Contacts of the strand formed by residues 241 - 250 (chain D) in PDB entry 4O2E
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 PHE 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D ASP* 4.2 21.1 - - + -
207D GLY 3.0 24.4 + - - -
208D PHE* 2.8 45.4 + - + -
209D TYR* 4.0 11.0 - + - -
210D PRO 4.3 0.2 - - - -
211D ALA* 3.7 38.4 - - + -
233D THR* 3.9 8.5 - - + -
234D ARG 3.3 17.0 - - - +
235D PRO* 3.8 22.2 - - + -
236D ALA 4.2 0.2 - - - +
239D ARG 3.9 17.3 - - - -
240D THR* 1.3 75.4 - - - +
242D GLN* 1.3 65.1 + - - +
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Residues in contact with GLN 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D TRP* 6.1 0.2 - - + -
205D ALA 3.3 6.3 - - - -
206D LEU* 3.6 26.0 - - + +
207D GLY 4.5 2.9 - - - +
208D PHE* 3.6 2.9 - - - -
233D THR* 3.5 3.6 - - - +
234D ARG* 2.8 71.5 + - + +
236D ALA* 3.6 21.1 - - + +
241D PHE* 1.3 79.1 - - - +
243D LYS* 1.3 64.7 + - - +
10E TYR* 3.3 11.4 - - - -
11E SER 3.4 10.8 + - - +
12E ARG* 2.9 29.3 + - - +
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Residues in contact with LYS 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D TRP* 3.9 2.5 - - - +
205D ALA* 2.8 32.0 + - - +
206D LEU* 4.9 0.4 - - - +
208D PHE* 4.1 11.4 - - + -
213D ILE* 3.7 24.0 - - + -
215D LEU* 3.6 21.7 - - + +
230D LEU* 3.7 29.1 - - - +
231D VAL* 2.8 38.4 + - - +
232D GLU* 3.8 5.1 + - - +
233D THR* 3.2 29.9 + - - +
234D ARG* 5.6 1.3 - - - +
242D GLN* 1.3 78.4 - - - +
244D TRP* 1.3 68.7 + - - +
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Residues in contact with TRP 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ARG* 3.2 44.9 - - + -
203D CYS 3.1 17.9 - - - +
204D TRP* 3.5 31.9 - + + -
215D LEU* 3.8 5.8 - - - -
229D GLU* 3.7 31.4 - - + -
230D LEU* 3.7 3.6 - - - +
231D VAL* 3.2 61.3 + - + +
234D ARG* 4.0 6.2 - - - +
243D LYS* 1.3 77.9 - - - +
245D ALA* 1.3 64.4 + - - +
246D ALA* 3.6 15.9 - - + -
99E MET* 3.0 47.2 + - + +
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Residues in contact with ALA 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ARG* 3.4 0.3 - - - -
203D CYS* 2.7 40.4 + - + +
215D LEU* 4.1 18.1 - - + +
216D THR 5.0 0.2 - - - +
217D TRP* 2.8 24.6 + - + +
228D THR* 3.9 8.1 - - + -
229D GLU 3.3 5.2 - - - -
230D LEU* 3.5 21.1 - - + -
244D TRP* 1.3 75.4 - - - +
246D ALA* 1.3 57.8 + - - +
259D CYS* 5.7 0.4 - - - -
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Residues in contact with ALA 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D THR* 3.8 18.8 - - + -
201D LEU 3.2 9.6 - - - +
202D ARG* 4.0 9.0 - - + +
217D TRP* 4.1 0.9 - - - -
227D ASP 4.2 0.3 - - - +
228D THR* 3.5 1.6 - - - +
229D GLU* 2.9 41.5 + - + +
244D TRP* 3.6 22.2 - - + -
245D ALA* 1.3 74.8 - - - +
247D VAL* 1.3 67.8 + - - +
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Residues in contact with VAL 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D THR* 3.5 4.0 - - - -
201D LEU* 3.0 35.0 + - + +
217D TRP* 3.8 34.8 - - + -
224D GLN* 4.7 7.2 - - + +
227D ASP* 3.8 14.6 - - + +
228D THR* 3.6 21.1 - - - +
246D ALA* 1.3 78.8 - - - +
248D VAL* 1.3 65.3 + - - +
249D VAL* 3.6 8.0 + - + +
257D TYR* 3.9 28.5 - - + -
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Residues in contact with VAL 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D ILE* 3.7 30.1 - - + -
198D GLU* 3.5 29.4 - - + +
199D ALA 3.5 4.0 - - - +
200D THR* 4.2 7.0 - - + +
227D ASP 4.8 3.6 + - - -
247D VAL* 1.3 76.4 - - - +
249D VAL* 1.3 63.4 + - - +
250D PRO* 3.9 6.8 - - - +
257D TYR* 4.2 4.9 + - - -
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Residues in contact with VAL 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D GLU* 3.3 4.1 - - - -
199D ALA* 2.7 40.4 + - + +
201D LEU* 3.8 21.8 - - + -
247D VAL* 3.9 8.5 - - + -
248D VAL* 1.3 75.9 - - - +
250D PRO* 1.3 84.7 - - + +
251D SER* 3.2 0.7 + - - -
253D GLU 3.9 0.4 - - - -
254D GLU* 3.7 27.9 - - + +
257D TYR* 3.5 45.5 - - + -
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Residues in contact with PRO 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D HIS* 3.8 11.2 - - + +
198D GLU* 4.4 4.0 - - + +
219D ARG* 6.1 1.1 - - - +
248D VAL* 3.9 5.2 - - + +
249D VAL* 1.3 90.1 - - + +
251D SER* 1.3 69.1 + - - +
252D GLY 3.1 0.2 + - - -
253D GLU* 2.8 52.3 + - + +
257D TYR* 3.7 15.9 - - - +
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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