Contacts of the helix formed by residues 291 - 302 (chain A) in PDB entry 4BPU
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A LEU* 4.0 22.4 - - + -
205A SER 3.2 28.4 + - - -
206A GLU* 3.5 21.3 + - - +
208A ILE* 3.9 14.5 - - + +
280A GLN* 3.3 32.3 - - - -
290A PRO* 1.3 84.2 - - + +
292A LEU* 1.3 62.0 + - - +
293A GLU* 3.3 2.9 - - - -
294A TRP* 3.2 45.0 + + + -
295A GLU* 3.0 26.6 + - - +
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Residues in contact with LEU 292 (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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200A LYS* 5.0 2.0 - - - +
246A LEU 4.2 11.4 - - - +
247A VAL* 4.1 15.9 - - + -
248A PRO* 3.7 35.9 - - + -
251A ILE* 4.3 7.4 - - + -
272A LEU* 5.5 0.2 - - + -
276A ALA* 4.1 27.8 - - + +
279A TYR* 4.2 17.9 - - + -
290A PRO 2.9 24.9 + - - +
291A TRP* 1.3 75.6 - - - +
293A GLU* 1.3 57.4 + - - +
295A GLU* 3.2 19.4 + - - +
296A ILE* 2.8 37.4 + - + +
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Residues in contact with GLU 293 (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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220A LYS* 5.1 3.6 - - - -
269A TRP* 3.5 25.7 - - + -
272A LEU* 4.7 7.6 - - + -
273A LYS* 3.6 26.3 - - + +
276A ALA* 4.9 7.4 - - + +
277A SER* 5.3 4.3 + - - -
291A TRP 3.3 1.0 - - - -
292A LEU* 1.3 77.2 - - - +
294A TRP* 1.3 72.7 + - + +
296A ILE* 3.2 6.7 + - - +
297A MET* 2.8 41.5 + - - +
1411A GOL 2.5 29.7 + - - -
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Residues in contact with TRP 294 (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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204A LEU* 3.8 10.3 - - + -
208A ILE* 4.3 20.0 - - + -
213A ARG* 6.5 1.1 - - + -
216A ILE* 3.7 47.4 - - + +
220A LYS* 4.2 21.4 - - - +
291A TRP* 3.2 56.5 + + + +
293A GLU* 1.3 87.2 + - + +
295A GLU* 1.3 60.7 + - - +
297A MET* 3.8 16.7 - - - +
298A LEU* 2.8 37.7 + - - +
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Residues in contact with GLU 295 (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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200A LYS* 2.7 34.8 + - - +
202A VAL* 3.4 32.9 - - + +
203A HIS* 3.5 3.9 - - - +
204A LEU* 2.8 45.2 + - + +
246A LEU* 5.7 0.4 - - - -
290A PRO* 5.0 6.1 - - - +
291A TRP 3.0 26.2 + - - +
292A LEU* 3.6 19.3 - - - +
294A TRP* 1.3 78.3 - - - +
296A ILE* 1.3 56.3 + - - +
299A GLN* 2.8 31.8 + - - +
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Residues in contact with ILE 296 (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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223A PHE* 5.2 0.9 - - + -
233A ILE* 5.2 2.5 - - + -
243A ILE* 3.9 17.9 - - + -
246A LEU* 4.3 21.1 - - + +
247A VAL* 3.8 25.1 - - + -
269A TRP* 3.7 20.2 - - + -
272A LEU* 3.9 32.3 - - + -
292A LEU 2.8 21.4 + - - +
293A GLU 3.5 3.8 - - - +
294A TRP 3.2 0.2 - - - -
295A GLU* 1.3 75.7 - - + +
297A MET* 1.3 60.9 + - - +
299A GLN* 3.2 4.1 + - - -
300A TYR* 2.8 47.0 + - + +
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Residues in contact with MET 297 (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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216A ILE* 4.6 6.3 - - + -
219A ILE* 4.0 19.3 - - + -
