Contacts of the helix formed by residues 249 - 264 (chain A) in PDB entry 1KOH
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ASN* 4.4 30.7 + - - +
203A GLU* 6.2 0.4 - - - +
246A VAL* 3.1 28.5 + - + +
247A LEU 3.4 4.0 - - - +
248A ASN* 1.3 86.5 + - - +
250A ARG* 1.3 82.3 + - - +
251A SER* 3.1 34.1 + - - +
252A SER* 3.4 2.5 + - - +
253A MET 3.3 15.4 + - - -
279A ARG* 5.2 0.4 - - - +
201B LEU 5.7 4.8 - - - +
250B ARG* 5.3 9.9 - - - +
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Residues in contact with ARG 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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248A ASN 3.6 2.2 + - - -
249A ARG* 1.3 87.6 - - - +
251A SER* 1.3 54.4 + - - +
253A MET* 3.4 0.7 + - - +
254A ALA* 2.5 41.3 + - + +
279A ARG* 2.8 41.8 - - - +
281A ASP* 2.9 24.4 + - - -
282A ASP* 3.0 40.6 + - + +
284A SER* 4.4 5.5 + - - -
285A SER* 5.8 0.2 + - - -
250B ARG* 5.1 16.0 - - - +
254B ALA* 3.8 27.3 + - - +
282B ASP 5.9 1.0 + - - -
285B SER* 5.6 3.0 + - - -
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Residues in contact with SER 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASN* 5.3 0.4 - - - -
203A GLU* 3.3 41.8 + - - +
204A LEU* 4.1 6.3 + - - +
249A ARG* 3.1 26.2 + - - +
250A ARG* 1.3 76.1 - - - +
252A SER* 1.3 72.2 + - - +
254A ALA* 2.8 15.9 - - - +
255A ALA* 3.2 6.1 + - - +
250B ARG* 4.0 15.8 + - - +
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Residues in contact with SER 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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204A LEU* 4.3 17.1 - - - +
212A LEU* 5.9 0.4 - - - -
244A ASP 4.7 0.3 + - - -
245A VAL* 3.8 12.2 - - - +
246A VAL* 3.0 47.2 + - - +
247A LEU* 3.9 8.5 - - - -
249A ARG 3.4 2.0 + - - -
251A SER* 1.3 78.1 + - - +
253A MET* 1.3 58.1 + - - +
254A ALA 2.5 16.4 + - - -
255A ALA* 2.7 16.9 + - - +
256A THR* 2.7 15.1 + - - -
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Residues in contact with MET 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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247A LEU* 3.1 49.2 - - + +
249A ARG 3.3 8.6 + - - +
250A ARG* 3.6 3.1 - - - +
252A SER* 1.3 78.1 - - - +
254A ALA* 1.3 59.0 + - - +
256A THR* 3.3 15.2 + - - -
257A LEU* 2.8 58.7 + - + +
272A LEU* 4.3 25.1 - - + -
277A LEU* 4.5 7.0 - - + -
282A ASP* 3.6 25.4 - - + +
283A MET* 3.8 15.7 - - + +
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Residues in contact with ALA 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 ARG* 2.5 18.8 + - + +
251A SER* 2.8 19.1 - - - +
252A SER 2.5 4.2 + - - -
253A MET* 1.3 68.0 - - - +
255A ALA* 1.3 66.6 + - - +
257A LEU* 2.6 21.1 + - - +
258A ARG* 2.9 10.5 + - - +
282A ASP 5.7 2.5 - - - -
289A LYS* 5.9 0.2 - - - -
250B ARG* 4.1 20.4 - - - +
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Residues in contact with ALA 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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204A LEU* 5.2 6.1 - - + -
209A VAL* 4.5 28.9 - - + -
212A LEU* 4.6 11.4 - - + -
251A SER 3.2 4.6 + - - +
252A SER* 2.7 10.8 + - - +
254A ALA* 1.3 74.5 - - - +
256A THR* 1.3 54.8 + - - +
257A LEU 2.5 2.4 + - - -
258A ARG* 2.4 39.1 + - - +
259A ILE* 3.0 14.2 + - + +
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Residues in contact with THR 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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212A LEU* 3.9 17.8 - - + +
216A MET* 4.0 16.0 - - + +
229A LEU* 4.0 25.1 - - + -
232A LEU* 5.4 1.6 - - + -
247A LEU* 3.0 27.7 - - + +
252A SER* 2.7 35.6 + - - -
253A MET* 3.5 16.4 - - - -
255A ALA* 1.3 71.8 - - - +
257A LEU* 1.3 56.9 + - + +
259A ILE 4.3 0.7 - - - -
260A ILE* 3.1 24.2 + - + +
272A LEU* 6.6 0.2 - - + -
