Contacts of the helix formed by residues 258 - 270 (chain D) in PDB entry 6CP3
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 ILE 258 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233D ALA* 4.7 7.2 - - + -
255D ILE* 3.9 26.7 - - + -
257D ASN* 1.3 82.2 + - - +
259D PHE* 1.3 65.8 + - - +
260D ARG 3.2 2.7 - - - -
261D PHE* 3.2 19.0 + - + +
262D THR* 3.8 5.7 + - - -
289D MET* 4.6 19.7 - - + -
292D LEU* 3.8 29.4 - - + -
293D GLN* 4.0 20.9 - - - +
308D GLN* 4.5 7.0 - - + +
309D ALA 3.2 6.7 + - - +
310D VAL* 3.6 35.0 - - + -
325D THR* 4.8 4.0 - - + +
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Residues in contact with PHE 259 (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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257D ASN* 3.4 3.7 + - - +
258D ILE* 1.3 82.7 - - + +
260D ARG* 1.3 69.5 + - - +
261D PHE 3.2 0.2 + - - -
262D THR* 3.2 7.6 + - - +
263D GLN* 2.9 53.6 + - + +
281D TYR* 3.4 26.0 - + - -
289D MET* 6.0 1.1 - - - -
310D VAL* 5.0 1.6 - - + -
311D TYR* 3.4 61.2 - + + +
313D PRO* 3.6 16.6 - - + -
321D ALA* 3.6 36.8 - - + -
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Residues in contact with ARG 260 (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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301C PHE* 3.4 31.6 - - - -
346C SER* 3.3 37.4 + - - -
187D VAL* 3.3 37.2 - - + +
188D GLY* 3.2 23.4 + - - +
222D MET* 4.4 1.6 - - - +
229D ARG* 4.2 11.1 - - + +
257D ASN* 4.4 16.3 - - + +
258D ILE 3.2 0.4 - - - -
259D PHE* 1.3 95.6 - - - +
261D PHE* 1.3 56.7 + - - +
263D GLN* 2.9 28.1 + - - +
264D ALA* 2.8 32.2 + - - +
311D TYR* 4.5 9.9 - - - +
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Residues in contact with PHE 261 (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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187D VAL* 4.3 3.6 - - + +
229D ARG 3.8 10.2 + - - +
230D ALA* 3.1 36.6 - - + +
231D ARG* 4.7 6.5 - - - -
233D ALA* 4.8 8.7 - - + -
234D LEU* 4.9 11.2 - - + -
258D ILE* 3.2 17.5 + - + +
259D PHE 3.1 0.8 - - - -
260D ARG* 1.3 78.1 - - - +
262D THR* 1.3 69.4 + - - +
264D ALA* 3.3 4.0 + - - +
265D GLY* 2.9 22.9 + - - -
282D GLN* 4.9 1.1 + - - -
288D ASP* 3.8 41.5 - - + -
289D MET* 4.5 6.5 - - + -
292D LEU* 3.6 37.7 - - + -
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Residues in contact with THR 262 (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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258D ILE 3.8 1.9 + - - -
259D PHE* 3.2 14.1 + - - -
261D PHE* 1.3 85.5 - - - +
263D GLN* 1.3 57.2 + - - +
265D GLY 3.1 1.6 + - - -
266D SER* 3.0 24.0 + - - -
281D TYR* 4.6 9.2 - - + -
282D GLN* 3.1 30.1 + - - +
285D LEU* 3.8 31.6 - - + +
289D MET* 3.3 31.0 + - + +
321D ALA* 4.9 6.7 - - + -
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Residues in contact with GLN 263 (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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301C PHE* 3.2 38.5 - - - +
339C TYR* 4.8 9.3 + - - +
343C ASN* 3.3 15.2 + - - -
259D PHE* 2.9 37.0 + - + +
260D ARG* 2.9 37.5 + - - +
262D THR* 1.3 78.3 - - - +
264D ALA* 1.3 56.8 + - - +
266D SER* 2.9 10.2 + - - +
267D GLU* 2.9 36.3 + - + +
281D TYR* 5.2 5.6 - - + -
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Residues in contact with ALA 264 (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 PRO* 3.3 34.3 - - + +
