Contacts of the helix formed by residues 260 - 272 (chain A) in PDB entry 3NC0
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 PHE 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ALA* 3.7 20.9 - - + -
222A VAL* 3.7 20.4 - - + -
223A HIS* 3.3 39.3 - + + -
226A LEU* 3.3 19.1 - - + -
254A PHE* 3.1 31.2 - + + +
257A VAL* 3.2 24.4 + - + -
258A PRO 2.7 2.6 + - - -
259A MET* 1.3 103.8 - - + +
261A ARG* 1.3 66.5 + - - +
262A ASN 3.1 3.5 + - - -
263A VAL* 3.5 6.9 + - - +
264A SER* 3.0 25.6 + - - -
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Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A PHE 4.3 1.1 - - - -
255A LEU* 3.4 26.5 - - - +
257A VAL 3.1 5.8 + - - +
258A PRO* 2.9 32.5 + - - +
260A PHE* 1.3 78.6 - - - +
262A ASN* 1.3 63.5 + - - +
264A SER* 3.8 2.8 - - - -
265A LEU* 3.1 28.2 + - - +
297A MET* 4.0 9.6 - - + +
298A LEU* 5.5 5.3 - - - +
314A ASP* 2.8 34.8 + - - +
315A GLU* 3.9 27.5 - - - +
318A PHE* 3.5 50.9 - - + +
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Residues in contact with ASN 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A PHE 3.2 1.2 - - - +
261A ARG* 1.3 78.2 - - - +
263A VAL* 1.3 69.6 + - + +
264A SER 3.1 1.1 - - - -
265A LEU* 3.1 2.9 + - - +
266A LYS* 2.8 35.1 + - - +
313A ASP 5.3 0.2 - - - +
314A ASP* 3.6 31.2 - - - +
317A ASN* 4.0 9.6 - - - +
318A PHE* 3.1 36.7 - - - +
321A ASN* 3.0 24.6 + - - +
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A HIS* 2.8 41.3 - - + +
226A LEU* 3.9 35.9 - - + +
227A GLU* 3.5 29.2 - - - +
230A LEU* 4.9 3.8 - - + -
259A MET 5.8 0.2 - - - -
260A PHE* 4.2 8.5 - - - +
262A ASN* 1.3 76.3 - - + +
264A SER* 1.3 64.3 + - - +
266A LYS* 3.4 11.7 + - - +
267A CYS* 3.0 30.8 + - - -
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Residues in contact with SER 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 5.4 3.9 - - - +
250A LEU* 3.4 21.3 + - - +
254A PHE* 3.9 11.9 - - - -
255A LEU* 3.2 39.8 - - - +
260A PHE 3.0 19.6 + - - -
261A ARG 3.8 2.0 - - - -
263A VAL* 1.3 79.0 - - - +
265A LEU* 1.3 62.2 + - - +
267A CYS* 3.3 6.7 + - - +
268A LEU* 3.1 23.3 + - - +
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LEU* 4.7 10.7 - - + +
261A ARG 3.1 14.8 + - - +
262A ASN* 3.1 6.0 + - - +
264A SER* 1.3 76.4 + - - +
266A LYS* 1.3 56.8 + - - +
268A LEU* 2.9 17.8 + - + +
269A THR* 2.7 36.8 + - - +
290A THR* 5.0 3.4 - - + -
294A LEU* 5.7 3.1 - - + -
318A PHE* 4.1 22.9 - - + +
321A ASN* 3.7 39.9 - - + +
322A LEU* 3.7 15.7 - - + +
325A PHE* 3.7 32.8 - - + -
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Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLU* 4.4 9.4 + - - -
230A LEU* 3.7 38.7 - - + +
231A ARG* 5.7 1.4 - - - +
262A ASN* 2.8 28.6 + - - +
263A VAL* 3.8 14.5 - - - +
265A LEU* 1.3 72.1 - - - +
267A CYS* 1.3 60.2 + - - +
269A THR* 3.5 9.7 + - - +
270A GLU* 3.2 18.9 + - - +
321A ASN* 3.6 32.5 - - + +
324A LEU* 6.4 0.2 - - + -
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Residues in contact with CYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A LEU* 3.8 14.4 - - - -
229A LEU* 4.5 7.2 - - - -
230A LEU* 3.8 35.9 - - - -
233A LEU* 3.7 16.2 - - + +
250A LEU* 4.0 19.7 - - + -
263A VAL* 3.0 17.2 + - - +
264A SER* 3.4 10.8 - - - +
265A LEU 3.1 0.2 - - - -
266A LYS* 1.3 75.4 - - - +
268A LEU* 1.3 65.6 + - - +
270A GLU* 3.1 5.4 + - - +
271A ILE* 3.0 27.5 + - - +
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ILE* 4.4 9.2 - - + -
250A LEU* 4.2 20.0 - - + -
251A ILE* 4.0 16.2 - - + -
255A LEU* 3.4 33.4 - - + -
264A SER* 3.1 15.2 + - - +
265A LEU* 2.9 13.1 + - + +
267A CYS* 1.3 78.5 - - - +
269A THR* 1.3 58.4 + - - +
271A ILE* 3.2 7.9 + - + +
272A ALA* 2.8 30.8 + - - +
286A LEU* 3.5 27.1 - - + +
290A THR* 3.9 15.7 - - + +
325A PHE* 4.3 13.2 - - + -
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Residues in contact with THR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LEU 2.7 20.4 + - - -
266A LYS* 3.7 9.8 - - - +
268A LEU* 1.3 73.6 - - - +
270A GLU* 1.3 66.8 + - - +
272A ALA* 3.2 11.3 + - - +
273A GLY* 3.4 9.0 + - - -
321A ASN* 4.0 3.8 + - - +
324A LEU* 4.1 18.1 - - + +
325A PHE* 3.0 47.0 + - - +
328A THR* 4.1 15.5 - - + +
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LEU* 4.6 13.7 - - + +
233A LEU* 4.3 21.2 - - + +
234A ASN* 3.7 29.0 + - - +
266A LYS 3.2 13.5 + - - +
267A CYS 3.1 9.2 + - - +
269A THR* 1.3 79.6 - - - +
271A ILE* 1.3 61.0 + - - +
273A GLY* 3.6 10.4 + - - -
274A VAL* 4.3 7.6 + - - +
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Residues in contact with ILE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 3.8 33.0 - - + -
241A ILE* 3.5 37.7 - - + -
242A PHE* 3.7 14.4 - - + -
246A LEU* 4.6 8.7 - - + -
247A ILE* 4.4 10.3 - - + -
250A LEU* 4.9 9.9 - - + -
267A CYS 3.0 16.8 + - - +
268A LEU* 3.7 10.5 - - + +
270A GLU* 1.3 74.3 - - - +
272A ALA* 1.3 60.3 + - - +
273A GLY 3.1 6.1 + - - -
274A VAL* 3.3 21.0 - - + +
283A PHE* 3.6 8.7 - - - -
286A LEU* 4.1 15.3 - - + -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LEU 2.8 16.1 + - - +
269A THR* 3.2 7.3 + - - +
271A ILE* 1.3 76.8 - - - +
273A GLY* 1.3 57.1 + - - +
274A VAL 3.4 0.7 - - - -
283A PHE* 4.7 1.8 - - - -
286A LEU* 4.8 4.9 - - + -
325A PHE* 4.2 12.8 - - + +
328A THR* 4.3 3.8 - - + -
329A PHE* 3.3 40.8 - - + -
332A GLU* 4.2 6.6 - - - +
333A HIS* 3.0 26.3 + - - -
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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