Contacts of the helix formed by residues 252 - 267 (chain A) in PDB entry 1BK6
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 TRP 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A PRO* 2.9 7.9 + - + +
251A ASP* 1.3 72.5 + - - +
253A SER* 1.3 55.9 + - - +
255A VAL* 3.8 14.6 - - + -
256A SER* 2.6 67.2 + - - -
259A LEU* 4.8 4.9 - - + -
284A LEU* 3.5 43.5 - - + -
288A PRO* 6.2 2.2 - - + -
290A GLU* 4.6 9.2 + - + +
291A ALA* 3.5 41.8 - - + +
294A ALA* 3.8 18.4 - - + +
295A VAL* 5.7 0.2 - - + -
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Residues in contact with SER 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ASP* 2.5 24.6 + - - -
252A TRP* 1.3 82.0 - - - +
254A VAL* 1.3 62.5 + - - +
256A SER* 3.5 9.4 + - - -
257A GLN* 3.4 16.1 - - - +
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Residues in contact with VAL 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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212A LEU* 4.1 30.5 - - + +
213A GLN* 4.9 7.4 - - - +
217A MET* 3.9 30.6 - - + +
251A ASP* 3.0 30.8 + - + +
253A SER* 1.3 80.1 - - - +
255A VAL* 1.3 67.8 + - - +
256A SER 3.2 1.3 - - - -
257A GLN* 3.0 31.5 + - - +
258A ALA 4.4 0.2 + - - -
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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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212A LEU* 4.2 17.9 - - + -
217A MET* 4.3 10.3 - - + -
242A LEU 3.9 22.4 - - - +
243A CYS* 4.2 13.0 - - - -
250A PRO* 4.0 19.5 - - + -
251A ASP 3.1 16.8 - - - +
252A TRP* 3.8 14.8 - - + -
254A VAL* 1.3 77.2 - - - +
256A SER* 1.3 63.2 + - - +
257A GLN 3.0 1.4 + - - -
258A ALA* 3.0 19.9 + - - +
284A LEU* 3.9 30.8 - - + +
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Residues in contact with SER 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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252A TRP* 2.6 63.5 + - - -
253A SER* 3.5 11.8 + - - -
255A VAL* 1.3 78.1 - - - +
257A GLN* 1.3 63.2 + - - +
258A ALA 3.2 1.0 + - - -
259A LEU* 3.3 28.7 + - - +
260A PRO* 4.4 1.0 - - - +
284A LEU* 5.0 0.7 - - - -
294A ALA* 5.7 0.4 - - - -
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Residues in contact with GLN 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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217A MET* 4.9 7.3 - - + +
221A LEU* 3.9 24.0 - - + +
253A SER 3.4 19.1 - - - +
254A VAL* 3.0 22.6 + - - +
255A VAL 3.0 0.8 + - - -
256A SER* 1.3 80.0 + - - +
258A ALA* 1.3 58.0 + - - +
259A LEU 3.3 0.4 - - - -
260A PRO* 3.4 14.3 - - - +
261A THR* 5.2 0.9 + - - -
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Residues in contact with ALA 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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217A MET* 4.5 7.3 - - + -
221A LEU* 4.1 15.9 - - + +
239A LEU* 4.1 22.9 - - + -
243A CYS* 5.4 4.5 - - - -
254A VAL 4.4 0.2 + - - -
255A VAL 3.0 13.0 + - - +
257A GLN* 1.3 78.1 - - - +
259A LEU* 1.3 65.1 + - - +
260A PRO* 3.4 0.9 - - - -
261A THR* 3.1 5.8 + - - -
262A LEU* 3.0 43.7 + - + +
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Residues in contact with LEU 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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252A TRP* 4.8 4.3 - - + -
255A VAL 4.4 0.4 + - - -
256A SER* 3.3 20.4 - - - +
258A ALA* 1.3 75.4 - - - +
260A PRO* 1.3 65.8 - - + +
262A LEU* 3.2 11.7 + - + +
263A ALA* 2.8 29.8 + - - +
281A ILE* 5.4 2.0 - - + -
284A LEU* 3.6 27.1 - - + -
294A ALA* 3.5 43.3 - - + +
295A VAL* 4.2 18.2 - - + +
298A VAL* 4.2 12.4 - - + +
300A ILE* 4.4 14.1 - - + +
