Contacts of the strand formed by residues 295 - 301 (chain B) in PDB entry 3CB4
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 295 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293B PRO 3.6 0.2 - - - -
294B GLN* 1.3 105.9 - - + +
296B TYR* 1.3 66.7 + - - +
341B GLY* 3.6 1.4 - - - -
342B PHE* 2.8 37.7 + - + +
344B GLY* 3.8 27.8 - - - +
348B MET* 4.9 8.5 - - + -
368B PRO* 3.7 15.3 - - + -
369B THR 3.9 6.3 - - - +
370B VAL* 4.5 2.5 - - + -
451B VAL* 3.6 41.1 - - + -
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Residues in contact with TYR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B LYS* 6.0 0.2 - - - +
293B PRO* 3.4 41.7 + - + +
295B VAL* 1.3 81.4 - - - +
297B ALA* 1.3 61.2 + - - +
325B PHE* 3.8 20.8 - + - -
339B ARG* 3.6 39.8 + - + +
340B CYS 3.2 16.8 - - - -
341B GLY* 3.8 4.0 - - - -
342B PHE* 5.2 0.7 - - - -
368B PRO* 3.1 5.5 - - - +
369B THR* 2.8 55.5 + - + +
370B VAL 5.6 0.2 - - - -
371B VAL* 4.2 9.6 - - + -
385B ASP* 3.4 39.0 + - + +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B TYR* 1.3 76.2 - - - +
298B GLY* 1.3 59.9 + - - +
299B LEU* 5.1 4.3 - - + -
339B ARG* 3.7 5.0 - - - +
340B CYS* 2.8 37.9 + - - +
342B PHE* 4.6 6.3 - - + -
348B MET* 3.8 27.4 - - - -
365B THR* 4.5 6.7 - - - +
366B THR* 4.0 19.1 - - - +
367B ALA 4.6 0.7 - - - -
368B PRO* 4.4 2.7 - - + -
369B THR* 5.1 2.0 - - - -
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B ALA* 1.3 72.1 - - - +
299B LEU* 1.3 62.6 + - - +
300B PHE* 3.7 12.3 - - - -
329B GLU* 4.4 10.1 - - - -
338B PHE 3.8 4.7 - - - -
339B ARG* 4.5 0.7 - - - -
364B ILE 3.6 0.7 - - - +
365B THR* 3.3 5.0 + - - -
366B THR* 2.8 53.6 + - - +
494B ALA* 5.1 1.5 + - - -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B ALA* 4.9 6.1 - - + +
298B GLY* 1.3 73.0 - - - +
300B PHE* 1.3 64.0 + - - +
310B PHE* 3.5 27.2 - - + -
314B LEU* 5.5 0.2 - - + -
337B GLY* 3.4 0.9 - - - -
338B PHE 2.7 43.7 + - - +
340B CYS* 3.7 30.7 - - + -
342B PHE* 4.4 11.4 - - + -
348B MET* 6.2 0.9 - - + -
351B ILE* 5.3 1.6 - - + -
352B GLN* 4.1 15.7 - - + +
355B LEU* 4.2 17.7 - - + -
363B LEU* 4.7 11.2 - - + -
364B ILE 3.5 1.8 - - - +
365B THR* 3.3 34.5 - - - +
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Residues in contact with PHE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B GLY* 3.7 23.6 - - - -
299B LEU* 1.3 75.8 - - - +
301B PRO* 1.3 68.0 - - + +
329B GLU* 3.4 38.4 - - + -
331B SER* 4.0 9.0 - - - -
334B LEU* 3.9 31.4 - - + +
335B GLY 3.7 14.6 - - - -
337B GLY* 3.4 21.1 - - - -
338B PHE 4.9 0.4 - - - -
363B LEU* 3.5 5.6 - - - +
364B ILE* 2.5 51.1 + - + +
366B THR* 3.8 16.8 - - + -
494B ALA* 3.7 22.4 - - + -
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Residues in contact with PRO 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A LYS* 4.6 2.6 - - - +
300B PHE* 1.3 88.3 - - + +
302B VAL* 1.3 65.9 + - - +
303B SER 3.5 21.4 + - - +
304B SER* 4.7 3.9 + - - +
306B ASP* 4.1 11.4 - - + -
307B TYR* 4.3 18.4 - - + +
310B PHE* 3.8 25.6 - - + -
334B LEU 4.5 7.7 - - - +
336B PHE 3.2 24.2 - - - +
337B GLY* 4.2 0.4 - - - -
362B ASP 4.6 0.7 - - - +
363B LEU* 3.8 14.1 - - + -
364B ILE* 4.6 2.7 - - - +
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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