 - - + -
246B GLY 3.8 0.2 - - - -
247B GLY* 1.3 73.9 - - - -
249B ALA* 1.3 63.5 + - - +
250B MET* 4.3 11.2 - - + -
339B GLY 3.2 20.1 + - - -
340B VAL* 3.2 30.7 + - + +
341B GLN* 3.2 32.8 + - + +
344B ILE* 4.7 10.3 - - + -
346B PHE* 4.0 24.5 - - + -
351B LEU* 5.5 3.1 - - + -
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B THR* 4.1 6.1 - - + -
187B LEU 2.9 11.1 + - - +
188B VAL* 3.3 20.1 - - + -
189B VAL 2.8 26.3 + - - -
248B LEU* 1.3 77.5 - - - +
250B MET* 1.3 68.7 + - - +
336B VAL* 4.3 4.7 - - + -
337B ILE 3.0 22.7 - - - +
338B THR* 3.9 14.4 - - + -
340B VAL* 4.3 1.3 - - - -
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Residues in contact with MET 250 (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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188B VAL* 4.7 0.2 - - - -
189B VAL* 3.9 12.1 - - + +
191B PRO* 4.1 22.0 - - + -
248B LEU* 4.3 9.0 - - + -
249B ALA* 1.3 79.0 - - - +
251B ILE* 1.3 67.4 + - - +
274B LEU 3.5 21.5 - - - +
275B LEU* 4.7 8.3 - - + -
276B ASP* 4.0 16.4 - - + +
277B VAL* 3.6 20.6 - - + -
336B VAL* 3.5 3.1 - - - +
337B ILE* 2.9 33.9 + - + +
340B VAL* 4.4 5.8 - - + +
344B ILE* 3.1 35.9 - - + -
351B LEU* 4.1 10.8 - - + -
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Residues in contact with ILE 251 (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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188B VAL* 3.4 27.4 - - + -
189B VAL 4.8 1.8 + - - +
190B ILE* 3.8 19.7 - - + -
214B VAL* 4.2 8.3 - - + -
218B ALA* 3.8 28.3 - - + -
222B LEU* 6.4 0.2 - - + -
250B MET* 1.3 81.0 - - - +
252B GLY* 1.3 60.3 + - - +
253B ILE* 4.2 21.5 - - + -
274B LEU* 3.2 40.1 + - + +
275B LEU* 3.2 8.3 + - - +
334B LEU* 4.3 6.1 - - + -
335B LEU 3.0 13.2 - - - +
336B VAL* 4.2 11.9 - - + -
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Residues in contact with GLY 252 (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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251B ILE* 1.3 75.3 - - - +
253B ILE* 1.3 63.1 + - - +
269B ALA* 3.5 24.6 - - - +
272B SER* 3.8 6.7 - - - -
275B LEU* 4.3 3.3 - - - +
333B VAL 3.6 0.7 - - - +
334B LEU* 3.6 3.3 - - - +
335B LEU* 2.7 41.5 + - - +
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Residues in contact with ILE 253 (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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198B ILE* 6.0 2.8 - - + +
214B VAL* 4.2 22.2 - - + +
217B ASN* 4.2 24.5 - - + -
218B ALA 5.0 0.4 - - - +
251B ILE* 4.2 20.2 - - + +
252B GLY* 1.3 78.6 - - - +
254B GLY* 1.3 66.0 + - - +
255B GLU* 5.8 3.1 - - + +
268B MET* 3.8 16.7 - - + +
269B ALA* 3.8 8.7 - - - -
272B SER* 3.6 14.3 + - - +
274B LEU* 4.7 6.7 - - + +
332B ARG* 5.0 15.0 - - + +
333B VAL 3.5 6.1 - - - +
334B LEU* 3.9 17.0 - - + -
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Residues in contact with GLY 254 (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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253B ILE* 1.3 79.8 - - - +
255B GLU* 1.3 61.2 + - - +
265B ALA* 3.5 22.3 - - - +
268B MET* 3.6 16.2 - - - -
269B ALA* 3.9 1.2 - - - +
332B ARG* 3.5 1.6 - - - +
333B VAL* 2.7 41.0 + - - +
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Residues in contact with GLU 255 (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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253B ILE* 5.8 2.7 - - + +
254B GLY* 1.3 76.1 - - - +
256B SER* 1.3 64.9 + - - +
264B GLU 5.1 0.3 - - - -
265B ALA* 3.9 6.2 - - - +
268B MET* 3.4 28.8 - - + +
330B THR* 3.7 19.4 + - + +
331B VAL 3.0 15.5 - - - +
332B ARG* 3.0 40.3 + - + +
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Residues in contact with SER 256 (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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255B GLU* 1.3 76.6 - - - +
257B ASP* 1.3 62.7 + - - +
258B SER* 3.2 22.7 + - - -
261B ARG* 3.5 19.8 - - - +
264B GLU* 3.2 30.9 + - - +
265B ALA* 3.9 1.5 - - - +
330B THR* 3.4 5.3 - - - -
331B VAL 2.9 29.5 + - - -
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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