Contacts of the strand formed by residues 297 - 306 (chain C) in PDB entry 1QPL
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 297 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C MET 3.8 1.6 - - - +
230C LEU* 4.2 9.2 - - + -
236C PHE* 3.7 26.5 - - + -
256C ILE* 4.3 0.9 - - + -
274C LEU 3.4 0.7 - - - +
275C THR* 3.4 3.7 - - - +
276C ILE* 2.7 43.4 + - + +
281C ALA* 3.6 29.4 - - + -
282C TYR* 3.8 22.2 - - + -
291C ILE* 3.9 15.0 - - + -
295C ALA* 3.8 11.0 + - + +
296C THR* 1.3 79.1 - - - +
298C VAL* 1.3 61.3 + - - +
299C PHE* 3.6 32.1 - - + -
308C 587 5.2 0.2 - - - +
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Residues in contact with VAL 298 (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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89A GLY* 6.1 0.9 - - - -
228C GLY* 3.4 2.8 - - - -
229C MET* 2.8 60.0 + - + +
230C LEU 4.5 9.4 - - - +
231C GLU* 4.7 12.8 - - + +
273C LYS* 3.7 39.9 - - + +
274C LEU 3.2 6.1 - - - +
275C THR* 4.3 16.6 - - + +
296C THR* 4.9 1.1 - - + +
297C LEU* 1.3 78.5 - - - +
299C PHE* 1.3 65.8 + - - +
300C ASP* 4.3 0.4 - - + -
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Residues in contact with PHE 299 (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 TYR* 4.3 3.8 - + - -
227C THR 3.5 1.3 - - - -
228C GLY* 3.5 26.5 - - - -
236C PHE* 4.1 7.4 - + - -
256C ILE* 4.0 3.1 - - + -
259C TRP* 3.2 40.6 - + - +
272C ALA 3.1 4.9 - - - +
273C LYS* 3.4 2.7 - - - -
274C LEU* 2.7 44.6 + - + +
276C ILE* 3.7 20.0 - - + -
297C LEU* 3.6 35.7 - - + -
298C VAL* 1.3 78.7 - - - +
300C ASP* 1.3 59.7 + - - +
301C VAL* 3.4 15.9 + - + -
308C 587 3.8 32.5 - - - -
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Residues in contact with ASP 300 (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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89A GLY 4.7 3.8 - - - +
90A ILE* 3.7 20.8 - - - +
207C ILE* 4.4 4.7 - - - +
225C HIS 3.5 1.6 - - - +
226C TYR* 3.0 23.6 - - - -
227C THR* 2.9 27.7 + - - +
229C MET* 4.5 10.6 - - + +
240C ARG* 5.5 0.2 + - - -
271C ARG* 2.7 54.0 + - - +
272C ALA 3.6 5.6 - - - +
273C LYS* 4.8 6.5 - - + +
298C VAL* 4.3 0.4 - - + -
299C PHE* 1.3 70.2 - - - +
301C VAL* 1.3 60.0 + - - +
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Residues in contact with VAL 301 (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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224C VAL* 3.9 30.1 - - + -
225C HIS 3.5 4.0 - - - +
226C TYR* 4.1 0.9 - - + -
259C TRP* 3.8 24.0 - - + -
263C VAL* 4.5 6.3 - - + -
266C MET* 4.0 23.0 - - + +
270C GLN 3.9 1.0 - - - +
271C ARG* 3.1 5.9 - - - +
272C ALA 2.9 32.1 + - - +
274C LEU* 4.0 15.0 - - + -
299C PHE* 3.8 23.3 - - + +
300C ASP* 1.3 76.1 - - - +
302C GLU* 1.3 63.7 + - - +
303C LEU 4.5 1.3 - - - +
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Residues in contact with GLU 302 (chain C).
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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37A ASP* 4.3 0.6 - - - +
38A SER 4.6 4.2 - - - +
41A ASP* 5.8 0.2 - - - +
42A ARG* 3.1 35.9 + - - -
108A 587 4.2 11.1 - - - +
208C SER* 5.7 0.2 - - - -
224C VAL* 3.4 1.2 - - - -
225C HIS* 2.8 32.0 + - + +
240C ARG* 2.9 40.5 + - - +
269C GLY* 4.8 6.8 - - - +
270C GLN 3.5 8.3 - - - +
271C ARG* 3.9 17.0 - - + +
300C ASP 4.1 0.2 + - - -
301C VAL* 1.3 74.3 - - - +
303C LEU* 1.3 62.0 + - - +
304C LEU* 3.1 32.4 + - + +
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Residues in contact with LEU 303 (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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216C PRO* 4.4 14.8 - - + -
222C CYS* 4.2 8.3 - - + -
223C VAL 4.0 0.9 - - - +
224C VAL* 3.8 24.2 - - + -
263C VAL* 4.7 7.6 - - + -
266C MET* 4.4 19.0 - - + +
267C SER 3.9 9.0 - - - +
268C VAL* 3.9 27.6 - - + +
269C GLY* 3.0 27.4 + - - -
270C GLN 2.9 15.4 + - - +
301C VAL* 4.0 2.4 + - - +
302C GLU* 1.3 69.9 - - - +
304C LEU* 1.3 60.6 + - - +
305C LYS 3.8 21.5 - - - +
306C LEU* 3.8 23.1 - - + -
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Residues in contact with LEU 304 (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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41A ASP* 4.5 16.4 - - + +
42A ARG* 4.2 27.4 - - + +
223C VAL* 2.8 25.4 + - + +
224C VAL 4.2 0.7 - - - -
225C HIS* 3.9 29.8 - - + +
245C PRO* 3.9 22.4 - - + -
268C VAL* 3.9 9.6 - - - +
269C GLY* 4.6 2.3 + - - -
302C GLU* 3.6 39.9 - - + +
303C LEU* 1.3 74.9 - - - +
305C LYS* 1.3 66.4 + - + +
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Residues in contact with LYS 305 (chain C).
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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41A ASP 5.9 1.3 - - - -
43A ASN* 4.7 17.0 - - - +
223C VAL* 3.0 50.6 + - + +
247C LYS* 6.1 0.2 - - - +
268C VAL* 4.2 9.2 - - + -
303C LEU* 3.7 3.1 - - - +
304C LEU* 1.3 85.4 - - - +
306C LEU* 1.3 69.6 + - - +
307C GLU* 3.9 28.5 + - + +
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Residues in contact with LEU 306 (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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214C THR* 4.1 11.4 - - + -
216C PRO* 3.6 35.4 - - + -
220C GLN* 3.7 22.4 + - + +
221C THR 3.4 5.2 - - - +
222C CYS* 3.6 30.5 - - - -
268C VAL* 3.5 32.0 - - + +
303C LEU* 3.8 13.9 - - + -
305C LYS* 1.3 85.2 - - - +
307C GLU* 1.3 65.4 + - - +
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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