Contacts of the helix formed by residues 263 - 273 (chain A) in PDB entry 1BKX
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 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A PHE 5.1 0.3 + - - -
262A SER* 1.3 72.9 - - - +
264A ASP* 1.3 63.6 + - - +
265A LEU 3.2 1.8 - - - -
266A LYS* 3.5 13.5 + - - +
267A ASP* 3.1 23.0 + - - +
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Residues in contact with ASP 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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262A SER* 3.4 2.5 + - - +
263A SER* 1.3 78.4 - - - +
265A LEU* 1.3 63.7 + - - +
267A ASP* 3.5 7.1 - - - +
268A LEU* 3.1 21.0 + - - +
294A HIS* 3.1 12.4 - - + -
295A LYS* 3.3 37.5 - - - +
296A TRP* 3.7 26.9 + - + +
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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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140A GLU* 3.2 28.5 - - - +
228A ILE* 4.0 21.8 - - + -
232A ALA* 4.2 11.4 - - + -
261A PHE* 3.0 42.6 - - + -
262A SER* 2.7 22.9 + - - +
264A ASP* 1.3 75.4 - - - +
266A LYS* 1.3 60.5 + - - +
267A ASP 2.9 9.5 + - - -
268A LEU* 3.3 3.3 + - + +
269A LEU* 3.1 30.9 + - + +
296A TRP* 3.6 26.6 - - + +
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Residues in contact with LYS 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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257A PHE* 4.0 35.9 + - + +
258A PRO 3.3 24.9 + - - -
259A SER* 4.1 8.5 + - - +
261A PHE* 3.3 28.6 + - + +
262A SER 2.8 23.1 + - - +
263A SER* 3.5 14.3 + - - +
265A LEU* 1.3 73.7 - - - +
267A ASP* 1.3 56.2 + - - +
269A LEU 4.2 0.9 - - - -
270A ARG* 2.8 44.6 - - - +
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Residues in contact with ASP 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 SER 3.1 13.2 + - - +
264A ASP* 3.4 10.1 - - - +
265A LEU 2.9 2.4 + - - -
266A LYS* 1.3 78.1 - - - +
268A LEU* 1.3 71.6 + - - +
269A LEU 3.2 0.3 + - - -
270A ARG* 3.6 4.4 + - - +
271A ASN* 3.2 28.3 + - - -
294A HIS* 2.4 35.0 + - + +
295A LYS* 4.5 6.6 - - - +
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Residues in contact with LEU 268 (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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228A ILE* 5.1 6.7 - - + -
264A ASP 3.1 8.2 + - - +
265A LEU* 3.6 10.5 - - + +
267A ASP* 1.3 82.1 - - - +
269A LEU* 1.3 60.8 + - + +
271A ASN* 2.6 30.3 + - - +
272A LEU* 3.3 23.8 + - + -
281A PHE* 4.1 13.7 - - + -
291A ILE* 4.9 7.2 - - + -
294A HIS* 3.1 29.0 + - + +
296A TRP* 3.7 33.9 - - + -
297A PHE* 3.8 25.1 - - + -
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Residues in contact with LEU 269 (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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225A GLY* 4.0 19.1 - - - +
228A ILE* 4.2 13.7 - - + -
229A TYR* 4.2 14.4 - - + -
257A PHE* 3.5 22.7 - - + -
261A PHE* 3.3 35.9 - - + -
265A LEU* 3.1 21.6 + - + +
266A LYS 4.2 0.7 - - - +
267A ASP 3.2 0.2 - - - -
268A LEU* 1.3 81.0 - - + +
270A ARG* 1.3 56.0 + - - +
271A ASN 2.5 13.2 + - - -
272A LEU* 2.6 28.8 + - + -
273A LEU* 2.9 28.5 + - + +
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Residues in contact with ARG 270 (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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255A VAL* 5.1 5.1 + - + -
257A PHE* 3.5 35.6 - - + -
266A LYS* 2.8 34.8 + - - +
267A ASP* 4.2 4.9 - - - +
268A LEU 3.2 0.4 + - - -
269A LEU* 1.3 72.4 - - - +
271A ASN* 1.3 62.6 + - - +
273A LEU* 4.3 13.0 - - - +
274A GLN* 3.9 21.3 + - - +
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Residues in contact with ASN 271 (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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267A ASP* 3.2 27.4 + - - +
268A LEU 2.6 15.0 + - - +
269A LEU 2.5 6.1 + - - -
270A ARG* 1.3 74.6 + - - +
272A LEU* 1.4 57.0 + - - +
274A GLN* 3.1 23.3 - - - +
279A LYS 4.0 1.6 - - - +
280A ARG* 3.4 15.9 - - - -
281A PHE* 2.9 53.9 + - + -
284A LEU* 5.6 0.3 - - - +
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Residues in contact with LEU 272 (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 TRP* 3.9 24.2 - - + +
222A TRP* 3.7 5.6 - - - -
224A LEU* 4.3 9.4 - - + -
225A GLY* 3.5 26.0 - - - +
228A ILE* 4.5 7.9 - - + -
268A LEU* 4.1 22.0 - - + +
269A LEU* 2.6 24.6 + - + +
271A ASN* 1.4 71.4 - - + +
273A LEU* 1.4 55.7 - - + +
274A GLN 2.3 20.4 + - - -
280A ARG* 3.3 26.8 + - - +
281A PHE* 4.4 8.7 - - + +
291A ILE* 4.1 33.0 - - + -
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Residues in contact with LEU 273 (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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222A TRP* 3.4 26.3 - - + +
225A GLY* 3.5 32.8 - - - +
226A VAL* 4.6 3.1 - - + +
229A TYR* 5.1 0.9 - - + -
237A PRO* 3.7 33.0 - - + -
238A PHE* 3.9 16.2 - - + -
253A GLY* 5.2 4.3 - - - +
255A VAL* 4.0 24.8 - - + +
257A PHE* 6.4 0.2 - - + -
269A LEU* 2.9 43.0 + - + +
270A ARG* 4.3 9.8 - - - +
272A LEU* 1.4 63.7 - - + +
274A GLN* 1.3 64.4 + - - +
275A VAL* 3.7 5.0 + - - +
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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