Contacts of the strand formed by residues 262 - 269 (chain A) in PDB entry 1BY7
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 VAL 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 6.5 0.2 - - + -
204A PHE* 3.9 21.1 - - + -
258A TYR* 2.8 36.5 + - + +
260A GLY* 3.3 7.3 - - - +
261A ASP* 1.3 82.4 - - - +
263A SER* 1.3 63.9 + - - +
398A ILE* 3.5 30.1 - - + -
399A MET 3.2 9.6 - - - +
400A HIS* 3.9 24.9 - - + -
407A LEU* 4.4 9.2 - - + -
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Residues in contact with SER 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLU* 2.6 39.5 + - - -
256A LEU 3.5 5.2 - - - -
257A PRO* 3.3 18.0 - - - +
258A TYR* 4.2 5.2 - - - -
261A ASP* 5.2 0.7 - - - -
262A VAL* 1.3 75.1 + - - +
264A MET* 1.3 62.0 + - - +
265A PHE* 3.8 5.2 + - - -
397A LEU 3.6 0.5 - - - +
398A ILE* 3.4 3.1 - - - -
399A MET* 2.8 40.2 + - - +
401A LYS* 3.9 15.6 - - - +
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Residues in contact with MET 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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208A TRP* 3.9 25.1 - - + -
254A LEU 3.6 1.2 - - - +
255A GLU* 3.4 3.8 - - - +
256A LEU* 2.9 33.7 + - - +
258A TYR* 3.3 32.7 - - + +
263A SER* 1.3 71.4 - - - +
265A PHE* 1.3 63.7 + - - +
266A LEU* 3.7 36.7 - - + +
309A ILE* 5.7 1.8 - - - -
312A PHE* 4.7 6.5 - - + -
362A VAL* 3.9 23.1 - - + -
396A PHE* 3.8 28.7 - - + -
397A LEU 3.1 11.7 - - - +
398A ILE* 4.2 9.9 - - + +
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Residues in contact with PHE 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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253A ILE* 4.4 8.3 - - + -
254A LEU 3.3 3.6 - - - +
255A GLU* 3.8 32.8 - - + -
263A SER* 4.1 15.7 - - - -
264A MET* 1.3 77.1 - - - +
266A LEU* 1.3 60.7 + - - +
267A LEU* 4.2 4.6 - - + +
295A THR* 3.9 28.5 - - + -
300A MET* 3.8 30.1 - - + -
396A PHE* 3.1 5.5 - - - +
397A LEU* 2.8 61.9 + - + +
399A MET* 4.0 25.4 - - + -
401A LYS* 4.3 11.2 - - + -
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Residues in contact with LEU 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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252A GLN 3.8 0.9 - - - +
253A ILE* 3.2 6.2 - - - +
254A LEU* 2.9 45.5 + - + +
256A LEU* 3.9 22.7 - - + -
264A MET* 3.7 37.5 - - + +
265A PHE* 1.3 75.4 - - - +
267A LEU* 1.3 60.9 + - - +
268A LEU 4.1 0.4 - - - -
309A ILE* 4.1 27.6 - - + -
312A PHE* 6.2 0.2 - - + -
388A PHE* 3.5 21.4 - - + -
394A PHE* 3.9 28.3 - - + -
395A LEU 3.5 6.5 - - - +
396A PHE* 4.4 2.7 - - + -
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Residues in contact with LEU 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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246A ILE* 4.9 2.2 - - + -
252A GLN 3.5 5.8 - - - +
253A ILE* 4.0 22.4 - - + -
265A PHE* 4.2 14.4 - - + +
266A LEU* 1.3 76.4 - - - +
268A LEU* 1.3 58.1 + - - +
269A PRO* 3.9 3.4 - - - +
282A LEU* 4.0 24.5 - - + +
286A ILE* 4.3 13.5 - - + -
291A LEU* 4.5 3.6 - - + -
294A TRP* 3.7 36.3 - - + -
394A PHE* 3.1 18.4 - - - +
395A LEU* 2.8 39.0 + - + +
396A PHE* 4.9 0.4 - - - -
397A LEU* 4.8 13.0 - - + -
409A PHE* 6.4 1.1 - - + -
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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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251A ALA* 4.0 1.8 - - - +
252A GLN* 2.9 41.3 + - - +
267A LEU* 1.3 71.7 - - - +
269A PRO* 1.3 78.9 - - - +
270A ASP* 4.4 0.2 - - - -
282A LEU* 4.5 0.6 - - - +
388A PHE* 3.6 32.5 - - + -
389A VAL* 3.4 35.9 - - + +
390A ALA* 3.9 11.2 - - - -
392A HIS* 3.4 48.7 - - + +
393A PRO 3.9 4.5 - - - +
394A PHE* 4.1 6.7 - - + -
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Residues in contact with PRO 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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249A LEU 5.5 1.8 - - - +
250A LYS 3.9 1.3 - - - +
251A ALA* 3.8 12.0 - - + -
267A LEU 3.9 0.7 - - - +
268A LEU* 1.3 90.7 - - + +
270A ASP* 1.3 60.3 + - - +
271A GLU 3.8 13.7 - - - +
272A ILE* 4.2 7.9 - - + -
278A GLY 3.4 28.0 - - - +
279A LEU* 3.7 20.0 - - + -
282A LEU* 4.0 10.8 - - + -
392A HIS* 2.7 33.0 + - + +
393A PRO 3.5 19.5 - - - +
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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