Contacts of the strand formed by residues 238 - 247 (chain C) in PDB entry 2WLM
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ARG* 3.1 20.7 - - - +
14C ILE* 2.8 34.0 + - - +
15C LEU* 3.0 44.6 + - + +
180C LEU* 3.5 6.4 - - - +
181C VAL* 2.7 33.2 + - + +
193C ARG* 4.1 7.5 + - - +
236C HIS* 4.1 8.9 - - + +
237C SER* 1.3 77.2 - - - +
239C PHE* 1.3 71.2 + - - +
259C ALA* 5.9 1.3 - - + -
260C TYR 3.3 15.0 - - - +
261C SER* 4.5 8.1 - - - +
262C CYS* 6.2 0.4 - - - -
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Residues in contact with PHE 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 5.9 0.4 - - - -
148C MET* 3.9 23.1 - - - -
159C LEU* 3.9 25.4 - - + -
178C LEU* 4.5 8.1 - - + -
179C VAL 3.4 4.3 - - - +
180C LEU* 3.9 34.8 - - + -
198C LEU* 4.1 10.1 - - + -
224C ILE* 4.2 16.6 - - + -
232C LEU* 4.3 12.8 - - + -
237C SER 4.4 9.4 - - - -
238C GLU* 1.3 83.4 - - - +
240C LEU* 1.3 61.0 + - - +
259C ALA* 3.2 4.3 - - - -
260C TYR* 2.6 49.2 + - + +
261C SER 5.0 1.3 - - - -
262C CYS* 4.9 1.6 - - - -
265C ILE* 3.3 33.9 - - + -
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.8 29.8 - - + -
19C GLY* 4.2 11.2 - - - +
177C HIS 3.4 2.8 - - - +
178C LEU* 3.7 1.0 - - - -
179C VAL* 2.7 51.9 + - + +
181C VAL* 4.9 3.6 - - + -
195C PHE* 5.2 12.1 - - + -
238C GLU 4.3 0.2 - - - -
239C PHE* 1.3 73.3 - - - +
241C VAL* 1.3 61.7 + - - +
242C LEU 4.1 0.4 + - - +
258C HIS 2.9 24.7 - - - +
259C ALA* 3.8 11.7 - - + -
207D ILE* 4.0 43.1 - - + +
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Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 3.7 25.1 - - + -
161C MET* 3.9 22.9 - - - -
163C LEU* 4.9 0.2 - - + -
176C VAL* 3.5 26.9 - - + -
177C HIS 3.3 4.0 - - - +
178C LEU* 3.4 26.2 - - + -
240C LEU* 1.3 75.8 - - - +
242C LEU* 1.3 62.0 + - - +
256C ALA 4.0 0.3 - - - +
257C ARG* 3.1 7.8 - - - +
258C HIS* 2.7 39.6 + - + +
260C TYR* 3.9 22.2 - - + -
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Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C ASP 3.9 0.5 - - - +
176C VAL* 3.2 6.9 - - - -
177C HIS* 2.9 45.4 + - + -
240C LEU* 4.1 1.0 + - + -
241C VAL* 1.3 74.0 - - - +
243C PHE* 1.3 80.7 + - - +
244C THR* 3.5 19.7 - - + +
255C HIS* 4.2 7.4 - - + -
256C ALA 3.4 10.8 - - - +
257C ARG* 4.5 2.5 - - + +
172D ILE* 4.7 5.6 - - + -
173D GLU* 4.3 10.1 - - + +
206D PRO* 3.1 54.1 - - + +
207D ILE* 4.0 16.8 - - + -
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Residues in contact with PHE 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ALA* 4.3 5.8 - - + -
142C VAL* 3.7 24.2 - - + -
144C PHE* 4.4 13.5 - - + -
163C LEU* 3.8 24.0 - - + -
171C ILE* 3.7 25.4 - - + -
174C ALA* 3.6 33.0 - - + -
175C ASP 3.6 10.8 - - - -
176C VAL* 4.2 8.3 - - + -
208C PHE* 3.8 17.7 - + - -
212C TRP* 4.7 2.7 - + - -
241C VAL* 4.1 1.0 - - - +
242C LEU* 1.3 72.3 - - - +
244C THR* 1.3 84.1 + - - +
245C GLY 4.1 2.2 - - - -
254C VAL* 4.7 1.6 - - + -
255C HIS* 3.0 1.2 - - - +
256C ALA* 2.7 47.9 + - + +
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Residues in contact with THR 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C GLU 4.2 0.7 - - - +
174C ALA* 3.3 2.3 - - - +
175C ASP* 2.8 49.4 + - - +
177C HIS* 6.2 0.9 - - + -
242C LEU* 3.5 24.0 - - + -
243C PHE* 1.3 89.4 - - - +
245C GLY* 1.3 58.3 + - - +
253C ASN* 5.5 3.3 + - - -
254C VAL 3.4 11.4 - - - -
255C HIS* 3.4 13.9 - - + -
172D ILE* 4.8 9.2 - - + -
173D GLU* 4.8 13.8 + - + +
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Residues in contact with GLY 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C ILE* 3.6 17.5 - - - -
172C ILE 3.9 7.0 - - - -
173C GLU* 4.0 4.0 - - - -
174C ALA* 3.9 3.1 - - - -
243C PHE* 4.1 2.0 - - - -
244C THR* 1.3 77.4 + - - +
246C HIS* 1.3 59.6 + - - -
253C ASN* 3.5 12.1 + - - +
254C VAL* 2.8 33.9 + - - +
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Residues in contact with HIS 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B HIS* 3.7 16.1 - + - -
171C ILE* 3.5 2.8 - - - +
172C ILE* 2.8 70.4 + - + +
173C GLU* 4.7 7.7 - - - +
245C GLY* 1.3 71.2 - - - -
247C HIS* 1.3 67.6 + - - +
248C GLU* 3.5 3.6 + - - -
251C ALA* 3.4 23.5 - - + +
252C GLN* 3.4 22.4 - - - -
253C ASN* 3.4 24.7 + - - +
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Residues in contact with HIS 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C ALA* 4.3 0.9 - - - -
141C GLY 4.2 7.5 + - - -
165C ASN* 4.8 2.0 + - - -
167C ARG* 3.7 36.9 + - - +
169C GLU* 3.5 25.7 + - + -
170C GLN 3.9 3.1 - - - -
171C ILE* 3.8 25.7 - - + +
245C GLY 3.7 2.4 + - - -
246C HIS* 1.3 71.6 - - - +
248C GLU* 1.3 55.2 + - - +
249C ALA* 3.0 38.8 + - + +
250C PHE* 3.8 11.4 - + + -
251C ALA* 2.7 34.8 + - - -
252C GLN 2.9 12.9 + - - +
254C VAL* 3.7 26.7 - - + -
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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