Contacts of the strand formed by residues 225 - 234 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192C GLU* 5.4 0.3 - - - +
193C GLY* 3.1 15.1 + - - -
195C TYR* 3.2 16.6 - - + +
196C ASP 3.7 3.4 - - - +
197C ALA* 3.5 36.3 - - - +
198C VAL* 3.7 10.8 - - + -
221C VAL* 2.9 24.8 + - + +
222C ALA 3.4 14.6 - - - +
223C ARG 3.2 0.7 - - - +
224C ALA* 1.3 78.5 - - - +
226C ARG* 1.3 70.3 + - - +
227C PRO* 4.5 0.7 - - - +
229C GLY* 3.6 20.2 - - - +
230C VAL 3.6 1.1 - - - +
231C VAL* 3.4 33.7 - - + -
282C THR* 4.3 7.6 - - + -
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Residues in contact with ARG 226 (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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118C ILE* 4.1 24.5 - - - +
119C PRO* 4.6 18.8 + - - +
121C PRO* 5.3 0.6 - - - +
193C GLY* 3.7 17.1 - - - +
195C TYR 2.8 18.6 + - - +
196C ASP* 3.0 38.1 + - - +
225C LEU* 1.3 77.0 - - - +
227C PRO* 1.3 87.3 + - + +
228C GLY* 3.7 19.8 + - - -
229C GLY* 2.8 20.1 + - - +
282C THR* 3.0 5.5 + - - -
285C PRO* 5.5 8.7 - - - +
287C VAL* 5.4 2.0 - - - +
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Residues in contact with PRO 227 (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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193C GLY* 5.1 3.8 - - - +
225C LEU 4.5 1.3 - - - +
226C ARG* 1.3 98.9 + - + +
228C GLY* 1.3 58.5 + - - +
282C THR* 3.7 3.4 - - - +
283C GLU 3.4 17.7 - - - +
284C GLY* 4.2 6.1 - - - -
285C PRO* 3.6 13.4 - - + +
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Residues in contact with GLY 228 (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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226C ARG* 3.7 16.0 + - - -
227C PRO* 1.3 73.6 - - - +
229C GLY* 1.3 66.1 + - - +
230C VAL* 3.7 2.6 + - - +
282C THR* 2.7 29.9 + - - -
283C GLU 3.4 1.6 + - - -
285C PRO* 3.8 21.8 - - - -
287C VAL* 3.6 20.3 - - - +
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Residues in contact with GLY 229 (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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196C ASP 3.6 12.1 - - - -
225C LEU* 3.6 20.7 - - - +
226C ARG* 2.8 23.6 + - - -
227C PRO 3.6 0.2 + - - -
228C GLY* 1.3 79.2 - - - +
230C VAL* 1.3 59.4 + - - -
231C VAL* 5.0 0.2 - - - +
280C CYS 3.5 0.5 - - - +
281C SER* 3.1 4.2 - - - -
282C THR* 2.9 25.0 + - - +
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Residues in contact with VAL 230 (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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114C PRO* 3.9 22.0 - - + +
118C ILE* 3.6 32.5 - - + -
196C ASP 3.3 7.1 + - - +
197C ALA* 3.2 21.9 - - + +
198C VAL 3.0 23.7 + - - -
225C LEU* 3.6 3.3 - - - +
228C GLY 4.0 3.8 - - - +
229C GLY* 1.3 77.0 - - - +
231C VAL* 1.3 63.5 + - - +
280C CYS 3.0 6.1 - - - +
281C SER* 4.4 0.2 - - - -
287C VAL* 3.9 10.3 - - + -
289C PHE* 3.7 28.5 - - + -
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Residues in contact with VAL 231 (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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114C PRO* 5.1 0.4 - - - -
198C VAL* 3.4 15.0 - - + +
200C VAL* 4.6 1.3 - - + -
218C PHE* 5.0 2.7 - - + -
221C VAL* 3.2 37.7 - - + -
225C LEU* 3.4 15.3 - - + -
230C VAL* 1.3 73.9 - - - +
232C CYS* 1.3 65.2 + - - +
233C THR* 3.7 22.7 - - + -
256C PHE* 3.4 24.9 - - + -
278C MSE 2.8 11.9 - - - +
279C LEU* 3.2 6.3 - - - +
280C CYS* 2.8 32.1 + - + +
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Residues in contact with CYS 232 (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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110C ILE* 3.5 35.7 - - - +
113C LEU* 5.0 1.8 - - - -
114C PRO* 3.8 20.2 - - + -
198C VAL 3.0 8.8 + - - +
199C ILE* 3.5 6.5 - - + +
200C VAL 2.9 24.6 + - - -
231C VAL* 1.3 75.7 - - - +
233C THR* 1.3 62.7 + - - +
277C PHE* 4.1 18.6 - - - -
278C MSE 2.9 3.1 - - - -
279C LEU* 3.7 23.8 - - + -
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Residues in contact with THR 233 (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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200C VAL* 3.3 36.1 - - + -
202C SER* 5.7 0.2 - - - -
212C LEU 5.4 1.8 - - - +
213C PHE* 6.0 1.4 - - - -
217C PHE* 5.3 0.2 - - + -
218C PHE* 3.8 25.1 - - + -
231C VAL* 3.7 16.6 - - + -
232C CYS* 1.3 76.7 - - - +
234C GLN* 1.3 72.6 + - - +
235C ALA* 3.0 5.0 + - - +
248C ILE* 5.2 1.9 - - - +
277C PHE* 3.1 8.7 - - - -
278C MSE 3.0 44.5 + - + +
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Residues in contact with GLN 234 (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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106C TYR* 3.5 35.2 - - + +
110C ILE* 4.6 1.4 - - - +
200C VAL 3.4 15.5 + - - +
202C SER* 3.9 16.1 + - - +
203C SER 3.4 25.2 + - - -
204C ASP* 4.4 3.8 + - - +
213C PHE* 3.6 19.8 - - - -
233C THR* 1.3 74.4 - - - +
235C ALA* 1.3 58.5 + - - +
236C GLU* 2.6 54.9 + - - +
270C TYR* 5.5 2.4 - - + -
275C ILE* 4.5 15.5 - - + +
276C GLY 3.7 4.4 - - - +
277C PHE* 3.9 7.3 - - - -
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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