Contacts of the strand formed by residues 293 - 297 (chain A) in PDB entry 6BHG
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 PHE 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A PRO* 5.7 1.1 - - + -
255A ALA* 3.9 26.5 - - + -
258A LEU* 3.8 29.2 - - + -
281A VAL* 3.9 19.7 - - + -
283A GLU 3.4 4.0 - - - +
284A THR* 4.1 6.7 - - + -
285A PRO* 3.5 26.2 - - + -
292A ARG* 1.3 73.1 - - - +
294A LEU* 1.3 61.7 + - - +
295A ILE* 3.7 17.6 + - + -
304A TYR* 3.3 3.7 - - - -
305A VAL* 2.9 38.8 + - + +
307A GLN* 3.6 31.2 - - + -
310A LEU* 3.7 30.1 - - + -
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Residues in contact with LEU 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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281A VAL* 3.6 1.0 - - - -
282A ALA* 2.7 37.5 + - + -
283A GLU* 3.0 40.8 + - + +
293A PHE* 1.3 70.8 - - - +
295A ILE* 1.3 61.4 + - - +
296A PHE* 3.7 29.8 - - + -
303A SER 3.6 20.6 - - - +
304A TYR* 3.6 16.2 - - + +
343A ARG* 4.8 2.9 - - - +
373A SER* 4.2 15.3 - - - -
374A LEU* 3.8 33.7 - - + -
389A TYR* 4.6 5.2 - - + -
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Residues in contact with ILE 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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264A VAL* 4.0 20.9 - - + -
266A ALA* 4.1 10.5 - - + -
279A GLY* 4.1 9.2 - - - -
280A ILE 3.5 5.8 - - - +
281A VAL* 4.1 10.8 - - + -
293A PHE* 4.0 17.3 - - + -
294A LEU* 1.3 81.4 - - - +
296A PHE* 1.3 73.0 + - - +
297A PHE* 3.7 36.6 + - + -
302A ALA* 3.3 6.4 - - - -
303A SER 2.8 35.9 + - - +
305A VAL* 3.7 23.1 - - + -
310A LEU* 4.1 6.5 - - + -
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Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLY* 3.3 0.3 - - - -
280A ILE* 2.8 40.8 + - + +
282A ALA* 3.5 22.9 - - + -
294A LEU* 3.7 22.6 - - + -
295A ILE* 1.3 81.3 - - - +
297A PHE* 1.3 63.4 + - - +
298A ASP* 4.8 0.2 - - - +
300A GLY* 6.2 0.7 - - - -
301A TYR 3.6 4.3 - - - +
302A ALA* 3.9 6.1 - - + -
332A PHE* 3.8 17.9 - + - -
333A ILE* 3.8 30.6 - - + +
336A TYR* 3.8 24.0 - + - -
389A TYR* 3.9 29.8 - + + -
14B ALY 3.7 27.4 - - + -
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Residues in contact with PHE 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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266A ALA* 3.7 22.4 - - + -
267A LYS 3.7 19.7 - - - -
268A TYR* 3.7 20.2 - + + -
277A TYR* 3.6 23.1 - - + -
278A ALA 3.5 16.4 - - - +
279A GLY* 3.8 0.4 - - - -
295A ILE* 3.7 26.7 - - + -
296A PHE* 1.3 75.7 - - - +
298A ASP* 1.3 59.4 + - - +
299A ASP* 3.2 17.5 - - - +
300A GLY* 2.9 20.6 + - - -
301A TYR* 2.8 37.1 + + + +
303A SER* 3.4 23.1 - - - -
305A VAL* 4.8 0.2 - - + -
505A UNX 3.0 11.4 - - - -
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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