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Residues in contact with PRO 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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256A SER 4.4 1.3 - - - +
257A GLN* 3.4 18.4 - - - +
258A ALA 3.5 0.9 - - - -
259A LEU* 1.3 93.6 - - + +
261A THR* 1.3 61.7 + - - +
263A ALA* 3.2 16.2 - - + +
264A LYS* 3.5 11.3 + - - +
298A VAL* 4.0 17.9 - - + -
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Residues in contact with THR 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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221A LEU* 3.5 26.2 + - + +
224A PHE* 3.7 43.6 - - + +
239A LEU* 5.5 0.2 - - + -
257A GLN 5.2 0.7 + - - -
258A ALA 3.1 9.1 + - - -
260A PRO* 1.3 75.0 - - - +
262A LEU* 1.3 70.7 + - + +
264A LYS* 2.9 18.5 + - + +
265A LEU* 3.0 21.3 + - + +
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Residues in contact with LEU 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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239A LEU* 3.3 34.5 - - + -
243A CYS* 5.4 1.1 - - - -
258A ALA* 3.0 30.8 + - + +
259A LEU* 3.5 11.7 - - + +
261A THR* 1.3 77.8 - - - +
263A ALA* 1.3 65.8 + - - +
265A LEU* 2.8 26.7 + - + +
266A ILE* 3.2 15.4 + - - +
277A ALA* 4.6 7.4 - - - +
280A ALA* 4.4 8.5 - - + -
281A ILE* 3.7 39.5 - - + +
284A LEU* 3.9 27.1 - - + -
300A ILE* 5.0 0.7 - - + -
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Residues in contact with ALA 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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259A LEU 2.8 13.3 + - - +
260A PRO* 3.2 14.8 - - + +
261A THR 3.1 0.2 - - - -
262A LEU* 1.3 75.6 - - - +
264A LYS* 1.3 57.0 + - + +
266A ILE* 3.1 24.6 - - - +
267A TYR* 3.4 14.2 - - - -
298A VAL* 4.0 27.1 - - + +
300A ILE* 4.3 13.4 - - + +
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Residues in contact with LYS 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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260A PRO 3.8 11.9 - - - +
261A THR* 2.9 9.6 + - + +
263A ALA* 1.3 74.1 - - + +
265A LEU* 1.3 69.7 + - + +
266A ILE 3.1 2.7 - - - -
267A TYR* 2.9 28.7 + - - +
268A SER 4.2 0.3 + - - -
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Residues in contact with LEU 265 (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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224A PHE* 3.8 38.6 - - + -
232A ILE* 4.4 11.2 - - + -
236A THR* 4.1 21.8 - - + +
239A LEU* 4.8 1.8 - - + -
261A THR* 3.0 26.1 + - + +
262A LEU* 2.8 23.2 + - + +
264A LYS* 1.3 78.0 - - + +
266A ILE* 1.3 57.4 + - - +
267A TYR 3.0 4.8 + - - -
268A SER* 3.2 24.4 + - - +
273A THR* 4.4 8.1 - - + +
274A LEU* 4.5 8.8 - - - -
277A ALA* 3.9 14.1 - - + -
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Residues in contact with ILE 266 (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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262A LEU 3.2 5.7 + - - +
263A ALA* 3.1 26.0 - - - +
264A LYS 2.9 0.2 + - - -
265A LEU* 1.3 75.8 - - - +
267A TYR* 1.3 56.3 + - + +
268A SER 3.5 0.9 - - - -
274A LEU* 4.6 9.7 - - + +
277A ALA* 4.2 10.3 - - + -
278A CYS* 4.0 24.0 - - - -
281A ILE* 3.8 24.2 - - + -
300A ILE* 4.1 26.9 - - + -
303A ARG* 3.0 51.3 + - + -
304A LEU* 4.4 4.7 - - + -
307A LEU* 3.9 13.3 - - + +
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Residues in contact with TYR 267 (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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263A ALA 3.4 24.9 - - - -
264A LYS* 2.9 14.5 + - - +
266A ILE* 1.3 79.1 - - + +
268A SER* 1.3 64.2 + - - +
269A MET* 3.9 5.9 + - - +
299A ARG 5.4 2.6 + - - -
303A ARG* 3.4 61.2 + - + +
306A GLU* 4.7 3.3 + - - -
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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