Contacts of the strand formed by residues 275 - 280 (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 VAL 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B GLU* 3.2 16.1 - - - +
245B VAL* 2.8 39.5 - - + +
246B ALA 3.1 12.2 + - - +
249B GLN* 3.7 33.4 - - - +
250B LYS 4.0 3.8 - - - +
270B ALA* 4.5 5.8 - - + -
271B HIS* 4.0 12.3 - - + +
273B ALA 3.9 4.0 - - - +
274B GLU* 1.3 75.2 - - - +
276B ASN* 1.3 58.8 + - - +
277B CYS 4.2 0.7 - - - +
290B THR* 3.1 35.0 - - + -
291B GLY 3.4 8.7 - - - +
292B SER* 4.3 1.1 - - - +
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Residues in contact with ASN 276 (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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230B GLU* 3.3 34.9 - - + +
231B ASP* 3.4 13.9 - - - +
245B VAL* 3.9 4.5 - - - -
247B ASP* 4.4 2.3 - - - +
274B GLU* 4.2 8.9 + - - +
275B VAL* 1.3 77.9 - - - +
277B CYS* 1.3 61.6 + - - +
291B GLY 2.9 6.7 + - - -
292B SER 4.1 0.2 - - - -
293B ALA* 4.0 23.0 - - - +
318B GLU* 4.5 1.8 + - - -
319B ILE 3.0 28.9 + - - +
320B PHE* 3.6 41.9 - - + +
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Residues in contact with CYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASP* 3.6 14.4 - - - +
245B VAL* 3.8 2.6 - - - +
275B VAL* 3.8 2.9 - - - +
276B ASN* 1.3 79.8 - - - +
278B LEU* 1.3 65.4 + - - +
290B THR* 3.5 6.6 - - - +
291B GLY* 3.0 41.1 + - - +
319B ILE* 4.3 1.8 - - - -
320B PHE* 3.4 33.9 - - - +
321B GLN* 3.6 16.6 - - - +
322B VAL* 3.6 19.7 - - + -
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Residues in contact with LEU 278 (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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231B ASP* 3.2 54.1 + - + +
232B VAL* 3.9 11.2 - - - +
233B ALA* 4.0 10.3 - - + +
243B GLY* 3.5 34.1 - - - +
244B SER 4.0 1.6 - - - +
245B VAL* 4.1 9.2 - - + -
251B LEU* 4.2 13.5 - - + -
277B CYS* 1.3 76.3 - - - +
279B SER* 1.3 63.2 + - - +
280B PHE* 4.1 14.6 - - + -
288B LEU* 4.0 7.2 - - + -
289B ALA 3.2 13.0 - - - +
290B THR* 4.1 5.8 - - - +
321B GLN* 5.4 1.2 + - - -
322B VAL* 3.9 5.3 - - - +
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Residues in contact with SER 279 (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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233B ALA* 5.4 1.1 - - - -
278B LEU* 1.3 73.7 - - - +
280B PHE* 1.3 58.0 + - - +
288B LEU* 3.8 4.0 - - - -
289B ALA* 3.0 24.5 + - - -
322B VAL* 3.2 36.4 + - - +
323B HIS* 3.7 6.4 + - - -
324B TRP* 2.7 47.8 + - - +
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Residues in contact with PHE 280 (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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233B ALA* 3.5 34.9 - - + +
234B TRP 3.3 17.5 - - - -
235B HIS* 3.6 33.7 - + + +
236B LEU* 3.5 28.4 - - + +
241B LEU* 6.3 0.4 - - + -
242B PHE* 4.5 3.4 - - - -
243B GLY* 3.8 19.7 - - - -
253B ILE* 5.4 4.0 - - + -
278B LEU* 4.1 7.6 - - + -
279B SER* 1.3 76.9 + - - +
281B ASN* 1.3 65.9 + - - +
282B PRO* 3.5 4.0 - - - +
286B PHE 6.2 0.2 - - - -
287B ILE 4.2 8.1 - - - -
288B LEU* 3.6 31.0 - - + -
302B LEU* 4.8 11.0 - - + -
324B TRP* 3.2 9.8 - - - -
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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