Contacts of the strand formed by residues 238 - 247 (chain B) in PDB entry 2WLJ
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 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B LEU* 3.5 5.5 - - - +
181B VAL* 2.7 45.4 + - + +
193B ARG* 4.4 14.8 + - - +
236B HIS 4.5 1.9 - - - +
237B SER* 1.3 77.5 - - - +
239B PHE* 1.3 68.0 + - - +
240B LEU* 4.2 12.1 - - + +
259B ALA* 4.9 7.7 - - + +
260B TYR 3.5 13.2 - - - +
261B SER* 4.3 12.1 - - - -
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Residues in contact with PHE 239 (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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148B MET* 3.8 22.2 - - - -
159B LEU* 3.6 28.7 - - + -
178B LEU* 4.2 8.7 - - + -
179B VAL 3.4 2.9 - - - -
180B LEU* 3.6 31.4 - - + -
198B LEU* 3.8 20.4 - - + -
224B ILE* 4.2 17.3 - - + -
232B LEU* 4.6 8.3 - - + -
237B SER* 4.6 9.6 - - - -
238B GLU* 1.3 78.7 - - - +
240B LEU* 1.3 63.7 + - - +
258B HIS 3.7 0.3 - - - +
259B ALA* 3.3 2.3 - - - -
260B TYR* 2.6 49.0 + - + +
261B SER 5.4 1.3 - - - -
262B CYS* 5.5 1.6 - - - -
265B ILE* 3.6 30.1 - - + -
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B HIS 3.4 1.4 - - - +
178B LEU* 3.3 5.8 - - - +
179B VAL* 2.8 49.8 + - + +
181B VAL* 4.1 22.7 - - + -
195B PHE* 4.6 11.9 - - + -
238B GLU* 4.7 10.3 - - + +
239B PHE* 1.3 74.8 - - - +
241B VAL* 1.3 62.8 + - - +
242B LEU* 3.8 23.7 - - + +
257B ARG* 6.2 0.4 - - + -
258B HIS 3.4 4.3 - - - +
259B ALA* 3.9 23.8 - - + -
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Residues in contact with VAL 241 (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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144B PHE* 4.0 23.6 - - + -
161B MET* 4.1 22.4 - - + -
163B LEU* 4.6 2.0 - - + -
176B VAL* 3.5 27.4 - - + -
177B HIS 3.2 4.3 - - - +
178B LEU* 4.2 13.0 - - + -
240B LEU* 1.3 76.1 - - - +
242B LEU* 1.3 65.5 + - - +
257B ARG* 3.1 8.9 - - - +
258B HIS* 2.9 28.5 + - + +
260B TYR* 3.6 33.4 - - + -
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Residues in contact with LEU 242 (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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175B ASP 3.7 0.5 - - - +
176B VAL* 3.1 7.5 - - - +
177B HIS* 2.8 46.6 + - + +
179B VAL* 4.3 15.5 - - + -
240B LEU* 3.8 32.3 - - + +
241B VAL* 1.3 79.7 - - - +
243B PHE* 1.3 61.8 + - - +
244B THR* 5.4 0.7 - - - +
256B ALA 3.6 3.4 - - - +
257B ARG* 3.8 26.9 - - + -
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Residues in contact with PHE 243 (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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140B ALA* 4.8 1.6 - - + -
142B VAL* 3.8 24.7 - - + -
144B PHE* 4.6 11.7 - - + -
163B LEU* 3.9 24.2 - - + -
171B ILE* 3.9 17.9 - - + -
174B ALA* 3.7 27.6 - - + -
175B ASP 3.3 11.4 - - - -
176B VAL* 4.8 2.0 - - + -
208B PHE* 3.8 33.7 - + - -
212B TRP* 4.5 4.9 - + - -
242B LEU* 1.3 76.4 - - - +
244B THR* 1.3 74.0 + - - +
245B GLY 4.3 2.5 - - - -
254B VAL* 4.4 7.0 - - + -
255B HIS* 3.3 6.6 - - - +
256B ALA* 2.8 47.9 + - + +
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Residues in contact with THR 244 (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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173B GLU 4.4 0.7 - - - +
174B ALA* 3.0 5.4 - - - +
175B ASP* 2.8 46.4 + - - +
242B LEU* 5.4 1.2 - - - +
243B PHE* 1.3 82.2 + - - +
245B GLY* 1.3 67.6 + - - +
253B ASN* 4.8 9.6 - - + +
254B VAL 3.4 14.1 - - - +
255B HIS* 4.1 22.3 + - + +
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Residues in contact with GLY 245 (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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171B ILE* 3.6 17.5 - - - -
172B ILE 3.8 0.2 - - - -
173B GLU 3.7 14.1 - - - -
174B ALA* 4.1 0.4 - - - -
243B PHE* 4.3 2.0 - - - -
244B THR* 1.3 80.9 - - - +
246B HIS* 1.3 62.1 + - - -
253B ASN* 3.1 8.1 - - - +
254B VAL* 2.7 31.6 + - - +
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Residues in contact with HIS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A HIS* 3.6 35.8 + + + -
171B ILE* 3.3 2.7 - - - +
172B ILE* 2.8 60.2 + - + +
173B GLU* 4.6 6.0 + - + +
245B GLY* 1.3 72.3 - - - -
247B HIS* 1.3 69.7 + - - +
248B GLU* 3.6 7.4 + - + +
251B ALA* 3.4 41.1 - - + +
252B GLN* 4.0 4.9 + - - -
253B ASN* 3.4 21.0 + - - +
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Residues in contact with HIS 247 (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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140B ALA 3.6 14.0 + - - -
165B ASN* 4.4 4.2 + - - -
167B ARG* 3.4 30.7 + - + -
169B GLU* 3.8 25.0 + - + -
170B GLN 3.9 2.2 + - - -
171B ILE* 3.4 30.2 - - + +
245B GLY 3.7 2.2 + - - -
246B HIS* 1.3 73.6 - - - +
248B GLU* 1.3 62.5 + - - +
249B ALA* 3.0 37.6 + - + +
250B PHE* 3.6 22.2 - + + -
251B ALA* 2.8 28.8 + - - -
252B GLN 3.2 12.6 + - - +
254B VAL* 3.9 11.4 - - + -
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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
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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