Contacts of the strand formed by residues 227 - 240 (chain A) in PDB entry 1QQW
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 GLY 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A VAL* 3.8 16.2 - - - -
224A ASN 3.1 5.7 + - - -
225A ALA 3.5 1.8 + - - -
226A ASN* 1.3 74.9 - - - +
228A GLU* 1.3 60.6 + - - +
229A ALA 3.6 0.3 + - - -
421A HIS* 3.4 23.8 + - - -
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Residues in contact with GLU 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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94A TYR 4.3 1.6 - - - +
222A LEU 3.6 0.7 - - - +
223A VAL* 3.3 2.5 - - - -
224A ASN* 2.8 51.7 + - - +
226A ASN* 3.4 17.1 - - + +
227A GLY* 1.3 76.9 - - - +
229A ALA* 1.3 60.4 + - - +
230A VAL* 5.4 4.1 - - + +
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Residues in contact with ALA 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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221A LYS* 4.0 7.0 - - + -
222A LEU 2.9 11.2 - - - +
223A VAL* 4.0 6.1 - - + -
227A GLY 3.6 1.6 + - - -
228A GLU* 1.3 74.0 - - - +
230A VAL* 1.3 68.8 + - - +
286A PHE* 3.3 28.9 + - + -
421A HIS* 3.5 39.7 - - + +
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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
----------------------------------------------------------
94A TYR* 4.0 33.2 - - + +
221A LYS* 3.6 1.0 - - - -
222A LEU* 2.7 50.8 + - + +
228A GLU* 5.4 4.3 - - + +
229A ALA* 1.3 80.1 - - - +
231A TYR* 1.3 68.2 + - - +
283A VAL* 4.2 9.6 - - + -
284A MET 3.9 8.7 - - - +
285A THR* 4.5 16.8 - - + -
286A PHE* 4.0 7.0 - - - +
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Residues in contact with TYR 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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219A THR* 3.9 13.0 - - + -
220A PHE 3.2 16.4 - - - +
221A LYS* 4.3 15.7 - - + -
230A VAL* 1.3 74.4 - - - +
232A CYS* 1.3 65.6 + - - +
283A VAL* 3.6 5.5 - - - +
284A MET* 2.8 39.6 + - + +
286A PHE* 3.4 35.0 - + - -
289A ALA* 4.2 20.4 - - + -
297A PHE* 3.7 31.6 - + - -
303A TRP* 3.8 17.0 - + + -
346A SER* 4.2 11.9 - - - -
347A PRO* 4.3 7.9 - - + +
423A ILE* 3.8 21.5 - - - +
425A TYR* 5.0 0.2 + - - -
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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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219A THR* 3.5 2.4 - - - -
220A PHE* 2.8 56.3 + - - -
222A LEU* 3.4 41.3 - - + -
231A TYR* 1.3 78.1 - - - +
233A LYS* 1.3 73.8 + - - +
234A PHE* 4.1 14.1 - - - -
281A ILE* 5.1 6.3 - - + -
282A GLN 2.9 14.6 - - - +
283A VAL* 4.9 1.8 - - + -
303A TRP* 4.0 1.8 - - - -
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Residues in contact with LYS 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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151A PRO 5.3 1.0 + - - -
217A SER 3.4 20.5 + - - +
218A HIS 3.4 22.3 - - - +
219A THR* 3.2 23.0 + - - +
232A CYS* 1.3 80.0 - - - +
234A PHE* 1.3 64.4 + - - +
235A HIS* 3.4 22.6 - - + +
281A ILE* 3.3 7.1 - - - +
282A GLN* 3.0 31.5 + - + +
296A PRO 4.3 3.4 + - - -
297A PHE* 6.0 0.4 - - - +
298A ASP 4.8 6.7 + - - -
299A LEU* 5.7 1.4 - - - +
301A LYS 4.2 16.0 + - - -
302A VAL* 5.4 0.4 - - - +
303A TRP* 3.5 50.1 - - + +
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Residues in contact with PHE 234 (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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100A PHE* 4.8 7.2 - + - -
143A TRP* 3.9 27.6 - + - -
