Contacts of the strand formed by residues 250 - 255 (chain B) in PDB entry 3VF0
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 PHE 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248B PRO* 3.4 7.9 - - - +
249B THR* 1.4 79.6 + - - +
251B CYS* 1.3 63.6 + - - +
252B GLN* 3.4 48.7 - - + -
266B VAL* 3.5 24.2 - - + -
267B LEU* 3.2 4.6 - - - -
268B GLU* 2.9 40.5 + - + +
303B GLY* 3.6 26.5 - - - -
304B ARG* 3.7 36.1 - - + -
307B LEU* 4.0 9.6 - - + -
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Residues in contact with CYS 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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235B VAL* 4.0 5.1 - - - +
238B LEU* 4.4 9.9 - - - -
239B CYS* 2.1 61.8 - - + -
248B PRO* 4.5 5.6 - - + -
250B PHE* 1.3 76.9 - - - +
252B GLN* 1.3 66.3 + - - +
266B VAL 3.5 6.3 - - - -
267B LEU* 3.7 24.2 - - + -
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Residues in contact with GLN 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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235B VAL* 4.4 4.9 - - - -
250B PHE* 3.4 29.9 - - + -
251B CYS* 1.3 81.1 - - - +
253B LEU* 1.3 64.8 + - - +
265B ALA* 3.3 5.9 - - - +
266B VAL* 3.1 31.7 + - - -
304B ARG* 5.8 2.6 - - - +
307B LEU* 3.6 28.9 - - + +
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Residues in contact with LEU 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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228B LEU* 4.0 15.9 - - + -
232B PHE* 3.9 32.8 - - + +
233B ASN* 5.0 4.0 - - - +
234B ASP 4.9 2.7 - - - +
235B VAL* 4.0 27.6 - - + +
238B LEU* 3.9 13.5 - - + -
252B GLN* 1.3 81.3 - - - +
254B ALA* 1.3 63.0 + - - +
255B CYS* 3.6 7.7 + - + +
261B LEU* 4.0 26.9 - - + -
264B PHE 3.8 2.5 - - - +
265B ALA* 3.8 20.2 - - + -
307B LEU* 4.2 4.7 - - - +
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Residues in contact with ALA 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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252B GLN 3.8 1.4 + - - -
253B LEU* 1.3 73.3 - - - +
255B CYS* 1.3 61.5 + - - +
261B LEU* 3.5 9.4 - - - +
262B LYS* 3.0 22.8 + - + -
263B GLY 4.6 0.2 + - - -
264B PHE* 2.8 56.7 + - + +
307B LEU* 3.5 18.4 - - + +
311B ILE* 3.8 7.2 - - + -
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Residues in contact with CYS 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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253B LEU* 3.6 6.4 + - + +
254B ALA* 1.3 76.7 - - - +
256B GLY* 1.3 71.7 + - - +
259B GLY* 3.5 23.1 - - - +
260B GLN 3.1 14.8 - - - +
261B LEU* 4.4 5.8 - - + -
262B LYS* 3.8 8.5 - - - +
311B ILE* 3.6 18.3 - - - +
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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