Contacts of the strand formed by residues 225 - 234 (chain B) in PDB entry 2Q41
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 LEU 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B GLY* 3.2 10.5 - - - -
195B TYR* 3.5 13.5 - - + +
196B ASP 4.1 2.7 - - - +
197B ALA* 3.9 8.7 - - - +
198B VAL* 3.6 26.2 - - + -
221B VAL* 3.1 30.5 - - + +
222B ALA 3.1 14.6 + - - +
223B ARG 3.7 1.4 - - - +
224B ALA* 1.3 76.5 - - - +
226B ARG* 1.3 70.7 + - - +
227B PRO* 4.7 0.3 - - - +
229B GLY* 4.2 6.1 - - - +
230B VAL 3.7 31.6 - - - +
231B VAL* 4.2 3.6 - - + +
256B PHE* 4.2 4.9 - - + -
282B THR* 3.9 22.2 + - + -
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Residues in contact with ARG 226 (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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118B ILE* 4.2 22.6 - - - +
119B PRO* 4.5 15.6 + - - +
193B GLY* 3.7 20.6 - - - +
195B TYR 2.7 15.6 + - - +
196B ASP* 2.7 63.1 + - - +
225B LEU* 1.3 79.5 - - - +
227B PRO* 1.3 84.6 + - + +
228B GLY 4.3 7.7 + - - -
229B GLY* 3.0 20.9 + - - +
282B THR* 3.2 5.5 + - - -
285B PRO* 6.2 2.6 - - - +
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Residues in contact with PRO 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLY* 5.3 3.4 - - - +
225B LEU 4.7 0.2 - - - +
226B ARG* 1.3 101.3 + - + +
228B GLY* 1.3 61.2 + - - +
229B GLY 3.3 0.5 + - - -
282B THR* 3.8 2.0 - - - +
283B GLU 3.4 16.4 - - - +
284B GLY* 4.3 5.8 - - - -
285B PRO* 3.5 15.0 - - + +
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Residues in contact with GLY 228 (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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118B ILE* 4.3 5.5 - - - +
226B ARG* 4.3 7.0 + - - -
227B PRO* 1.3 72.1 - - - +
229B GLY* 1.3 64.2 + - - +
230B VAL* 4.1 1.7 - - - +
282B THR* 3.1 18.9 + - - -
283B GLU 3.0 11.5 + - - -
285B PRO* 3.6 27.3 - - - +
287B VAL* 3.5 20.4 - - - +
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Residues in contact with GLY 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE* 5.4 0.2 - - - -
196B ASP 3.7 11.2 - - - -
225B LEU* 4.2 12.2 - - - +
226B ARG* 3.0 29.0 + - - -
227B PRO 3.1 1.0 + - - -
228B GLY* 1.3 81.1 - - - +
230B VAL* 1.3 60.0 + - - -
281B SER* 3.0 4.9 - - - -
282B THR* 3.0 27.1 + - - +
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Residues in contact with VAL 230 (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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114B PRO* 3.9 26.9 - - + +
118B ILE* 3.4 45.5 - - + -
196B ASP 3.3 5.3 + - - +
197B ALA* 3.2 24.1 - - + +
198B VAL 3.4 2.3 + - - +
225B LEU* 3.7 7.7 - - - +
229B GLY* 1.3 79.0 - - - +
231B VAL* 1.3 60.6 + - - +
280B CYS 3.0 8.1 - - - +
281B SER* 3.9 2.7 - - - -
287B VAL* 3.7 10.3 - - + -
289B PHE* 3.4 26.7 - - + -
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Residues in contact with VAL 231 (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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114B PRO* 5.1 1.3 - - - -
198B VAL* 3.5 13.9 - - + +
200B VAL* 4.3 14.8 - - + -
218B PHE* 6.0 4.3 - - + -
221B VAL* 3.8 26.9 - - + -
225B LEU* 4.2 2.0 - - + +
230B VAL* 1.3 76.4 - - - +
232B CYS* 1.3 72.6 + - - +
233B THR* 4.3 7.2 - - - +
256B PHE* 3.6 21.1 - - + -
278B MSE 3.4 2.9 - - - +
279B LEU* 3.5 5.5 - - - +
280B CYS* 2.9 55.6 + - + +
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Residues in contact with CYS 232 (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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110B ILE* 3.6 22.1 - - + +
113B LEU* 4.1 5.2 - - - -
114B PRO* 3.9 18.6 - - + +
198B VAL 3.2 8.2 + - - +
199B ILE* 3.8 5.1 - - - +
200B VAL 2.9 26.8 + - - +
231B VAL* 1.3 77.1 - - - +
233B THR* 1.3 62.8 + - - +
234B GLN 4.2 0.2 + - - -
277B PHE* 3.9 34.3 - - - -
278B MSE 3.1 3.8 - - - -
279B LEU* 3.8 19.7 - - + -
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Residues in contact with THR 233 (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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200B VAL* 3.3 30.6 - - + +
212B LEU 5.5 1.8 - - - +
213B PHE* 5.1 7.9 - - + -
218B PHE* 4.1 24.2 - - + -
231B VAL* 4.1 7.2 - - - +
232B CYS* 1.3 72.6 - - - +
234B GLN* 1.3 78.3 + - - +
235B ALA* 4.5 0.9 - - + -
248B ILE* 4.9 4.7 - - + -
252B CYS* 6.0 0.2 - - - -
277B PHE* 3.0 8.1 - - - -
278B MSE 2.5 60.9 + - + -
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Residues in contact with GLN 234 (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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97B GLN* 5.8 1.0 - - - +
106B TYR* 3.3 31.3 + - + +
110B ILE* 4.9 1.0 - - + +
200B VAL* 3.3 15.9 + - - +
201B ASP* 4.7 0.2 + - - -
202B SER* 3.1 31.5 + - - +
203B SER* 2.9 25.3 + - - +
204B ASP* 5.4 0.2 + - - -
213B PHE* 3.8 14.9 - - - -
232B CYS 4.2 0.2 + - - -
233B THR* 1.3 82.2 - - - +
235B ALA* 1.3 59.4 + - - +
236B GLU* 3.2 10.8 - - - +
270B TYR* 5.5 3.4 + - - -
275B ILE* 3.7 31.7 - - + +
276B GLY 3.6 5.4 - - - +
277B PHE* 4.0 6.0 - - + -
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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