145A LEU* 4.0 24.7 - - + -
215A TYR* 3.0 8.7 - - - +
216A GLY* 2.8 36.0 + - - +
217A SER 4.5 0.7 + - - +
218A HIS 5.0 1.0 + - - -
220A PHE* 3.8 39.9 - + + -
222A LEU* 4.7 13.0 - - + -
232A CYS* 4.1 14.8 - - - -
233A LYS* 1.3 71.3 - - - +
235A HIS* 1.3 65.2 + - - +
236A TYR* 4.5 2.0 - - + -
279A PHE* 3.3 33.0 - + + -
280A TYR 3.9 1.6 - - - -
281A ILE* 3.5 21.1 - - + -
343A ILE* 4.8 6.5 - - + -
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Residues in contact with HIS 235 (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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151A PRO* 5.2 7.9 - - + -
214A GLY 3.4 5.4 - - - -
215A TYR* 3.2 32.1 - + + -
233A LYS* 3.4 28.0 + - + +
234A PHE* 1.3 76.3 + - - +
236A TYR* 1.3 64.5 + - - +
237A LYS* 4.1 10.7 + - + +
278A THR 3.6 0.7 - - - +
279A PHE* 3.7 1.2 - - - -
280A TYR* 2.8 40.9 + - + +
282A GLN* 3.6 34.1 + - - +
305A HIS* 5.2 7.4 + + - -
310A LEU* 3.6 28.4 - - + +
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Residues in contact with TYR 236 (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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132A PHE* 3.3 57.6 + + - +
134A VAL* 4.7 7.4 - - + -
145A LEU* 4.1 21.4 + - + +
147A GLY* 3.5 17.0 + - - -
214A GLY* 2.8 67.7 + - - -
215A TYR* 3.6 12.4 + - - -
216A GLY 4.2 2.7 - - - -
234A PHE 4.4 1.3 - - - -
235A HIS* 1.3 79.0 - - - +
237A LYS* 1.3 62.7 + - - +
277A TRP* 3.3 20.1 - + + -
278A THR 3.0 10.8 - - - +
279A PHE* 3.8 26.0 - + + -
316A LEU* 4.3 8.1 - - + -
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Residues in contact with LYS 237 (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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213A ASN* 3.2 30.8 - - + +
215A TYR* 5.1 8.9 + - + -
235A HIS* 4.8 11.3 + - + +
236A TYR* 1.3 73.0 - - - +
238A THR* 1.3 64.9 + - - +
239A ASP* 3.4 2.6 + - - +
277A TRP* 2.9 6.5 - - - -
278A THR* 2.8 32.4 + - - +
280A TYR* 3.5 31.9 - - + -
305A HIS* 4.5 10.7 + - - -
310A LEU* 4.2 23.4 - - + +
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Residues in contact with THR 238 (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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210A ARG 2.6 28.1 + - - -
212A MET* 3.4 22.7 - - - +
213A ASN* 3.0 16.8 + - - +
237A LYS* 1.3 72.7 - - - +
239A ASP* 1.3 59.9 + - - +
240A GLN* 2.9 15.6 + - - +
241A GLY* 3.2 33.3 + - - +
242A ILE* 4.0 4.9 - - + +
276A SER 3.7 0.7 - - - -
277A TRP* 3.3 13.6 - - - +
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Residues in contact with ASP 239 (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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237A LYS* 3.5 7.4 - - - +
238A THR* 1.3 71.1 - - - +
240A GLN* 1.3 65.9 + - - +
241A GLY 3.4 0.7 - - - -
276A SER* 2.7 44.6 + - - +
277A TRP 4.0 0.2 - - - -
278A THR* 2.8 21.2 + - - -
315A LYS* 3.2 22.6 - - - +
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Residues in contact with GLN 240 (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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210A ARG* 3.2 29.7 + - - +
211A HIS* 3.2 35.7 + - + +
238A THR* 2.9 5.6 + - - +
239A ASP* 1.3 85.3 - - - +
241A GLY* 1.3 59.0 - - - +
243A LYS* 5.3 2.1 - - - +
273A LYS 6.0 0.9 - - - +
274A TYR 4.7 1.0 - - - +
275A PRO* 3.4 22.5 - - + +
276A SER* 2.7 47.4 + - - +
277A TRP* 4.0 3.2 - - - -
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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