Contacts of the strand formed by residues 225 - 234 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A GLY* 3.7 3.5 - - - -
195A TYR 3.7 10.8 - - - +
197A ALA* 3.9 7.2 - - - +
198A VAL* 3.9 20.9 - - + +
221A VAL* 3.1 31.5 + - + +
222A ALA* 3.0 16.8 + - - +
223A ARG 3.7 4.3 - - - +
224A ALA* 1.3 78.7 - - - +
226A ARG* 1.3 65.0 + - - +
227A PRO* 4.8 0.3 - - - +
229A GLY* 3.9 4.0 - - - +
230A VAL* 3.3 44.6 - - - +
231A VAL* 4.0 4.0 - - + -
256A PHE* 4.2 4.9 - - + -
282A THR* 3.5 31.4 + - + +
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Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 4.6 16.4 - - - +
119A PRO* 4.9 13.3 + - - +
121A PRO* 5.9 0.4 - - - +
193A GLY* 3.5 26.5 - - - +
194A SER 6.2 0.2 - - - -
195A TYR 3.3 10.0 + - - +
196A ASP* 2.8 64.5 + - - +
225A LEU* 1.3 73.3 - - - +
227A PRO* 1.3 76.5 + - + +
228A GLY 4.5 9.6 + - - -
229A GLY* 2.9 17.4 + - - +
282A THR* 2.6 23.4 + - - -
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Residues in contact with PRO 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLY* 5.4 1.3 - - - -
225A LEU 4.8 0.2 - - - +
226A ARG* 1.3 98.4 + - + +
228A GLY* 1.3 59.7 + - - +
229A GLY 3.2 0.4 + - - -
282A THR* 3.3 2.9 - - - +
283A GLU 3.0 21.1 - - - +
284A GLY* 4.1 7.2 - - - -
285A PRO* 3.7 12.0 - - + +
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Residues in contact with GLY 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 4.3 5.9 - - - +
226A ARG* 4.5 7.4 + - - -
227A PRO* 1.3 72.1 - - - +
229A GLY* 1.3 66.4 + - - +
230A VAL* 3.9 2.4 - - - +
282A THR* 2.8 18.7 + - - -
283A GLU 3.4 6.7 + - - -
285A PRO* 3.9 26.0 - - - -
287A VAL* 3.6 20.6 - - - +
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Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ASP 3.5 13.5 - - - -
225A LEU* 3.9 11.4 - - - -
226A ARG* 2.9 28.5 + - - +
227A PRO 3.2 1.2 + - - -
228A GLY* 1.3 80.5 - - - +
230A VAL* 1.3 59.3 + - - -
281A SER* 3.1 5.0 - - - -
282A THR* 3.0 26.0 + - - +
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PRO* 3.9 24.2 - - + +
118A ILE* 3.6 34.5 - - + -
196A ASP 3.3 4.0 + - - -
197A ALA* 3.0 24.5 - - + -
198A VAL 2.8 29.1 + - - -
225A LEU* 3.3 6.9 - - - +
228A GLY 3.9 3.8 - - - +
229A GLY* 1.3 80.4 - - - +
231A VAL* 1.3 55.0 + - - +
280A CYS 3.0 7.6 - - - +
281A SER* 4.0 6.7 - - - -
287A VAL* 4.0 2.9 - - + -
289A PHE* 3.5 27.1 - - + -
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PRO* 5.1 0.9 - - - -
198A VAL* 3.1 18.4 - - + +
200A VAL* 4.5 0.4 - - + -
218A PHE* 6.0 2.0 - - + -
221A VAL* 3.6 29.8 - - + -
225A LEU* 4.0 1.6 - - + -
230A VAL* 1.3 75.5 - - - +
232A CYS* 1.3 62.9 + - - +
233A THR* 3.6 24.2 - - + -
252A CYS* 5.8 0.9 - - - -
256A PHE* 3.7 19.7 - - + -
278A MSE 3.3 3.8 - - + +
279A LEU* 3.4 4.8 - - - +
280A CYS* 2.8 54.1 + - + +
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Residues in contact with CYS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ILE* 3.6 30.4 - - - +
113A LEU* 5.1 1.3 - - - -
114A PRO* 3.4 28.4 - - + +
198A VAL 2.8 8.6 + - - +
199A ILE* 3.4 5.6 - - + +
200A VAL 3.0 24.3 + - - -
231A VAL* 1.3 72.4 - - - +
233A THR* 1.3 66.2 + - - +
277A PHE* 4.0 20.6 - - - -
278A MSE 3.0 6.3 - - - -
279A LEU* 3.6 20.2 - - + -
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Residues in contact with THR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ILE* 5.2 0.4 - - - -
200A VAL* 3.5 35.7 - - + -
202A SER* 5.7 0.9 - - - -
212A LEU 5.3 2.9 - - - +
213A PHE* 5.8 2.7 - - - -
217A PHE* 5.3 0.9 - - + -
218A PHE* 4.7 21.8 - - + -
231A VAL* 3.6 16.8 - - + -
232A CYS* 1.3 81.8 - - - +
234A GLN* 1.3 67.8 + - - +
235A ALA* 4.9 0.3 - - - +
248A ILE* 5.3 1.2 - - - +
277A PHE* 3.2 5.8 - - - -
278A MSE 2.7 49.9 + - + +
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Residues in contact with GLN 234 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLN* 5.6 0.8 + - - -
106A TYR* 2.8 30.7 + - - +
110A ILE* 4.5 1.0 - - + +
200A VAL 3.8 7.2 + - - +
202A SER* 2.5 36.3 + - - +
203A SER* 3.5 20.5 + - - +
204A ASP* 4.3 3.6 + - - +
213A PHE* 3.7 16.7 - - + -
233A THR* 1.3 80.0 + - - +
235A ALA* 1.3 58.5 + - - +
236A GLU* 3.8 10.0 - - - +
270A TYR* 5.7 2.6 + - - -
275A ILE* 3.4 23.0 - - + +
276A GLY 3.3 12.3 - - - +
277A PHE* 3.3 13.6 - - + -
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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