Contacts of the strand formed by residues 287 - 292 (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 ILE 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B PHE* 4.2 6.1 - - - -
281B ASN* 3.3 54.3 + - + +
284B SER* 3.6 17.2 + - - +
285B GLU 5.3 0.2 - - - -
286B PHE* 1.3 81.2 - - + +
288B LEU* 1.3 61.1 + - - +
299B LEU* 4.1 10.3 - - + -
300B TRP 3.1 9.9 - - - +
301B ASP* 4.0 16.4 - - - +
303B ARG* 5.6 0.4 - - - +
309B LEU* 4.8 7.4 - - + -
324B TRP* 3.7 17.3 - - + -
346B LEU* 4.3 2.5 - - + -
29F ILE* 3.8 29.8 - - + -
30F THR* 4.3 11.9 - - - +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 4.3 29.6 - - + -
253B ILE* 4.5 14.1 - - + -
278B LEU* 4.0 13.2 - - + -
279B SER 3.4 21.3 - - - +
280B PHE* 3.6 34.1 - - + +
286B PHE 4.6 2.9 - - - +
287B ILE* 1.3 77.1 - - - +
289B ALA* 1.3 92.5 + - - +
290B THR* 4.4 2.2 - - - +
299B LEU* 3.4 7.4 - - - +
300B TRP* 2.7 44.5 + - + +
302B LEU* 4.7 4.7 - - + -
305B LEU* 5.8 0.2 - - + -
324B TRP* 4.3 1.8 - - - -
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU* 3.2 1.3 - - - -
279B SER 3.0 31.1 + - - +
288B LEU* 1.3 81.2 - - - +
290B THR* 1.3 64.7 + - - +
297B VAL* 4.2 2.2 - - + -
298B ALA 3.4 7.0 - - - +
299B LEU* 5.3 1.8 - - + -
312B PHE* 5.9 0.2 - - + -
322B VAL* 4.1 13.5 - - + -
324B TRP* 3.7 26.2 - - + +
332B LEU* 3.9 20.6 - - + -
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Residues in contact with THR 290 (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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245B VAL* 4.6 0.6 - - + +
251B LEU* 4.2 12.1 - - - +
270B ALA* 4.6 4.7 - - + -
271B HIS* 3.1 26.9 - - + +
275B VAL* 3.1 28.7 - - + -
277B CYS 3.5 5.2 - - - +
278B LEU* 4.1 10.3 - - - +
288B LEU* 4.4 1.6 - - - +
289B ALA* 1.3 79.9 + - - +
291B GLY* 1.3 58.1 + - - +
297B VAL* 3.1 10.1 - - - +
298B ALA 2.9 32.8 + - - -
300B TRP* 3.5 25.3 + - - +
322B VAL* 4.8 1.5 - - - +
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Residues in contact with GLY 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL* 3.4 4.9 - - - +
276B ASN 2.9 24.1 + - - -
277B CYS* 3.0 30.4 + - - -
290B THR* 1.3 74.3 - - - +
292B SER* 1.3 61.7 + - - -
296B THR 3.9 3.8 - - - -
297B VAL* 4.6 2.9 - - - -
319B ILE* 4.0 17.0 - - - -
322B VAL* 4.5 1.5 - - - +
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Residues in contact with SER 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B HIS* 3.2 46.2 - - - +
273B ALA 3.4 3.5 + - - -
274B GLU 2.8 15.3 + - - -
275B VAL* 4.4 0.9 - - - -
276B ASN* 4.1 7.2 - - - +
291B GLY* 1.3 73.0 - - - -
293B ALA* 1.3 69.9 + - - +
294B ASP* 3.1 21.3 + - - -
295B LYS* 3.6 6.6 + - - -
296B THR 3.3 6.9 + - - -
319B ILE* 3.1 24.3 + - - +
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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