Contacts of the helix formed by residues 245 - 261 (chain A) in PDB entry 5K9S
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 PRO 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A ASP* 3.8 21.1 - - - +
201A ILE* 4.0 23.1 - - + -
243A ALA 3.6 1.3 - - - +
244A PRO* 1.3 87.8 - - + +
246A LEU* 1.3 67.0 + - - +
247A ASP* 4.4 8.7 - - + +
248A ALA* 2.9 22.5 + - + +
249A VAL* 3.1 10.4 + - - +
285A ARG* 4.4 0.2 - - - +
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Residues in contact with LEU 246 (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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244A PRO 3.5 1.2 + - - -
245A PRO* 1.3 71.8 - - - +
247A ASP* 1.3 65.6 + - - +
249A VAL* 3.2 3.6 + - + +
250A GLU* 2.9 26.9 + - - +
284A GLU* 6.2 3.6 - - + -
285A ARG* 3.4 37.7 - - + +
288A MET* 3.7 29.4 - - - +
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Residues in contact with ASP 247 (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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245A PRO* 3.2 6.4 - - + +
246A LEU* 1.3 79.8 - - - +
248A ALA* 1.3 62.4 + - - +
250A GLU* 3.9 4.8 - - - +
251A GLN* 3.0 25.3 + - - +
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Residues in contact with ALA 248 (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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201A ILE* 4.2 14.6 - - + -
206A ILE* 3.4 27.1 - - + -
236A LEU 6.1 0.2 - - - +
244A PRO* 5.3 1.3 - - + -
245A PRO* 2.9 27.7 + - + +
247A ASP* 1.3 76.1 - - - +
249A VAL* 1.3 67.9 + - + +
251A GLN* 3.1 6.3 + - - +
252A ILE* 2.9 31.8 + - + +
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Residues in contact with VAL 249 (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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237A CYS* 6.0 1.6 - - - -
244A PRO* 3.9 17.9 - - + -
245A PRO 3.1 13.7 + - - +
246A LEU* 3.2 4.0 + - - +
248A ALA* 1.3 75.9 - - - +
250A GLU* 1.3 62.0 + - - +
252A ILE* 3.0 9.0 + - + +
253A LEU* 2.9 29.9 + - + +
278A LEU* 3.8 44.1 - - + +
285A ARG* 4.2 17.7 - - + +
288A MET* 3.3 26.9 - - + -
289A VAL* 5.6 1.1 - - + -
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Residues in contact with GLU 250 (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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246A LEU 2.9 17.4 + - - +
247A ASP* 3.9 5.2 - - - +
249A VAL* 1.3 76.9 - - - +
251A GLN* 1.3 60.0 + - - +
253A LEU* 4.3 2.9 - - - +
254A PRO* 3.4 14.7 - - - +
288A MET* 3.6 25.8 - - + +
292A LYS* 3.1 35.5 + - - -
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Residues in contact with GLN 251 (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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206A ILE* 3.5 32.4 - - + +
207A ASP* 2.5 37.4 + - - +
210A LEU* 3.4 16.9 - - + +
247A ASP 3.0 18.8 + - - +
248A ALA* 3.5 6.6 - - - +
249A VAL 3.1 0.2 - - - -
250A GLU* 1.3 78.9 - - - +
252A ILE* 1.3 59.8 + - - +
254A PRO* 3.8 8.1 - - - +
255A THR* 5.0 1.7 + - - -
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Residues in contact with ILE 252 (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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206A ILE* 3.7 37.0 - - + -
210A LEU* 4.3 5.4 - - + -
233A LEU* 4.2 25.8 - - + -
236A LEU* 4.3 22.9 - - + +
237A CYS* 4.3 25.4 - - - -
248A ALA* 2.9 24.1 + - + +
249A VAL* 3.8 5.2 - - + +
251A GLN* 1.3 76.6 - - - +
253A LEU* 1.3 68.2 + - - +
254A PRO 3.4 0.4 - - - -
255A THR* 3.2 6.9 + - - -
256A LEU* 3.1 28.4 + - + -
278A LEU* 5.9 0.9 - - + -
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Residues in contact with LEU 253 (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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249A VAL* 2.9 25.2 + - + +
250A GLU* 4.3 3.8 - - - +
252A ILE* 1.3 77.4 - - - +
254A PRO* 1.3 70.4 - - + +
256A LEU* 3.0 13.6 + - + +
257A VAL* 2.9 28.6 + - + +
275A ILE* 4.5 8.5 - - + -
278A LEU* 4.1 19.3 - - + -
288A MET* 3.9 46.2 - - + +
289A VAL* 4.1 14.8 - - + +
