Contacts of the helix formed by residues 235 - 247 (chain A) in PDB entry 5KOQ
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A GLY* 1.3 73.9 - - - -
236A THR* 1.3 56.2 + - - +
237A SER* 3.4 10.5 + - - -
238A SER* 2.7 35.4 + - - -
239A ILE* 2.7 32.6 + - - +
303A MET 4.4 1.3 - - - -
304A ASP* 3.3 19.1 - - - -
311A PRO* 4.7 15.9 - - - -
312A THR 4.4 6.0 + - - +
313A TRP* 5.2 1.0 - - - +
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Residues in contact with THR 236 (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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234A GLY 4.0 0.6 + - - -
235A SER* 1.3 71.6 - - - +
237A SER* 1.3 58.1 + - - +
239A ILE* 3.9 1.0 - - - +
240A GLU* 2.9 52.6 + - + +
250A LYS* 5.6 2.9 - - - +
255A TYR* 5.0 0.6 + - - +
302A ALA* 4.0 22.9 - - + +
304A ASP* 2.6 30.2 + - - +
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Residues in contact with SER 237 (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* 5.0 0.2 - - - +
235A SER* 3.4 9.7 + - - -
236A THR* 1.3 75.1 - - - +
238A SER* 1.3 66.0 + - - +
240A GLU* 4.2 8.5 - - - +
241A LYS* 3.3 23.0 + - - +
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Residues in contact with SER 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 3.4 28.6 - - - +
235A SER* 2.7 35.2 + - - -
237A SER* 1.3 78.0 + - - +
239A ILE* 1.3 58.8 - - - +
241A LYS 3.5 0.3 + - - -
242A LEU* 3.1 22.5 + - - +
313A TRP* 3.7 31.6 + - - -
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Residues in contact with ILE 239 (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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234A GLY* 3.5 24.9 - - - +
235A SER 2.7 21.5 + - - +
236A THR 4.0 2.5 - - - +
238A SER* 1.3 70.3 - - - +
240A GLU* 1.3 54.9 + - - +
242A LEU* 3.0 25.2 + - + +
243A MET* 2.8 48.8 + - + +
255A TYR* 3.5 33.9 - - + +
300A ILE* 3.8 13.2 - - + -
301A HIS 3.4 16.2 - - - +
302A ALA* 3.8 15.7 - - + +
313A TRP* 3.9 8.1 - - + -
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Residues in contact with GLU 240 (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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236A THR* 2.9 39.8 + - + +
237A SER* 4.2 7.6 - - - +
238A SER 3.5 0.2 - - - -
239A ILE* 1.3 75.5 - - - +
241A LYS* 1.3 57.4 + - - +
243A MET* 4.1 3.2 - - - +
244A GLU* 3.1 27.2 + - - +
250A LYS* 4.0 21.1 + - + -
255A TYR* 3.5 20.7 + - + +
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Residues in contact with LYS 241 (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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215A LEU* 4.6 6.2 - - + +
216A LEU* 4.4 17.0 - - + -
237A SER 3.3 17.6 + - - +
238A SER 3.9 3.6 - - - +
239A ILE 3.2 0.6 - - - -
240A GLU* 1.3 74.6 - - - +
242A LEU* 1.3 63.6 + - - +
243A MET 3.3 0.2 - - - -
244A GLU* 3.9 5.9 - - - +
245A ALA* 3.3 21.5 + - - +
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Residues in contact with LEU 242 (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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208A VAL* 4.8 6.7 - - + -
210A VAL* 3.6 25.8 - - + -
215A LEU* 5.1 0.2 - - - -
216A LEU* 3.8 11.6 - - + +
232A ILE* 5.8 0.7 - - + -
238A SER 3.1 14.2 + - - +
239A ILE* 3.0 19.6 + - + +
241A LYS* 1.3 75.4 - - - +
243A MET* 1.3 61.6 + - + +
245A ALA* 3.4 7.5 - - - +
246A LEU* 3.2 35.5 + - + +
268A ILE* 3.8 28.0 - - + -
270A PHE* 6.1 0.7 - - + -
300A ILE* 3.8 33.7 - - + -
313A TRP* 4.0 14.4 - - + -
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Residues in contact with MET 243 (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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239A ILE* 2.8 29.6 + - + +
240A GLU 4.2 2.9 - - - +
242A LEU* 1.3 74.5 - - + +
244A GLU* 1.3 60.4 + - - +
245A ALA 3.2 1.1 - - - -
246A LEU* 3.0 9.4 + - + +
247A GLY 2.9 24.8 + - - -
248A ALA* 3.1 20.9 + - - +
255A TYR* 3.4 54.5 - - + -
298A LEU* 3.7 21.8 - - + -
300A ILE* 3.4 50.5 - - + +
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Residues in contact with GLU 244 (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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240A GLU 3.1 20.2 + - - +
241A LYS* 3.9 7.6 - - - +
243A MET* 1.3 73.4 - - - +
245A ALA* 1.3 62.7 + - - +
247A GLY* 3.3 13.2 + - - +
248A ALA 5.4 1.6 - - - -
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Residues in contact with ALA 245 (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 VAL* 4.2 28.8 - - + +
215A LEU* 4.3 14.8 - - + -
241A LYS 3.3 12.5 + - - +
242A LEU 3.4 11.2 - - - +
243A MET 3.2 0.2 - - - -
244A GLU* 1.3 81.0 - - - +
246A LEU* 1.3 59.5 + - - +
247A GLY 3.6 0.2 + - - -
266A PRO* 5.4 2.1 - - - +
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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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210A VAL* 4.1 11.4 - - + -
242A LEU* 3.2 19.7 + - + +
243A MET* 3.0 18.8 + - + +
245A ALA* 1.3 75.2 - - - +
247A GLY* 1.3 61.4 + - - +
248A ALA* 3.6 6.6 + - + +
257A VAL* 4.3 1.0 - - - +
265A LEU* 3.3 28.2 - - + +
266A PRO* 3.7 26.7 - - + -
268A ILE* 3.8 26.7 - - + -
284A TYR* 3.7 23.3 - - + +
298A LEU* 4.1 22.9 - - + -
300A ILE* 4.9 0.9 - - + -
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Residues in contact with GLY 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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243A MET 2.9 4.5 + - - -
244A GLU* 3.3 12.3 + - - -
245A ALA 3.4 1.2 + - - -
246A LEU* 1.3 78.5 - - - +
248A ALA* 1.3 61.6 + - - +
249A LYS* 3.8 1.7 + - - +
256A VAL 4.8 0.2 - - - +
257A VAL* 4.1 7.7 - - - +
261A GLU* 4.6 7.3 - - - +
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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