Contacts of the helix formed by residues 243 - 255 (chain A) in PDB entry 1KKQ
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 ASP 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A ILE* 3.6 0.8 - - - +
242A HIS* 1.3 106.4 + - + +
244A MET* 1.3 58.0 + - - +
245A GLU* 2.7 36.3 + - - +
246A THR* 3.1 13.5 + - - +
247A LEU* 3.0 29.5 + - - +
343A PHE* 3.3 18.0 - - - -
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Residues in contact with MET 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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243A ASP* 1.3 75.9 - - - +
245A GLU* 1.3 65.3 + - - +
247A LEU* 3.8 8.9 - - + +
248A CYS* 3.1 22.6 + - - -
266A LYS 5.5 0.2 - - - +
268A ALA* 2.9 39.3 - - + -
269A GLU* 5.1 5.4 - - - +
271A ARG* 3.1 21.1 - - - +
343A PHE* 3.7 10.7 - - + -
347A LEU* 5.6 4.5 - - + -
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Residues in contact with GLU 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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243A ASP* 2.7 19.3 + - - +
244A MET* 1.3 71.2 - - - +
246A THR* 1.3 61.9 + - + +
248A CYS* 3.0 20.6 + - - +
249A MET* 3.2 37.9 + - + +
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Residues in contact with THR 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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239A PHE* 3.8 11.9 - - + -
240A VAL 3.8 20.4 - - - +
241A ILE* 3.6 2.9 - - - -
242A HIS* 3.1 39.0 + - + +
243A ASP* 3.1 17.8 + - - +
245A GLU* 1.3 76.2 - - + +
247A LEU* 1.3 64.1 + - - +
248A CYS 3.0 2.0 - - - -
249A MET* 3.2 27.3 + - + +
250A ALA* 3.0 24.9 + - - +
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Residues in contact with LEU 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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241A ILE* 3.6 22.9 - - + -
243A ASP 3.0 21.4 + - - +
244A MET* 3.8 7.0 - - + +
245A GLU 3.2 0.2 - - - -
246A THR* 1.3 77.3 + - - +
248A CYS* 1.3 58.6 + - - +
250A ALA* 4.1 1.8 - - - -
251A GLU* 3.1 30.8 + - + +
268A ALA* 3.9 23.3 - - + +
271A ARG* 4.4 5.8 - - + +
272A ILE* 3.6 39.7 - - + -
339A ILE* 5.0 0.7 - - + -
343A PHE* 3.7 13.7 - - + -
775A 471 4.1 25.4 - - + -
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Residues in contact with CYS 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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244A MET* 3.1 14.5 + - - +
245A GLU* 3.0 13.0 + - + +
247A LEU* 1.3 77.8 - - - +
249A MET* 1.3 55.3 + - + +
251A GLU* 4.3 1.1 - - - +
252A LYS* 2.7 48.3 + - - +
264A GLN* 3.9 16.8 - - - +
265A ASN* 5.2 0.7 - - - -
271A ARG* 2.6 46.3 + - - +
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Residues in contact with MET 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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239A PHE* 4.3 16.2 - - + -
245A GLU* 3.4 34.1 - - + +
246A THR* 3.2 33.4 + - + +
248A CYS* 1.3 75.5 - - + +
250A ALA* 1.3 67.4 + - - +
252A LYS* 2.8 29.1 + - - +
253A THR* 3.0 20.9 + - + +
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Residues in contact with ALA 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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239A PHE* 4.0 13.3 - - + -
241A ILE* 3.4 35.4 - - + -
246A THR 3.0 12.4 + - - +
247A LEU 3.9 3.8 - - - +
249A MET* 1.3 82.9 - - - +
251A GLU* 1.3 63.7 + - - +
252A LYS 3.0 0.3 + - - -
253A THR* 3.3 7.6 + - - +
254A LEU* 3.1 23.7 + - + +
775A 471 4.3 7.6 - - + -
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Residues in contact with GLU 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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247A LEU* 3.1 21.5 + - + +
248A CYS 4.3 1.6 - - - +
250A ALA* 1.3 78.8 - - - +
252A LYS* 1.3 63.4 + - + +
254A LEU* 3.5 7.1 - - - +
255A VAL* 3.4 33.1 + - - +
258A LEU* 3.8 13.6 - - - +
263A ILE* 4.4 8.9 - - - +
271A ARG* 2.6 60.0 + - + +
274A HIS* 5.0 4.3 - - - +
275A CYS* 4.1 21.7 - - - -
775A 471 4.3 5.1 - - + -
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Residues in contact with LYS 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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248A CYS* 2.7 34.9 + - - +
249A MET* 2.8 21.6 + - - +
251A GLU* 1.3 77.6 - - + +
253A THR* 1.3 66.5 + - + +
254A LEU 3.1 1.7 + - - -
255A VAL 3.6 0.7 + - - -
256A ALA* 3.6 13.3 + - - -
258A LEU* 2.9 47.9 + - + +
259A VAL* 3.5 22.9 - - + +
263A ILE 4.7 5.2 - - - +
264A GLN* 5.0 14.1 - - + -
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Residues in contact with THR 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 MET* 3.0 24.0 - - + +
250A ALA* 3.5 7.7 + - - +
252A LYS* 1.3 77.1 - - + +
254A LEU* 1.3 68.5 + - - +
256A ALA* 3.1 19.3 + - - +
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Residues in contact with LEU 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 ALA* 3.1 17.5 + - + +
251A GLU 3.5 7.6 - - - +
252A LYS 3.1 0.2 - - - -
253A THR* 1.3 85.9 + - - +
255A VAL* 1.3 64.9 + - + +
256A ALA* 3.1 3.2 + - - +
275A CYS* 3.9 18.6 - - + -
278A CYS* 5.5 7.9 - - + +
279A THR* 5.3 4.7 - - - +
333A ALA* 4.7 16.2 - - + -
775A 471 3.2 37.7 - - + -
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Residues in contact with VAL 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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251A GLU* 3.4 26.2 + - - +
252A LYS 3.6 0.4 + - - -
253A THR 3.4 0.6 - - - -
254A LEU* 1.3 80.7 - - + +
256A ALA* 1.3 53.7 + - - +
257A LYS* 2.6 31.7 + - + +
258A LEU* 3.5 32.1 - - + -
274A HIS* 4.4 27.6 - - + +
275A CYS* 6.0 2.2 - - - -
278A CYS* 5.2 10.3 - - - -
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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