220A LYS* 3.7 39.5 - - + +
223A PHE* 3.7 35.4 - - + -
269A TRP* 3.9 8.3 - - + -
293A GLU* 2.8 32.3 + - - +
294A TRP* 3.8 17.3 - - - +
296A ILE* 1.3 73.7 - - - +
298A LEU* 1.3 55.1 + - + +
300A TYR 3.1 1.7 + - - -
301A CYS* 2.7 41.7 + - - +
1411A GOL 3.7 21.5 - - - +
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Residues in contact with LEU 298 (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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191A LEU* 3.9 13.5 - - + -
192A VAL* 4.0 3.1 - - - +
202A VAL* 4.1 17.0 - - + -
204A LEU* 3.9 34.1 - - + -
212A ILE* 4.1 11.2 - - + -
215A SER* 4.9 1.1 - - - -
216A ILE* 4.0 21.5 - - + +
219A ILE* 4.0 13.7 - - + -
294A TRP 2.8 20.9 + - - +
295A GLU 3.9 2.5 - - - +
297A MET* 1.3 77.2 - - - +
299A GLN* 1.3 62.3 + - - +
302A PHE* 2.9 59.2 + - + +
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Residues in contact with GLN 299 (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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118A VAL* 3.6 7.1 - - + +
192A VAL* 4.6 2.9 - - + -
199A LYS 2.8 26.0 + - - -
200A LYS* 3.6 2.8 + - - +
201A LYS* 2.7 44.6 + - + +
202A VAL* 3.5 16.4 + - + +
246A LEU* 3.6 29.4 - - + +
295A GLU 2.8 23.1 + - - +
296A ILE 3.8 3.1 - - - +
298A LEU* 1.3 72.8 - - - +
300A TYR* 1.3 62.2 + - + +
304A ARG* 3.0 34.7 + - - +
1410A GOL 4.1 12.3 - - - -
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Residues in contact with TYR 300 (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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117A ASP 4.9 0.2 + - - -
118A VAL* 3.5 51.3 - - + +
120A ARG* 6.4 0.7 - - + -
134A LEU* 3.6 13.2 - - - +
223A PHE* 4.8 6.5 - - + -
226A TYR* 4.1 7.9 + + + -
227A ALA* 5.7 0.7 - - + -
233A ILE* 3.8 32.6 + - + +
239A SER 4.5 2.1 + - - -
242A LYS* 3.8 13.3 - - - +
243A ILE* 3.7 25.4 - - + +
246A LEU* 3.9 23.6 - - + -
296A ILE* 2.8 26.9 + - + +
297A MET* 3.9 3.4 - - - +
299A GLN* 1.3 83.1 - - + +
301A CYS* 1.3 68.0 + - - +
304A ARG* 4.7 1.6 - - - -
1410A GOL 3.5 21.8 + - - -
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Residues in contact with CYS 301 (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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115A TYR* 4.3 3.8 + - - -
134A LEU* 3.8 17.3 - - - +
137A MET* 3.7 28.9 - - + +
141A ILE* 4.8 0.2 - - - +
219A ILE* 3.7 20.8 - - + +
223A PHE* 3.8 26.2 - - - -
226A TYR* 3.8 28.7 - - - -
297A MET 2.7 20.0 + - - +
300A TYR* 1.3 81.4 - - - +
302A PHE* 1.3 62.9 + - - +
303A PRO* 3.8 3.5 - - - +
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Residues in contact with PHE 302 (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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115A TYR* 3.5 4.2 - - - -
141A ILE* 3.8 26.5 - - + -
142A ILE* 5.9 0.4 - - + -
189A LEU 3.1 28.7 - - - -
190A SER* 4.5 0.9 - - - -
191A LEU* 3.5 38.1 - - + -
192A VAL* 4.1 7.6 - - + +
211A PHE* 3.6 10.5 - + - -
215A SER* 3.8 10.8 - - - -
219A ILE* 4.1 3.1 - - + +
298A LEU* 2.9 44.9 + - + +
301A CYS* 1.3 79.5 - - - +
303A PRO* 1.3 105.1 - - + +
304A ARG* 3.0 24.6 + - - -
305A LEU* 6.0 0.7 - - + -
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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