Contacts of the helix formed by residues 241 - 253 (chain B) in PDB entry 1KB2
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 CYS 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224B CYS* 3.2 11.2 - - + +
227B CYS* 3.8 5.8 - - - -
229B ASP* 3.6 24.5 - - + +
230B ARG 3.7 15.9 - - - +
231B ALA* 3.8 0.7 - - - +
232B THR* 3.8 1.6 - - - -
240B THR* 1.3 79.0 - - - +
242B GLU* 1.3 63.8 + - - +
243B GLY* 3.4 8.5 - - - -
244B CYS* 3.1 20.6 - - - -
245B LYS* 3.2 20.8 + - - +
273B ARG* 3.9 9.0 - - - -
350B ZN 2.5 32.3 - - - -
421D A 5.9 0.4 - - - +
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B THR* 3.3 23.4 + - + +
241B CYS* 1.3 73.9 - - - +
243B GLY* 1.3 64.2 + - - +
245B LYS* 3.0 39.2 + - - +
246B GLY* 3.1 20.4 + - - -
249B ARG* 5.3 0.5 + - - -
414C G 4.5 0.2 - - - +
415C T 4.2 3.6 - - - +
420D G 4.3 3.8 - - + +
421D A 3.4 46.5 + - + +
422D A 3.1 28.5 + - - +
423D C 4.6 3.6 + - - -
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Residues in contact with GLY 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B CYS* 3.4 7.5 - - - -
242B GLU* 1.3 78.1 - - - +
244B CYS* 1.3 53.3 + - - +
246B GLY* 3.1 2.8 + - - -
247B PHE* 2.7 35.0 + - - +
250B ARG* 4.7 2.1 + - - -
273B ARG* 4.9 2.2 - - - +
280B ARG* 3.6 6.9 + - - -
420D G 3.6 38.8 + - - +
421D A 4.3 3.0 + - - -
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Residues in contact with CYS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B CYS* 4.2 5.4 - - - -
226B VAL* 3.7 26.5 - - + -
227B CYS* 3.9 5.6 - - - -
240B THR* 4.5 5.8 - - - -
241B CYS* 3.1 9.4 - - - +
243B GLY* 1.3 72.0 - - - +
245B LYS* 1.3 68.7 + - - +
247B PHE* 3.9 3.3 - - - +
248B PHE* 3.0 23.0 + - - +
280B ARG* 3.4 30.0 - - - +
284B CYS* 4.5 4.6 - - - -
289B MET* 3.9 4.5 - - - +
350B ZN 2.3 35.4 - - - -
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Residues in contact with LYS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B HIS* 3.1 48.2 - - + +
236B PHE* 3.8 16.7 - - + -
240B THR* 4.3 5.6 + - - -
241B CYS 3.2 14.3 + - - +
242B GLU* 3.0 37.8 + - - +
244B CYS* 1.3 79.6 - - - +
246B GLY* 1.3 65.1 + - - +
248B PHE* 3.2 2.8 + - - +
249B ARG* 3.2 27.4 + - - +
289B MET* 4.5 6.5 - - - -
413C G 4.5 12.7 + - - -
414C G 3.0 38.9 + - - -
415C T 5.1 0.2 - - - -
423D C 4.6 2.4 - - - +
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Residues in contact with GLY 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B GLU* 3.1 9.2 + - - -
243B GLY* 3.1 6.7 + - - -
245B LYS* 1.3 80.2 - - - +
247B PHE* 1.3 58.9 + - - +
249B ARG* 3.4 19.8 + - - +
250B ARG* 2.8 52.6 + - - +
420D G 5.7 1.8 - - - -
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Residues in contact with PHE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B GLY 2.7 20.3 + - - +
244B CYS 3.9 2.2 - - - +
246B GLY* 1.3 73.1 - - - +
248B PHE* 1.3 63.8 + - - +
250B ARG* 3.7 14.8 - - + +
251B SER* 2.9 53.9 + - - -
258B PHE* 3.6 25.1 - + - -
277B GLN* 3.8 28.3 - - - -
280B ARG* 3.4 44.0 - - + +
281B LEU* 3.7 32.3 - - + -
284B CYS* 4.3 7.4 - - - -
419D T 4.1 13.2 - - - -
420D G 4.8 0.2 - - - +
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Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B PHE* 4.0 12.1 - + + -
244B CYS 3.0 10.4 + - - +
245B LYS 3.6 1.8 - - - +
247B PHE* 1.3 83.8 - - - +
249B ARG* 1.3 65.9 + - - +
251B SER* 3.7 2.8 - - - -
252B MET* 3.2 55.4 + - + +
281B LEU* 4.1 6.7 - - + -
284B CYS* 3.7 26.7 - - + -
285B VAL* 4.1 4.9 - - + -
289B MET* 3.2 61.5 - - + -
290B MET 3.8 8.3 - - - -
291B LYS* 3.6 27.4 - - - -
294B ILE* 4.2 5.4 - - + -
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Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B PHE* 3.7 14.5 - - + -
242B GLU* 5.3 0.8 + - - -
245B LYS* 3.2 25.7 + - - +
246B GLY* 3.7 21.1 + - - +
248B PHE* 1.3 81.7 - - - +
250B ARG* 1.3 81.2 + - - +
252B MET* 3.6 1.0 + - - +
253B LYS* 3.2 37.1 + - + +
294B ILE* 3.8 23.6 - - + -
414C G 2.9 45.4 + - - +
415C T 3.3 40.0 + - - +
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B GLY 4.7 0.6 + - - -
246B GLY* 2.8 34.7 + - - +
247B PHE* 3.7 21.0 - - + +
249B ARG* 1.3 88.6 - - - +
251B SER* 1.3 64.6 + - - +
253B LYS* 3.3 12.7 + - - +
254B ARG* 3.4 16.5 + - - +
419D T 3.5 66.8 + - - +
420D G 3.3 27.1 + - - -
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Residues in contact with SER 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B PHE* 2.9 47.3 + - - -
248B PHE 3.7 0.7 - - - -
250B ARG* 1.3 75.8 - - - +
252B MET* 1.3 58.6 + - - +
254B ARG* 3.0 6.1 + - - +
255B LYS 2.9 23.1 + - - -
256B ALA* 3.3 19.1 + - - -
258B PHE* 3.5 13.8 - - - -
281B LEU* 3.6 24.7 - - - -
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Residues in contact with MET 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B PHE* 3.2 51.9 + - + +
251B SER* 1.3 76.4 - - - +
253B LYS* 1.3 59.6 + - - +
254B ARG 3.1 0.9 + - - -
255B LYS* 3.3 21.6 + - - +
281B LEU* 3.6 30.5 - - + -
285B VAL* 4.1 12.1 - - + -
291B LYS* 4.0 31.0 - - + +
294B ILE* 3.5 20.4 - - + -
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Residues in contact with LYS 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ARG* 3.2 38.2 + - + +
250B ARG* 3.8 7.4 - - - +
251B SER 3.2 0.4 - - - -
252B MET* 1.3 75.4 - - - +
254B ARG* 1.3 58.2 + - - +
255B LYS* 3.6 3.3 + - - +
294B ILE* 4.1 17.9 - - + -
295B LEU 4.7 8.2 + - - -
297B ASP* 4.3 17.7 + - - -
300B VAL* 4.6 19.6 - - - +
414C G 5.5 3.0 + - - -
415C T 4.5 13.7 + - - -
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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