Contacts of the strand formed by residues 210 - 226 (chain D) in PDB entry 6OY5
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 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176D ASP* 3.3 21.8 + - - +
208D PRO* 4.5 0.7 - - - +
209D ARG* 1.3 79.1 - - - +
211D VAL* 1.3 67.5 + - - +
212D ARG* 2.9 43.5 - - - +
344D ASP* 3.7 28.6 + - + -
345D TYR 3.5 8.1 - - - +
346D ARG* 4.4 11.2 - - - +
388D HIS* 3.1 62.9 + - - +
389D GLU* 3.2 29.3 + - - +
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Residues in contact with VAL 211 (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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208D PRO* 4.9 2.2 - - + -
209D ARG 4.3 0.2 - - - -
210D ARG* 1.3 75.5 - - - +
212D ARG* 1.3 60.7 + - - +
213D VAL* 4.0 11.6 + - + -
343D LYS 3.8 1.2 - - - +
344D ASP* 3.6 0.7 - - - -
345D TYR* 2.9 45.7 + - + +
347D VAL* 3.9 22.2 - - + -
353D VAL* 4.0 13.5 - - + -
367D ILE* 4.1 16.2 - - + -
368D VAL* 4.5 4.3 - - + -
385D VAL* 3.9 26.9 - - + -
386D HIS 3.7 4.5 - - - +
387D LEU* 3.9 20.2 - - + -
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Residues in contact with ARG 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D ARG* 2.9 35.1 + - - +
211D VAL* 1.3 71.0 - - - +
213D VAL* 1.3 63.8 + - - +
214D GLU* 3.6 24.5 - - + +
342D PRO* 4.0 22.1 - - + +
343D LYS 3.6 1.3 - - - +
344D ASP* 3.0 33.9 + - - +
386D HIS* 3.1 37.7 + - + +
388D HIS* 4.0 31.1 + - + +
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Residues in contact with VAL 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D VAL* 4.1 14.1 - - + -
212D ARG* 1.3 75.1 - - - +
214D GLU* 1.3 66.6 + - - +
215D TYR* 3.5 41.7 + - + +
341D GLU 3.5 0.3 - - - +
342D PRO* 3.4 1.0 - - - +
343D LYS 2.8 38.8 + - - +
345D TYR* 4.1 14.8 - - + -
361D VAL* 5.2 3.4 - - + -
367D ILE* 4.0 26.9 - - + -
383D GLY* 4.6 3.6 - - - -
384D VAL 3.5 17.5 - - - +
385D VAL* 4.9 8.3 - - + -
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Residues in contact with GLU 214 (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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212D ARG* 3.6 13.8 + - + -
213D VAL* 1.3 72.1 - - - +
215D TYR* 1.3 61.3 + - - +
216D VAL* 3.8 2.9 + - - +
316D GLN* 3.9 12.3 + - - -
340D THR* 3.7 25.2 + - + +
341D GLU 3.7 2.6 - - - -
342D PRO* 3.3 38.9 - - - +
383D GLY* 3.3 1.2 - - - -
384D VAL* 2.9 44.1 + - + +
386D HIS* 3.8 24.5 - - + +
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Residues in contact with TYR 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D VAL* 3.7 31.6 - - + +
214D GLU* 1.3 71.5 - - - +
216D VAL* 1.3 64.1 + - - +
217D LYS* 3.7 17.4 + - + +
340D THR* 3.2 6.5 - - - -
341D GLU* 3.0 39.1 + - + +
343D LYS* 3.7 28.3 - - + -
345D TYR* 2.9 27.0 + - - -
367D ILE* 5.2 0.2 - - - +
379D ALA* 4.1 4.6 - - + -
380D GLU* 3.1 26.3 + - + +
381D ALA* 3.3 37.2 - - + -
382D GLU 3.5 16.8 - - - +
383D GLY* 3.9 0.2 - - - -
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Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D GLU 4.5 2.0 - - - +
215D TYR* 1.3 71.1 - - - +
217D LYS* 1.3 65.3 + - - +
218D LYS* 4.0 24.2 - - + -
339D TRP 4.1 3.4 - - - +
340D THR* 4.4 14.4 - - + -
360D ARG* 6.0 1.1 - - - +
381D ALA* 6.0 0.9 - - - +
382D GLU* 3.1 44.7 + - + +
383D GLY* 4.1 17.0 - - - -
384D VAL* 4.9 3.4 - - + +
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Residues in contact with LYS 217 (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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215D TYR* 4.3 13.8 - - + +
216D VAL* 1.3 79.7 - - - +
218D LYS* 1.3 64.0 + - - +
219D GLU* 5.1 2.9 - - + -
262D LYS* 4.2 11.6 - - - +
338D GLU* 3.5 2.1 - - - +
339D TRP* 3.1 80.1 + - + +
341D GLU* 3.3 40.0 + - + +
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Residues in contact with LYS 218 (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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216D VAL* 4.0 24.4 + - + -
