Contacts of the strand formed by residues 250 - 255 (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 LYS 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225B HIS* 3.4 16.8 + - - -
245B VAL* 3.8 2.1 - - - +
246B ALA 3.6 13.7 + - - +
248B ASP* 2.9 44.4 + - + +
249B GLN* 1.3 78.6 - - - +
251B LEU* 1.3 59.0 + - - +
252B MSE 3.9 18.4 - - + -
267B LEU* 3.8 30.0 - - + +
268B VAL 3.2 11.9 - - - +
269B ASP* 3.4 29.7 + - - +
275B VAL* 4.0 5.2 - - - +
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Residues in contact with LEU 251 (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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244B SER 3.6 15.3 - - - +
245B VAL* 4.0 17.5 - - + -
250B LYS* 1.3 71.6 - - - +
252B MSE 1.3 69.6 + - - +
253B ILE* 4.7 4.7 - - + -
266B HIS 4.3 0.2 - - - +
267B LEU* 3.8 0.3 - - - -
268B VAL* 2.9 49.8 + - + +
270B ALA* 3.9 16.6 - - + +
278B LEU* 4.2 15.3 - - + -
288B LEU* 4.3 17.5 - - + -
290B THR* 4.2 5.6 - - - +
300B TRP* 4.0 39.9 - - + +
305B LEU* 4.9 4.9 - - + -
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Residues in contact with MSE 252 (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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224B GLY 3.2 35.4 - - - +
225B HIS* 3.6 32.1 - - + +
243B GLY* 3.4 2.8 - - - -
244B SER* 2.7 48.7 + - - +
248B ASP* 3.8 9.0 - - - +
250B LYS* 4.0 12.8 - - + -
251B LEU* 1.3 79.0 - - - +
253B ILE* 1.3 63.7 + - - +
254B TRP* 3.7 16.2 - - - +
264B PRO* 3.9 20.4 - - + -
266B HIS 3.6 4.5 - - - +
267B LEU* 3.9 24.5 - - + -
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Residues in contact with ILE 253 (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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241B LEU* 4.2 17.3 - - + -
242B PHE 3.5 9.9 - - - +
243B GLY* 4.6 7.9 - - - -
251B LEU* 4.7 10.8 - - + +
252B MSE 1.3 77.9 - - - +
254B TRP* 1.3 70.6 + - - +
264B PRO* 3.3 2.5 - - - +
265B SER* 3.0 27.3 + - - -
266B HIS* 3.2 30.7 + - + -
268B VAL* 5.8 0.9 - - + -
280B PHE* 5.4 3.8 - - + -
288B LEU* 4.5 11.0 - - + -
302B LEU* 3.3 35.7 - - + -
305B LEU* 4.1 21.5 - - + -
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Residues in contact with TRP 254 (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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201B VAL* 5.9 1.7 - - + +
222B PHE* 3.4 39.5 - + + -
224B GLY* 3.3 40.6 - - - -
225B HIS* 4.7 4.5 - - - -
240B SER 4.4 0.2 - - - -
241B LEU* 3.4 14.2 - - - +
242B PHE* 2.8 71.5 + + + -
244B SER* 2.6 28.1 + - - -
252B MSE 3.7 19.3 - - - +
253B ILE* 1.3 77.3 - - - +
255B ASP* 1.3 61.7 + - - +
260B THR 4.7 3.1 - - - -
261B THR 4.2 0.2 - - - -
262B SER 4.0 5.4 - - - -
263B LYS 3.7 13.9 - - - -
264B PRO* 3.7 34.5 - - + -
265B SER* 4.5 3.1 - - - +
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Residues in contact with ASP 255 (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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222B PHE* 4.8 7.0 - - - -
240B SER* 3.4 8.5 - - - +
241B LEU* 4.1 12.2 - - + +
242B PHE* 5.3 0.2 - - - -
254B TRP* 1.3 78.3 - - - +
256B THR* 1.3 75.6 + - - +
257B ARG* 2.8 50.3 + - - +
258B SER* 3.4 28.9 + - - +
260B THR 5.5 1.4 - - - +
265B SER* 3.7 19.0 + - - +
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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