292A LYS* 4.0 26.7 - - + -
294A VAL* 5.6 0.7 - - + -
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Residues in contact with PRO 254 (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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250A GLU* 3.4 17.3 - - - +
251A GLN 3.8 7.0 - - - +
252A ILE 3.6 3.1 - - - -
253A LEU* 1.3 94.0 - - + +
255A THR* 1.3 63.0 + - - +
257A VAL* 3.2 17.7 + - + +
258A ARG* 3.3 18.3 + - - +
292A LYS* 4.1 19.5 - - + +
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Residues in contact with THR 255 (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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210A LEU* 3.6 31.7 + - + +
213A LEU* 3.6 41.0 - - + +
233A LEU* 4.1 6.1 - - + -
251A GLN 5.0 0.7 + - - -
252A ILE 3.2 8.8 + - - -
254A PRO* 1.3 79.3 - - - +
256A LEU* 1.3 62.2 + - - +
258A ARG* 3.2 16.2 + - + +
259A LEU* 3.0 27.0 + - + +
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Residues in contact with LEU 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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230A THR* 5.7 2.5 - - + +
233A LEU* 5.0 11.9 - - + +
234A SER* 5.6 0.4 - - - +
237A CYS* 4.4 4.9 - - - -
252A ILE* 3.1 22.3 + - + +
253A LEU* 3.0 16.0 + - + +
255A THR* 1.3 78.0 - - - +
257A VAL* 1.3 61.8 + - - +
259A LEU* 3.3 16.0 + - + +
260A LEU* 3.0 24.9 + - - +
271A SER* 4.5 14.1 + - - +
274A ALA* 3.7 33.9 - - + -
275A ILE* 3.7 26.0 - - + -
278A LEU* 3.9 20.4 - - + -
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Residues in contact with VAL 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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253A LEU* 2.9 22.9 + - + +
254A PRO* 3.5 10.5 - - + +
255A THR 3.2 0.2 - - - -
256A LEU* 1.3 73.7 - - + +
258A ARG* 1.3 67.7 + - + +
260A LEU* 3.2 12.0 + - + +
261A HIS* 3.2 38.3 + - + +
275A ILE* 6.1 0.2 - - + -
292A LYS* 4.0 26.7 - - + +
293A GLY 6.1 0.9 - - - -
294A VAL* 3.6 30.3 - - + -
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Residues in contact with ARG 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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213A LEU* 2.7 27.7 + - - +
214A ALA* 4.4 4.9 - - - +
215A VAL 2.7 24.8 + - - -
216A PRO* 3.5 17.1 + - - +
218A LEU* 3.5 38.5 - - + +
254A PRO 3.3 12.3 + - - +
255A THR* 3.2 18.1 + - + +
257A VAL* 1.3 79.8 - - + +
259A LEU* 1.3 62.1 + - + +
261A HIS* 3.1 16.7 + - - +
262A HIS 3.3 7.8 + - - -
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Residues in contact with LEU 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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213A LEU* 4.5 8.3 - - + -
218A LEU* 3.9 16.4 - - + -
226A LEU* 3.9 23.1 - - + -
230A THR* 3.7 33.9 - - + +
233A LEU* 4.3 15.3 - - + -
255A THR* 3.0 36.7 + - + +
256A LEU* 3.3 10.1 + - + +
257A VAL 3.3 0.2 - - - -
258A ARG* 1.3 75.7 - - - +
260A LEU* 1.3 61.6 + - - +
262A HIS* 3.1 20.3 + - - +
267A VAL* 3.6 16.8 - - + +
268A LEU* 3.9 3.8 - - - +
271A SER* 3.2 18.1 + - - +
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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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256A LEU 3.0 15.7 + - - +
257A VAL 3.5 7.0 - - - +
258A ARG 3.2 0.4 - - - -
259A LEU* 1.3 75.5 - - - +
261A HIS* 1.3 60.5 + - + +
268A LEU* 3.1 15.0 - - + +
271A SER* 3.7 24.2 + - - +
272A CYS* 3.7 30.1 - - - +
275A ILE* 4.3 14.8 - - + -
294A VAL* 4.0 33.4 - - + +
297A GLN* 2.9 37.3 + - + -
298A LEU* 4.4 11.0 - - + -
301A LEU* 3.8 8.1 - - + -
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Residues in contact with HIS 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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257A VAL* 3.2 32.6 + - + +
258A ARG* 3.1 10.9 + - - +
260A LEU* 1.3 79.1 - - + +
262A HIS* 1.3 67.2 + - - +
293A GLY 5.5 5.8 - - - -
294A VAL* 5.7 2.0 - - - -
297A GLN* 3.8 43.2 + - + +
300A LYS* 5.2 3.6 - - - -
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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