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Residues in contact with LEU 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 MET* 2.8 38.9 + - + +
254A ALA* 2.6 11.9 + - - +
255A ALA 2.5 4.0 + - - -
256A THR* 1.3 74.5 - - + +
258A ARG* 1.3 64.2 + - - +
259A ILE 3.1 2.5 - - - -
260A ILE* 3.1 22.5 + - + +
261A GLU* 2.9 23.7 + - - +
270A LEU* 5.1 2.7 - - + -
272A LEU* 6.1 1.1 - - + -
282A ASP 4.3 4.7 - - - +
283A MET* 3.6 33.9 - - + -
285A SER* 5.3 3.4 - - - +
286A ILE* 4.2 32.3 - - + +
289A LYS* 3.9 21.0 - - + +
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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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254A ALA 2.9 6.6 + - - +
255A ALA* 2.4 34.1 + - - +
257A LEU* 1.3 69.7 - - - +
259A ILE* 1.3 51.8 + - + +
261A GLU* 3.4 8.0 - - + +
262A GLU* 2.7 78.9 + - - +
289A LYS* 4.7 8.8 - - - +
281B ASP* 4.1 17.2 + - - +
307B ARG* 5.9 3.6 - - - +
311B LYS* 3.1 42.5 - - - +
336D THR* 5.6 8.7 + - - +
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Residues in contact with ILE 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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209A VAL* 4.0 17.9 - - + +
212A LEU* 4.2 6.7 - - + -
213A LYS* 3.3 56.8 - - + +
216A MET* 3.4 36.3 - - + -
255A ALA 3.0 11.8 + - - +
256A THR 4.4 0.2 - - - +
258A ARG* 1.3 75.2 - - + +
260A ILE* 1.3 60.2 + - - +
261A GLU 3.2 0.2 - - - -
262A GLU* 4.3 5.8 - - - +
263A ASN* 2.8 46.9 + - + +
264A ILE* 5.6 3.8 - - + -
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Residues in contact with ILE 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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216A MET* 4.6 5.8 - - - -
227A LEU* 3.7 25.4 - - + -
229A LEU* 4.6 6.5 - - + -
256A THR* 3.1 23.6 - - + +
257A LEU* 3.1 24.6 + - + +
259A ILE* 1.3 75.9 - - - +
261A GLU* 1.3 55.1 + - - +
264A ILE* 2.6 61.4 + - + +
267A LEU* 3.6 24.2 - - + -
270A LEU* 4.2 14.8 - - + -
289A LYS* 4.9 3.8 - - + +
290A ALA* 4.7 10.5 - - + -
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Residues in contact with GLU 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 LEU 2.9 12.4 + - - +
258A ARG* 3.4 12.6 - - + +
260A ILE* 1.3 77.5 - - - +
262A GLU* 1.3 60.4 + - + +
265A PRO* 3.1 35.0 - - - +
288A GLN* 3.9 7.8 - - - +
289A LYS* 2.8 69.4 + - + +
291A PRO* 5.2 0.2 - - - +
310B ASP 5.3 4.3 - - - +
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Residues in contact with GLU 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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213A LYS* 5.3 9.8 + - - +
258A ARG* 2.7 66.8 + - - +
259A ILE* 4.0 6.4 - - - +
261A GLU* 1.3 76.5 - - + +
263A ASN* 1.3 66.2 + - - +
265A PRO* 4.7 3.7 - - - +
307B ARG* 5.3 6.1 + - - +
336D THR* 6.2 0.2 - - - +
339D SER* 5.2 9.3 + - - +
343D GLU* 6.1 0.7 - - - +
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Residues in contact with ASN 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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213A LYS* 3.1 48.6 + - - +
259A ILE* 2.8 24.6 + - + +
262A GLU* 1.3 77.4 - - - +
264A ILE* 1.3 65.2 + - + +
265A PRO* 3.0 15.5 - - - +
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Residues in contact with ILE 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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216A MET* 6.0 3.8 - - + -
220A TYR* 3.2 59.5 - - + +
227A LEU* 4.3 15.9 - - + -
259A ILE* 5.0 4.7 - - + +
260A ILE* 2.6 47.8 + - + +
263A ASN* 1.3 82.0 - - + +
265A PRO* 1.3 56.4 - - - +
266A GLU* 3.1 8.7 + - + +
267A LEU* 3.6 25.4 + - + +
289A LYS 4.2 4.2 - - - +
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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