217D LYS* 1.3 75.0 - - - +
219D GLU* 1.3 70.4 + - - +
337D LEU 3.4 6.5 - - - +
338D GLU* 3.4 36.1 - - + +
382D GLU* 4.6 9.7 + - - -
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Residues in contact with GLU 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D LYS* 5.1 2.2 - - + -
218D LYS* 1.3 82.5 - - - +
220D ARG* 1.3 62.9 + - - +
221D ALA* 4.0 0.9 - - - -
269D PHE* 4.8 9.0 - - + -
281D THR* 6.1 2.0 - - + -
335D LEU 3.9 0.2 - - - +
336D PHE* 3.7 3.1 - - - -
337D LEU* 2.8 43.1 + - - +
339D TRP* 3.5 30.2 - - + -
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Residues in contact with ARG 220 (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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219D GLU* 1.3 75.1 + - - +
221D ALA* 1.3 61.6 + - - +
222D GLY 4.4 8.7 - - - +
280D ALA* 5.5 2.8 - - - +
281D THR* 4.1 32.6 + - - +
332D TYR* 3.2 28.5 + - - -
334D THR* 3.5 42.0 + - + +
335D LEU 3.4 7.0 - - - +
336D PHE* 4.0 24.0 - - + -
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Residues in contact with ALA 221 (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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219D GLU 3.9 1.8 + - - +
220D ARG* 1.3 77.4 - - - +
222D GLY* 1.4 59.8 + - - +
269D PHE* 4.2 9.0 - - + -
281D THR* 3.5 27.4 - - + +
283D PHE* 4.0 13.4 - - + +
335D LEU* 3.0 38.0 + - - +
337D LEU* 3.8 21.7 - - + +
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Residues in contact with GLY 222 (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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220D ARG* 4.4 5.9 - - - -
221D ALA* 1.4 72.2 - - - +
223D LEU* 1.3 60.3 + - - -
281D THR 2.8 13.1 + - - -
282D TYR* 3.1 14.4 - - - +
283D PHE* 3.0 23.0 + - - -
332D TYR* 3.6 21.5 + - - -
333D LEU 3.2 10.5 - - - -
334D THR* 4.5 0.4 - - - -
335D LEU* 5.9 0.7 - - - -
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Residues in contact with LEU 223 (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* 1.3 74.5 - - - +
224D ARG* 1.4 66.6 + - - +
225D LEU* 3.8 32.1 - - + -
242D LEU* 4.4 9.2 - - + -
251D PHE* 3.7 27.8 - - + -
283D PHE* 3.2 23.3 - - + +
284D LEU* 4.5 0.4 - - + -
285D PRO* 3.8 25.6 - - + -
288D MET* 4.1 15.3 - - + -
332D TYR* 3.3 8.6 - - - -
333D LEU* 2.7 49.3 + - + +
335D LEU* 5.3 5.6 - - + -
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Residues in contact with ARG 224 (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 LEU* 1.4 76.3 - - - +
225D LEU* 1.3 68.7 + - - +
249D TYR* 3.3 32.5 - - - +
251D PHE* 3.4 23.5 - - + +
254D GLU* 2.6 40.4 + - - +
288D MET* 6.1 0.2 - - - +
325D GLU 5.5 0.2 + - - -
327D GLU* 3.5 34.6 + - - +
330D THR* 2.7 43.2 + - - +
331D VAL 3.3 10.3 - - - +
332D TYR* 3.7 37.6 - - + +
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Residues in contact with LEU 225 (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 LEU* 3.8 26.5 - - + -
224D ARG* 1.3 79.0 - - - +
226D PRO* 1.3 84.8 - - + +
229D ALA* 6.2 0.4 - - + -
230D TRP* 4.0 10.1 - - + +
242D LEU* 4.6 7.4 - - + -
243D ALA* 3.8 24.7 - - + -
245D LEU* 4.8 6.3 - - + -
249D TYR* 4.6 5.2 - - + -
288D MET* 4.9 5.4 - - - -
307D ALA* 5.5 0.7 - - + -
311D LEU* 4.1 24.5 - - + -
330D THR* 3.4 6.7 - - - -
331D VAL* 2.8 31.7 + - + +
333D LEU* 3.9 26.2 - - + -
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Residues in contact with PRO 226 (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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225D LEU* 1.3 100.0 - - + +
227D LEU* 1.3 63.7 + - - +
228D ALA* 4.4 4.7 - - + +
229D ALA* 4.4 13.0 - - + -
230D TRP* 4.2 6.4 + - - +
245D LEU* 3.8 20.0 - - + -
246D PRO* 6.3 1.1 - - + -
249D TYR* 3.6 41.3 - - + -
329D GLU 3.8 9.9 - - - +
330D THR* 4.2 5.6 - - + -
331D VAL* 3.3 9.5 - - - +
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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