229D ARG* 3.8 13.2 - - + +
230D ALA* 3.7 17.4 - - - +
260D ARG 2.8 18.8 + - - +
261D PHE 3.7 2.5 - - - +
263D GLN* 1.3 73.2 - - - +
265D GLY* 1.3 64.6 + - - +
267D GLU* 3.8 13.3 + - - +
268D VAL* 3.6 16.6 - - - +
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Residues in contact with GLY 265 (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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230D ALA* 4.6 4.0 - - - +
261D PHE 2.9 13.7 + - - -
262D THR 3.1 5.7 + - - -
264D ALA* 1.3 77.7 - - - +
266D SER* 1.3 55.6 + - - +
268D VAL* 3.5 4.9 + - - +
269D SER* 3.0 32.1 + - - -
274D ARG* 4.8 2.5 + - - -
282D GLN* 3.2 19.7 - - - -
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Residues in contact with SER 266 (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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298C GLY* 4.4 5.3 - - - +
339C TYR* 6.2 0.4 - - - -
262D THR 3.0 6.5 + - - -
263D GLN* 2.9 14.6 + - - -
265D GLY* 1.3 76.3 - - - +
267D GLU* 1.3 63.2 + - - +
268D VAL 3.1 1.4 + - - -
269D SER* 3.5 15.8 + - - -
270D ALA* 3.7 10.9 + - - +
280D GLY 4.1 13.7 - - - -
281D TYR* 3.3 26.8 - - - -
282D GLN* 2.6 19.7 + - - -
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Residues in contact with GLU 267 (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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298C GLY 3.3 29.3 - - - +
299C ASP* 4.1 11.2 - - - +
301C PHE* 3.2 40.0 - - + +
302C TYR* 3.8 9.0 + - - +
339C TYR* 5.9 0.9 - - - +
226D PRO* 3.3 22.0 - - + +
229D ARG* 2.4 30.8 + - - -
263D GLN* 2.9 26.8 + - + +
264D ALA* 3.8 3.1 + - - -
265D GLY 3.3 0.8 - - - -
266D SER* 1.3 75.8 - - - +
268D VAL* 1.3 62.2 + - - +
271D LEU* 3.9 15.8 - - - +
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Residues in contact with VAL 268 (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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19D ALA* 4.7 5.2 - - + +
20D ILE* 3.8 25.1 - - + -
62D ILE* 4.6 25.6 - - + -
226D PRO* 3.7 27.8 - - + -
230D ALA* 6.2 0.9 - - + -
264D ALA 3.6 15.3 - - - +
265D GLY* 3.8 4.9 - - - +
267D GLU* 1.3 83.5 - - - +
269D SER* 1.3 57.9 + - - +
270D ALA 3.1 2.9 - - - -
271D LEU* 2.7 25.3 + - - +
272D LEU* 2.9 25.3 + - + +
274D ARG* 6.0 1.1 - - - +
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Residues in contact with SER 269 (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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265D GLY 3.0 20.2 + - - -
266D SER* 3.5 8.0 + - - -
268D VAL* 1.3 75.1 - - - +
270D ALA* 1.3 65.5 + - - +
272D LEU* 4.0 4.0 + - - +
274D ARG* 3.3 63.5 + - - +
276D PRO* 6.1 0.2 - - - +
281D TYR 5.0 0.5 - - - -
282D GLN* 3.3 24.1 - - - +
283D PRO* 4.9 0.6 - - - +
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Residues in contact with ALA 270 (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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290C PRO* 3.5 46.5 - - + +
291C PRO 5.0 5.6 - - - +
292C GLY* 5.0 3.6 - - - -
298C GLY* 4.7 10.1 - - - -
266D SER 3.7 10.5 + - - +
268D VAL 3.1 0.4 - - - -
269D SER* 1.3 83.3 + - - +
271D LEU* 1.3 68.1 + - + +
272D LEU 3.7 0.3 + - - -
273D GLY* 3.7 7.4 + - - -
274D ARG 4.4 6.4 - - - +
276D PRO* 5.0 9.6 - - + -
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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