Contacts of the strand formed by residues 236 - 245 (chain D) 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 ARG 236 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D HIS* 5.7 2.2 - - - -
205D ASP* 2.9 25.1 + - - -
207D VAL* 3.6 15.7 - - - +
228D SER* 2.8 41.5 + - - -
229D TYR 3.3 9.6 - - - +
230D PRO* 3.6 27.4 - - + +
231D ILE* 3.9 4.7 - - - -
232D THR 5.3 0.9 - - - +
233D LYS 6.4 0.4 - - - -
234D HIS 5.2 0.4 - - - -
235D VAL* 1.3 80.5 - - - +
237D LEU* 1.3 63.3 + - - +
263D VAL* 3.2 8.8 - - - +
264D MET* 2.7 48.1 + - + +
265D LEU 3.8 17.5 - - - +
266D ASN* 4.8 0.2 - - - +
267D ASP* 4.0 18.8 - - - +
269D PHE 5.3 2.9 + - - -
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Residues in contact with LEU 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D LEU 3.8 0.4 - - - +
228D SER* 3.0 7.8 - - - -
229D TYR* 2.7 45.7 + - + +
231D ILE* 3.7 33.9 - - + +
236D ARG* 1.3 71.6 - - - +
238D TYR* 1.3 58.9 + - - +
261D VAL* 5.6 7.9 - - + -
262D GLY 3.7 12.3 - - - +
263D VAL* 4.8 3.1 - - + +
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Residues in contact with TYR 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D THR* 5.5 0.7 + - - -
39D TYR* 3.7 32.2 - + + -
41D ILE* 3.6 21.3 - - + +
209D SER* 4.9 5.3 + - - -
224D GLU* 4.0 9.2 + - - -
226D GLY* 4.0 15.6 - - - -
227D LEU 3.4 14.4 - - - -
228D SER* 4.0 4.0 - - - -
237D LEU* 1.3 77.1 - - - +
239D THR* 1.3 79.0 + - - +
240D GLN* 2.9 38.7 + - + +
260D GLY 4.1 0.2 - - - +
261D VAL* 3.4 3.8 - - - +
262D GLY 2.8 40.8 + - - +
263D VAL 4.3 1.8 - - - -
264D MET* 3.7 43.9 - - + +
267D ASP* 5.0 2.0 - - - -
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Residues in contact with THR 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D GLY* 3.3 4.0 - - - -
227D LEU* 2.9 45.7 + - + +
238D TYR* 1.3 78.9 + - - +
240D GLN* 1.3 70.1 + - - +
241D VAL* 4.9 8.1 - - + -
259D VAL* 5.1 5.2 - - + -
260D GLY 3.3 11.7 - - - +
261D VAL* 3.6 22.0 - - + +
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Residues in contact with GLN 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D TYR* 3.1 21.3 + - - -
41D ILE* 3.7 22.0 - - + +
43D THR* 5.6 0.6 - - - +
68D LYS* 2.9 33.3 - - - +
224D GLU* 3.6 28.2 + - + +
225D LEU 3.4 4.7 - - - +
238D TYR* 2.9 31.3 + - + +
239D THR* 1.3 75.7 - - - +
241D VAL* 1.3 71.0 + - - +
242D TYR* 4.2 8.3 - - - +
247D GLU* 4.9 0.2 + - - -
258D ARG* 3.8 3.9 + - - +
259D VAL* 3.4 3.8 - - - +
260D GLY 2.8 37.5 + - - +
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Residues in contact with VAL 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D ALA 3.8 0.9 - - - +
224D GLU* 3.3 2.1 - - - -
225D LEU* 2.8 53.5 + - + +
239D THR* 4.9 7.9 - - + -
240D GLN* 1.3 81.5 - - - +
242D TYR* 1.3 67.1 + - - +
243D SER* 5.3 3.4 - - - -
257D THR* 4.5 12.6 - - + -
258D ARG 3.2 9.2 - - - +
259D VAL* 4.3 16.4 - - + -
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Residues in contact with TYR 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LYS* 4.7 1.3 - - - -
211D LYS 5.5 0.4 - - - -
213D GLN* 4.5 10.5 + - - -
222D GLY* 4.0 7.7 - - - -
223D ALA* 3.3 14.6 - - - -
224D GLU* 3.6 33.4 - - + -
240D GLN* 4.2 11.5 - - - +
241D VAL* 1.3 74.4 - - - +
243D SER* 1.3 83.8 + - - +
244D GLY 4.0 12.6 - - - -
245D TYR 2.8 25.4 + - - -
246D GLY 3.4 10.4 + - - -
247D GLU* 3.5 45.5 - - + +
256D GLN* 4.5 5.4 - - + -
257D THR* 3.2 4.5 - - - +
258D ARG* 2.7 51.3 + - + +
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Residues in contact with SER 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D GLY* 3.3 1.6 - - - -
223D ALA* 2.8 42.3 + - - +
241D VAL* 5.3 4.0 - - - -
242D TYR* 1.3 79.8 - - - +
244D GLY* 1.3 60.8 + - - +
255D ASN* 5.0 1.4 + - - -
256D GLN 3.5 3.8 - - - -
257D THR* 2.8 25.6 + - - +
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Residues in contact with GLY 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D GLY 3.5 9.0 - - - -
222D GLY* 3.9 0.2 - - - -
242D TYR* 4.0 7.1 - - - -
243D SER* 1.3 77.9 + - - +
245D TYR* 1.3 63.7 - - - -
247D GLU 5.1 0.5 + - - -
254D PHE 3.6 1.7 - - - +
255D ASN* 3.2 19.5 + - - -
256D GLN* 3.0 31.3 + - - +
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Residues in contact with TYR 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D TYR* 3.6 32.7 - + + +
192D MET* 4.9 1.9 - - - +
213D GLN* 5.6 0.9 + - - -
219D GLY 5.9 0.2 - - - -
220D TYR* 3.4 38.4 - + - -
221D GLY 2.8 23.6 + - - +
222D GLY* 3.9 7.3 + - - -
242D TYR* 2.8 18.4 + - - -
244D GLY* 1.3 77.4 - - - -
246D GLY* 1.3 60.7 + - - +
247D GLU 3.5 1.6 - - - -
252D TYR 3.6 6.7 - - - +
253D ASN 3.9 10.8 - - - -
254D PHE* 3.5 21.5 - - - -
255D ASN* 3.5 33.6 + - + +
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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