Contacts of the helix formed by residues 255 - 270 (chain A) in PDB entry 1NBF
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 SER 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A ASP* 3.2 31.2 + - - -
251A ASP 3.0 13.9 + - - -
252A SER* 4.5 2.7 - - - +
253A SER 3.7 1.4 - - - +
254A LYS* 1.3 78.3 - - - +
256A VAL* 1.3 57.0 + - - +
257A PRO* 3.4 8.7 - - - +
258A LEU* 3.0 30.0 + - - +
259A ALA* 3.0 26.7 + - - +
282A SER* 3.5 4.7 - - - -
310A LYS* 6.4 0.7 - - - +
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Residues in contact with VAL 256 (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 LYS 3.5 3.0 + - - +
255A SER* 1.3 72.1 - - - +
257A PRO* 1.3 68.2 - - + +
259A ALA* 3.2 1.6 + - - +
260A LEU* 2.8 39.7 + - + +
279A LEU* 4.7 1.3 - - + -
282A SER* 3.4 33.9 - - - +
283A PHE* 3.8 26.2 - - + -
303A LEU* 4.4 11.0 - - + -
306A ASN* 3.8 28.9 - - - +
307A VAL* 4.7 4.5 - - + -
310A LYS* 5.8 3.3 - - + +
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Residues in contact with PRO 257 (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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242A VAL* 4.4 1.3 - - + +
245A MET* 3.8 38.8 - - + -
247A THR* 4.1 12.6 - - + -
250A ASP* 4.9 2.9 - - - +
255A SER* 3.4 11.4 - - - +
256A VAL* 1.3 98.3 - - + +
258A LEU* 1.3 55.2 + - - +
260A LEU* 3.9 7.7 - - + +
261A GLN* 3.0 36.0 + - - +
307A VAL* 6.0 4.5 - - + -
310A LYS* 4.0 29.4 - - + -
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Residues in contact with LEU 258 (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 THR* 3.9 17.4 - - + +
250A ASP* 4.4 2.0 - - + +
252A SER* 3.5 20.4 - - - +
255A SER* 3.0 23.3 + - - +
257A PRO* 1.3 76.5 - - - +
259A ALA* 1.3 58.1 + - - +
261A GLN* 3.4 18.1 + - - +
262A ARG* 2.9 53.7 + - - +
540A LEU* 4.7 3.1 - - + -
543A ARG* 3.5 40.6 - - - +
544A LEU* 4.5 13.9 - - + -
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Residues in contact with ALA 259 (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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252A SER 6.1 0.4 - - - +
255A SER 3.0 18.2 + - - +
256A VAL* 3.4 5.4 - - - +
258A LEU* 1.3 77.9 - - - +
260A LEU* 1.3 56.0 + - - +
262A ARG* 3.4 16.7 + - - +
263A VAL* 3.0 35.3 + - - +
278A LYS* 3.8 8.1 - - - +
279A LEU* 3.7 23.3 - - + +
282A SER* 3.5 17.3 - - - +
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Residues in contact with LEU 260 (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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229A LEU* 3.7 29.8 - - + -
232A LEU* 6.1 4.3 - - + -
242A VAL* 4.1 18.8 - - + -
245A MET* 6.5 0.2 - - - -
256A VAL* 2.8 25.6 + - + +
257A PRO* 3.9 6.1 - - + +
259A ALA* 1.3 71.9 - - - +
261A GLN* 1.3 60.5 - - - +
263A VAL* 3.2 3.1 + - + +
264A PHE* 2.8 51.3 + - + -
279A LEU* 4.5 13.2 - - + -
303A LEU* 4.7 11.4 - - + -
307A VAL* 3.7 34.5 - - + -
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Residues in contact with GLN 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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242A VAL* 3.0 39.1 - - + +
243A TYR* 3.5 12.1 - - - +
245A MET* 3.1 21.6 - - - +
247A THR* 2.7 35.9 + - - +
257A PRO 3.0 21.2 + - - +
258A LEU* 3.5 17.2 - - - +
260A LEU* 1.3 77.1 - - - +
262A ARG* 1.3 56.8 + - - +
264A PHE* 3.4 4.3 + - - +
265A TYR* 2.8 32.2 + - - +
540A LEU* 4.0 26.7 - - + +
544A LEU* 5.0 2.5 - - - -
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Residues in contact with ARG 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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252A SER* 2.6 33.8 + - - -
258A LEU* 2.9 36.1 + - - +
259A ALA* 3.5 26.5 - - - +
261A GLN* 1.3 74.0 - - - +
263A VAL* 1.3 67.5 + - + +
265A TYR* 3.3 1.9 + - - +
266A GLU* 3.0 38.6 + - + +
278A LYS* 3.5 41.5 - - - +
544A LEU* 4.0 23.1 - - + +
547A GLU* 3.0 31.0 + - - -
