Contacts of the strand formed by residues 235 - 245 (chain C) in PDB entry 1QD6
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 VAL 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230C PRO* 3.6 1.4 - - - +
231C ILE* 2.8 41.3 + - + -
232C THR* 2.9 32.6 + - + +
234C HIS* 1.3 84.5 - - + +
236C ARG* 1.3 66.9 + - - +
263C VAL* 4.1 19.1 - - + -
264C MET 3.5 7.2 - - - +
265C LEU* 5.3 4.7 - - + -
75D PHE* 6.2 0.4 - - + -
76D PRO 3.7 19.1 - - - +
77D LEU* 4.2 24.0 - - + +
270D HDS 4.8 6.1 - - + -
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Residues in contact with ARG 236 (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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202C HIS* 5.6 2.0 - - - -
205C ASP* 2.8 25.6 + - - +
207C VAL* 3.5 16.3 - - - +
228C SER* 2.8 39.9 + - - -
229C TYR 3.2 8.3 - - - +
230C PRO* 3.7 26.0 - - + +
231C ILE* 3.9 5.4 - - - +
232C THR 5.1 0.7 - - - +
234C HIS 5.3 0.4 - - - -
235C VAL* 1.3 80.7 - - - +
237C LEU* 1.3 64.5 + - - +
263C VAL* 3.2 8.3 - - - +
264C MET* 2.7 47.9 + - + +
265C LEU 3.9 17.3 - - - +
266C ASN* 4.8 0.2 - - - +
267C ASP* 4.2 17.7 - - - +
269C PHE 5.4 2.5 + - - -
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Residues in contact with LEU 237 (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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227C LEU 4.5 0.2 - - - -
228C SER* 3.0 6.6 - - - -
229C TYR* 2.8 43.0 + - + +
230C PRO 5.9 1.1 - - - +
231C ILE* 3.4 31.7 - - + +
236C ARG* 1.3 75.0 - - - +
238C TYR* 1.3 58.7 + - - +
261C VAL* 6.4 2.0 - - + -
262C GLY 3.6 10.5 - - - +
263C VAL* 4.7 4.0 - - + -
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Residues in contact with TYR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C THR* 5.5 0.2 + - - -
39C TYR* 3.7 32.6 - + + -
41C ILE* 3.6 20.2 - - + -
209C SER* 4.9 4.8 + - - -
224C GLU* 4.0 9.2 + - - +
226C GLY* 3.9 15.2 - - - -
227C LEU 3.3 18.6 - - - -
228C SER* 4.0 2.9 - - - -
237C LEU* 1.3 76.0 - - - +
239C THR* 1.3 73.3 + - - +
240C GLN* 3.0 39.6 + - + +
261C VAL* 3.4 4.6 - - - +
262C GLY 2.8 41.1 + - - +
263C VAL 4.2 2.5 - - - -
264C MET* 3.7 42.5 - - + +
267C ASP* 4.7 3.6 - - - -
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Residues in contact with THR 239 (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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225C LEU 4.1 0.2 - - - +
226C GLY* 3.3 3.5 - - - -
227C LEU* 2.9 45.9 + - + +
238C TYR* 1.3 79.2 + - - +
240C GLN* 1.3 69.7 + - - +
241C VAL* 4.9 8.1 - - + -
259C VAL* 5.0 5.4 - - + -
260C GLY 3.3 11.4 - - - +
261C VAL* 3.7 20.7 - - + +
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Residues in contact with GLN 240 (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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39C TYR* 3.2 22.7 + - - -
41C ILE* 3.8 21.9 - - + +
43C THR* 5.5 1.0 - - - +
68C LYS* 3.0 32.3 - - - +
224C GLU* 3.7 28.2 + - + +
225C LEU 3.3 6.1 - - - +
238C TYR* 3.0 30.3 + - + +
239C THR* 1.3 75.8 - - - +
241C VAL* 1.3 69.5 + - - +
242C TYR* 4.6 7.3 - - - +
247C GLU* 4.9 0.2 + - - -
258C ARG* 4.0 4.2 + - - +
259C VAL* 3.4 3.3 - - - +
260C GLY 2.8 36.3 + - - +
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Residues in contact with VAL 241 (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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223C ALA 3.8 0.9 - - - +
224C GLU* 3.3 1.7 - - - -
225C LEU* 2.7 51.9 + - + +
239C THR* 4.9 7.0 - - + -
240C GLN* 1.3 82.1 - - - +
242C TYR* 1.3 67.6 + - - +
243C SER* 5.3 2.7 - - - -
257C THR* 4.5 12.1 - - + -
258C ARG 3.3 9.6 - - - +
259C VAL* 4.2 17.3 - - + -
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Residues in contact with TYR 242 (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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68C LYS* 4.7 1.1 - - - -
211C LYS 5.5 0.9 - - - -
213C GLN* 4.5 10.7 + - - -
222C GLY* 3.9 7.3 - - - -
223C ALA 3.3 15.3 - - - -
224C GLU* 3.7 34.1 - - + -
240C GLN* 4.3 11.3 - - - +
241C VAL* 1.3 74.0 - - - +
243C SER* 1.3 83.5 + - - +
244C GLY 4.0 16.2 - - - -
245C TYR 2.9 20.3 + - - -
246C GLY 3.5 9.6 + - - -
247C GLU* 3.6 48.5 - - + +
256C GLN* 4.6 5.2 - - + -
257C THR* 3.2 5.2 - - - +
258C ARG* 2.7 50.0 + - + +
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Residues in contact with SER 243 (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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222C GLY* 3.3 1.0 - - - -
223C ALA* 2.8 41.8 + - - +
241C VAL* 5.3 4.0 - - - -
242C TYR* 1.3 80.3 - - - +
244C GLY* 1.3 59.6 + - - +
255C ASN* 5.0 1.0 + - - -
256C GLN 3.4 4.7 - - - -
257C THR* 2.8 26.3 + - - +
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Residues in contact with GLY 244 (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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221C GLY 3.5 9.2 - - - -
242C TYR* 4.0 7.3 - - - -
243C SER* 1.3 79.5 + - - +
245C TYR* 1.3 63.8 + - - -
247C GLU 5.1 0.5 + - - -
254C PHE 3.5 1.9 - - - +
255C ASN* 3.2 18.9 + - - -
256C GLN* 3.0 31.3 + - - +
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Residues in contact with TYR 245 (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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191C TYR* 3.5 40.4 - + + +
192C MET* 4.9 1.6 - - - +
213C GLN* 5.6 1.0 + - - -
220C TYR* 3.6 32.9 - + + -
221C GLY 2.8 23.4 + - - +
222C GLY* 3.8 8.1 + - - -
242C TYR* 2.9 17.9 + - - -
244C GLY* 1.3 77.2 - - - -
246C GLY* 1.3 60.9 + - - +
247C GLU 3.5 2.0 - - - -
252C TYR 3.7 6.7 - - - +
253C ASN 3.8 13.5 - - - -
254C PHE 3.4 21.3 - - - -
255C ASN* 3.5 31.0 + - + +
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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