Contacts of the helix formed by residues 243 - 253 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242D HIS* 1.3 112.3 - - + +
244D MET* 1.3 66.9 + - - +
245D GLU* 2.8 39.7 + - - +
246D THR* 2.8 18.5 + - - +
247D LEU* 3.0 19.9 + - - +
343D PHE* 3.8 9.5 - - - -
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Residues in contact with MET 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D ASP* 1.3 73.6 - - - +
245D GLU* 1.3 58.8 + - - +
247D LEU* 3.6 6.7 - - + +
248D CYS* 3.1 29.9 + - - -
268D ALA* 3.0 52.9 - - + +
269D GLU* 4.6 8.1 - - - +
343D PHE* 3.8 18.7 - - + -
347D LEU* 4.3 10.3 - - - -
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Residues in contact with GLU 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D ASP* 2.8 20.6 + - - +
244D MET* 1.3 69.6 - - - +
246D THR* 1.3 58.9 + - - +
247D LEU 2.9 3.8 - - - -
248D CYS* 2.6 33.0 + - + +
249D MET* 3.2 29.4 + - + +
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Residues in contact with THR 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D PHE* 3.7 17.7 - - + -
240D VAL 3.7 14.1 - - - +
241D ILE* 3.2 5.4 - - - +
242D HIS* 2.9 40.4 + - + +
243D ASP* 2.8 33.9 + - - +
245D GLU* 1.3 77.4 - - + +
247D LEU* 1.3 58.8 + - - +
249D MET* 3.5 6.9 + - - -
250D ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D ILE* 3.5 18.4 - - + -
243D ASP 3.0 11.6 + - - +
244D MET* 3.6 9.4 - - + +
245D GLU 2.8 0.8 + - - -
246D THR* 1.3 80.1 + - - +
248D CYS* 1.3 50.6 + - - +
250D ALA* 4.0 0.7 - - + -
251D GLU* 2.5 51.4 + - + +
268D ALA* 3.3 42.6 - - + +
271D ARG* 4.5 1.3 - - + +
272D ILE* 4.0 22.2 - - + -
339D ILE* 5.0 0.9 - - + -
343D PHE* 4.0 19.7 - - + -
778D 471 3.8 28.7 - - + -
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Residues in contact with CYS 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D MET* 3.1 24.0 - - - -
245D GLU* 2.6 20.5 + - + +
247D LEU* 1.3 69.6 - - - +
249D MET* 1.3 50.2 + - + +
251D GLU* 2.5 23.6 - - - +
252D LYS* 2.6 30.4 - - + +
264D GLN 4.5 11.2 - - - +
265D ASN* 6.0 2.9 - - - -
268D ALA* 4.7 3.4 - - - -
271D ARG* 3.9 20.0 + - - +
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Residues in contact with MET 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D PHE* 4.3 23.1 - - + -
245D GLU* 3.2 25.4 + - + +
246D THR* 4.0 11.2 - - - +
248D CYS* 1.3 74.4 - - + +
250D ALA* 1.3 72.4 + - - +
252D LYS* 3.0 7.0 + - - -
253D THR* 2.9 34.4 + - + +
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Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D PHE* 3.8 18.1 - - + -
241D ILE* 3.9 27.4 - - + -
246D THR 2.9 20.3 + - - +
247D LEU* 3.6 9.0 - - - +
249D MET* 1.3 79.2 - - - +
251D GLU* 1.3 60.2 + - - +
253D THR* 3.4 14.3 + - - -
254D LEU* 3.4 12.0 + - - +
778D 471 4.5 6.5 - - + -
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Residues in contact with GLU 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D LEU* 2.5 41.5 - - + +
248D CYS* 2.5 24.1 - - - +
250D ALA* 1.3 69.9 - - - +
252D LYS* 1.3 62.8 + - - +
253D THR 3.0 2.7 - - - -
254D LEU* 2.7 24.5 + - + +
255D VAL* 6.1 0.2 - - + -
258D LEU* 2.6 35.3 - - + +
271D ARG* 2.7 46.2 + - + +
272D ILE* 6.3 0.2 - - + -
275D CYS* 3.4 31.9 - - - -
778D 471 4.1 7.4 - - + -
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Residues in contact with LYS 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D CYS* 2.6 22.2 - - + +
249D MET* 3.0 7.3 + - - +
251D GLU* 1.3 83.3 + - - +
253D THR* 1.3 60.9 + - + +
254D LEU 3.2 0.2 - - - -
255D VAL 3.8 2.8 - - - +
258D LEU* 2.8 31.4 + - + +
259D VAL* 3.7 43.1 + - + +
264D GLN* 4.0 29.3 - - + +
271D ARG* 6.2 0.7 - - - +
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Residues in contact with THR 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D MET* 2.9 27.5 + - + +
250D ALA* 3.4 8.1 + - - -
252D LYS* 1.3 79.6 - - + +
254D LEU* 1.3 63.9 + - - +
255D VAL 4.8 2.1 - - - -
256D ALA* 5.1 1.8 + - - +
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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