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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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216A LEU* 4.1 24.9 - - + -
229A LEU* 4.4 15.7 - - + -
259A ALA 3.0 24.2 + - - +
260A LEU* 3.7 6.1 - - + +
262A ARG* 1.3 76.8 - - + +
264A PHE* 1.3 64.3 + - + +
266A GLU* 3.4 2.3 + - - +
267A LEU* 3.0 36.5 + - + +
274A VAL* 4.2 10.2 - - + +
275A GLY 4.2 15.0 - - - +
276A THR* 4.8 1.8 - - + -
278A LYS* 6.5 0.2 - - + -
279A LEU* 4.2 26.7 - - + +
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Residues in contact with PHE 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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229A LEU* 4.1 15.5 - - + -
232A LEU* 4.2 13.5 - - + -
233A PHE* 3.3 49.1 - + + -
238A LEU* 5.2 2.9 - - + -
239A ARG* 3.5 34.8 - - + -
242A VAL* 4.1 27.6 - - + -
243A TYR* 3.1 25.5 + + + +
260A LEU* 2.8 40.7 + - + +
261A GLN 3.7 0.2 - - - +
263A VAL* 1.3 81.5 - - + +
265A TYR* 1.3 65.2 + - - +
267A LEU* 3.3 1.2 + - + -
268A GLN 3.0 18.0 + - - -
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Residues in contact with TYR 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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243A TYR* 3.3 10.3 + - + +
261A GLN 2.8 21.9 + - - +
262A ARG 3.7 2.5 - - - +
264A PHE* 1.3 72.5 - - - +
266A GLU* 1.3 75.3 + - - +
268A GLN 3.1 1.2 + - - -
269A HIS* 2.9 77.1 + + + +
533A ASP* 5.1 3.0 + - - -
536A ILE* 3.9 20.0 - - + -
540A LEU* 5.6 0.2 - - + -
541A VAL* 3.7 25.2 - - + +
544A LEU* 3.5 33.7 - - + -
545A GLN* 3.5 24.8 + - + -
548A LYS* 5.0 9.9 - - - -
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Residues in contact with GLU 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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262A ARG* 3.0 27.8 + - + +
265A TYR* 1.3 90.0 - - + +
267A LEU* 1.3 60.6 + - - +
269A HIS* 5.6 0.5 - - - +
270A SER* 2.6 47.2 + - - +
274A VAL* 3.6 31.6 - - + +
548A LYS* 3.4 37.1 + - - -
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Residues in contact with LEU 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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213A TYR* 5.6 1.9 - - - -
214A VAL* 3.5 39.8 + - + +
215A GLY 3.8 3.6 - - - +
216A LEU* 3.8 22.9 - - + -
229A LEU 4.7 3.1 - - - +
230A GLN* 3.7 29.4 - - - +
233A PHE* 3.6 48.4 - - + -
263A VAL* 3.0 32.4 + - + +
264A PHE* 3.3 6.3 + - + +
266A GLU* 1.3 75.9 - - - +
268A GLN* 1.3 58.7 + - - +
269A HIS 3.8 0.2 + - - -
270A SER 4.8 2.1 + - - +
274A VAL* 3.7 4.2 - - + +
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Residues in contact with GLN 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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233A PHE* 3.9 7.9 - - + -
239A ARG* 2.9 28.3 - - - +
243A TYR* 2.7 37.6 + - - +
264A PHE 3.0 14.5 + - - +
265A TYR 3.6 4.0 - - - +
267A LEU* 1.3 78.1 - - - +
269A HIS* 1.3 78.6 + - + +
270A SER 5.0 0.4 - - - -
531A VAL* 3.4 20.3 - - - +
532A THR 4.0 14.9 - - - +
533A ASP* 4.2 2.6 - - - +
536A ILE* 4.0 1.8 - - - +
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Residues in contact with HIS 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 TYR* 2.9 69.5 + + + +
266A GLU* 5.1 1.1 - - - +
268A GLN* 1.3 95.4 + - + +
270A SER* 1.3 68.2 + - - +
271A ASP* 5.0 1.2 - - - +
533A ASP* 3.0 36.0 + - - -
536A ILE* 3.6 20.6 - - + -
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Residues in contact with SER 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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214A VAL* 3.8 12.9 - - - +
266A GLU* 2.6 41.4 + - - +
267A LEU 4.8 1.4 - - - +
268A GLN 5.0 0.7 - - - -
269A HIS* 1.3 81.1 + - - +
271A ASP* 1.3 68.8 + - - +
272A LYS* 3.0 27.3 + - - +
273A PRO 4.7 1.2 + - - -
274A VAL* 4.3 5.3 - - - +
548A LYS* 6.3 0.2 - - - -
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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