Contacts of the helix formed by residues 247 - 259 (chain A) in PDB entry 2B69
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 ILE 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A VAL* 4.4 11.9 - - + -
193A PHE* 3.9 16.7 - - + -
205A VAL* 4.5 9.2 - - + -
209A GLY* 3.3 4.2 + - - +
211A GLN* 2.9 44.8 + - + +
212A THR 5.1 0.2 - - - +
213A ARG* 4.1 16.4 - - + +
215A PHE* 4.5 0.2 - - + -
246A THR* 1.3 68.7 - - - +
248A LEU* 1.3 60.8 + - - +
250A PHE* 3.3 20.0 + - + +
251A ALA* 3.0 26.9 + - - +
900A UDP 3.6 50.7 - - - +
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Residues in contact with LEU 248 (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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205A VAL* 4.8 4.7 - - + -
208A SER 4.5 6.5 - - - +
209A GLY* 3.0 25.7 + - - +
246A THR* 4.2 3.6 - - - +
247A ILE* 1.3 76.8 - - - +
249A GLU* 1.3 61.4 + - - +
251A ALA* 3.2 3.5 + - + +
252A GLN* 3.0 53.6 + - + +
264A ILE* 4.1 19.5 - - + -
266A PHE* 4.0 30.7 - - + -
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Residues in contact with GLU 249 (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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245A HIS* 3.5 24.5 + - + +
246A THR* 3.0 50.5 + - + +
248A LEU* 1.3 75.6 - - - +
250A PHE* 1.3 58.0 + - - +
252A GLN* 3.4 16.5 + - - +
253A LEU* 2.9 29.5 + - - +
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Residues in contact with PHE 250 (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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189A VAL* 6.1 1.8 - - + -
193A PHE* 4.5 6.7 - - + -
213A ARG 3.3 22.0 - - - -
215A PHE* 3.1 47.1 - + + -
243A GLU 4.9 0.7 - - - -
245A HIS* 3.3 43.5 - + + -
246A THR 3.0 25.0 + - - -
247A ILE* 3.6 16.8 - - + +
248A LEU 3.3 0.2 - - - -
249A GLU* 1.3 77.6 - - - +
251A ALA* 1.3 55.7 + - - +
253A LEU* 3.3 12.4 + - + +
254A ILE* 3.0 39.3 + - + +
296A LEU* 3.9 20.4 - - + -
300A LEU* 5.5 3.6 - - + -
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Residues in contact with ALA 251 (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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193A PHE* 3.6 30.9 - - + -
203A LEU* 3.6 16.4 - - + +
205A VAL* 4.4 12.1 - - + -
247A ILE 3.0 9.9 + - - +
248A LEU* 3.2 9.2 + - - +
250A PHE* 1.3 75.3 - - - +
252A GLN* 1.3 57.1 + - - +
254A ILE* 3.5 0.4 + - - -
255A LYS* 3.0 30.7 + - - +
264A ILE* 4.2 15.4 - - + +
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Residues in contact with GLN 252 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A LEU* 3.0 43.5 + - + +
249A GLU* 3.7 18.4 + - - +
251A ALA* 1.3 76.7 - - - +
253A LEU* 1.3 60.9 + - - +
255A LYS* 3.5 6.6 + - - +
256A ASN* 3.1 35.2 + - - +
264A ILE* 4.0 17.4 - - + +
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Residues in contact with LEU 253 (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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245A HIS* 6.0 0.9 - - + -
249A GLU 2.9 17.8 + - - +
250A PHE* 3.3 13.0 + - + +
252A GLN* 1.3 72.5 - - - +
254A ILE* 1.3 60.5 + - - +
256A ASN* 3.2 12.8 + - + +
257A LEU* 2.9 48.9 + - + +
296A LEU* 4.0 21.1 - - + -
297A GLU* 4.1 22.4 - - + +
300A LEU* 3.7 24.9 - - + -
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Residues in contact with ILE 254 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A VAL* 5.1 5.2 - - + -
193A PHE* 3.8 43.1 - - + +
194A ILE* 3.9 24.7 - - + -
197A ALA* 4.3 2.9 - - + -
203A LEU* 4.8 1.8 - - + -
250A PHE* 3.0 26.2 + - + +
251A ALA 3.9 3.4 - - - +
253A LEU* 1.3 71.0 - - - +
255A LYS* 1.3 68.7 + - - +
257A LEU* 3.3 4.1 + - + +
258A VAL* 2.9 33.1 + - + +
300A LEU* 3.6 41.3 - - + -
304A ILE* 5.1 4.0 - - + -
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Residues in contact with LYS 255 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ALA* 4.7 4.0 - - - -
203A LEU* 4.8 8.0 - - + +
251A ALA 3.0 18.7 + - - +
252A GLN* 3.7 6.5 - - - +
253A LEU 3.4 0.2 - - - -
254A ILE* 1.3 77.0 - - - +
256A ASN* 1.3 62.4 + - - +
259A GLY* 3.0 23.0 + - - -
260A SER* 3.1 47.1 + - - +
261A GLY* 4.3 5.5 + - - -
262A SER* 2.9 31.6 + - - +
263A GLU* 4.9 2.0 - - - +
264A ILE* 4.6 19.5 - - + +
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Residues in contact with ASN 256 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A GLN* 3.1 27.0 + - - +
253A LEU* 3.5 15.2 - - + +
254A ILE 3.2 0.2 - - - -
255A LYS* 1.3 79.7 - - - +
257A LEU* 1.3 64.2 + - + +
259A GLY* 3.3 12.6 + - - -
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Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A LEU* 2.9 35.1 + - + +
254A ILE* 4.0 2.9 - - - +
256A ASN* 1.3 75.5 - - + +
258A VAL* 1.3 60.3 + - - +
297A GLU* 4.1 29.2 - - + +
300A LEU* 3.8 40.4 - - + -
301A ASN* 4.0 24.0 - - - +
304A ILE* 3.8 17.5 - - + +
308A ARG* 5.3 2.6 + - - -
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Residues in contact with VAL 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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194A ILE* 4.7 6.5 - - + +
197A ALA* 4.1 21.3 - - + +
198A LEU* 3.8 37.9 - - + +
254A ILE* 2.9 26.3 + - + +
255A LYS 4.2 1.6 - - - +
257A LEU* 1.3 77.2 - - - +
259A GLY* 1.3 59.7 + - - +
260A SER* 4.1 6.1 - - - -
304A ILE* 3.9 28.9 - - + -
308A ARG* 4.4 15.5 + - - +
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Residues in contact with GLY 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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255A LYS 3.0 8.1 + - - -
256A ASN* 3.3 11.2 + - - -
258A VAL* 1.3 80.0 - - - +
260A SER* 1.3 59.4 + - - +
261A GLY 4.3 0.2 + - - -
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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