Contacts of the strand formed by residues 296 - 301 (chain B) in PDB entry 3CFV
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 THR 296 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B HIS* 3.5 13.2 + - - -
291B GLY* 3.9 0.2 - - - -
292B SER 3.3 23.4 + - - -
294B ASP* 2.5 35.7 + - - +
295B LYS* 1.3 84.9 - - + +
297B VAL* 1.3 60.5 + - - +
308B LYS* 5.5 0.5 + - - -
311B THR* 3.8 26.0 - - + +
312B PHE 3.4 9.6 - - - +
313B GLU* 4.0 13.7 - - + +
319B ILE* 3.6 9.3 - - - +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B HIS* 4.4 0.4 - - - -
289B ALA* 4.2 2.0 - - + -
290B THR 3.1 25.6 - - - +
291B GLY* 4.8 0.9 - - - -
296B THR* 1.3 78.9 - - - +
298B ALA* 1.3 60.4 + - - +
311B THR* 3.4 4.7 - - - +
312B PHE* 2.8 59.3 + - + +
319B ILE* 3.7 21.1 - - + -
322B VAL* 4.2 6.5 - - + -
332B LEU* 4.1 18.6 - - + -
334B SER* 3.9 24.9 - - - +
344B TRP* 4.5 4.5 - - + +
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B HIS* 3.5 21.0 + - + +
289B ALA* 3.4 3.6 - - - +
290B THR 2.9 31.5 + - - -
297B VAL* 1.3 76.3 - - - +
299B LEU* 1.3 59.8 + - - +
300B TRP* 3.3 36.4 - - + +
308B LYS* 3.8 17.0 - - + +
310B HIS 3.5 4.0 - - - -
311B THR* 5.0 0.7 - - - +
312B PHE* 4.9 0.9 - - - -
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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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287B ILE* 4.1 18.2 - - + -
288B LEU 3.4 13.2 - - - +
289B ALA* 4.8 1.3 - - + +
297B VAL 4.2 0.4 + - - -
298B ALA* 1.3 72.1 - - - +
300B TRP* 1.3 84.7 + - - +
308B LYS* 3.9 2.4 - - - +
309B LEU* 3.2 39.1 + - + -
310B HIS* 3.0 32.7 + - + +
312B PHE* 4.3 14.0 - - + -
324B TRP* 4.4 13.5 - - + -
346B LEU* 3.9 29.2 - - + -
349B ILE* 4.8 3.6 - - + -
29F ILE* 5.5 4.3 - - + -
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Residues in contact with TRP 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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251B LEU* 4.0 15.8 - - + +
268B VAL* 3.6 14.6 - - + -
269B ASP 4.6 2.0 - - - -
270B ALA* 3.5 34.8 - - + -
286B PHE 3.8 0.2 - - - +
287B ILE* 3.1 7.8 - - - +
288B LEU* 2.7 54.2 + - + +
290B THR* 3.5 23.8 + - - -
298B ALA* 3.3 37.7 + - + +
299B LEU* 1.3 78.0 - - - +
301B ASP* 1.3 61.3 + - - +
305B LEU* 3.3 41.7 - - + -
306B LYS 4.8 1.6 - - - -
307B LEU 4.1 1.8 - - - -
308B LYS* 3.6 45.8 - - + -
309B LEU* 4.2 6.1 - - - -
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Residues in contact with ASP 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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29A PHE* 3.3 28.0 - - + -
286B PHE* 3.7 10.5 - - - +
287B ILE* 4.0 9.9 - - + +
300B TRP* 1.3 74.5 - - - +
302B LEU* 1.3 68.8 + - - +
303B ARG* 2.7 34.5 + - - -
304B ASN 3.2 20.1 + - - +
305B LEU* 3.8 8.1 - - - +
307B LEU 5.1 0.4 + - - -
309B LEU* 3.7 30.6 - - + +
30F THR* 5.4 0.5 + - - -
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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