Contacts of the strand formed by residues 247 - 252 (chain v) in PDB entry 6FF7
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 GLY 247 (chain v).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173v VAL* 5.3 14.6 - - - +
174v ASP 5.9 1.0 - - - +
237v THR* 4.2 1.6 - - - -
238v VAL* 2.9 33.5 + - - +
245v PRO 3.2 6.3 + - - -
246v SER* 1.3 73.9 - - - +
248v VAL* 1.3 61.6 + - - +
260v ASN* 4.6 13.5 - - - -
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Residues in contact with VAL 248 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171v VAL* 5.9 2.7 - - + -
173v VAL* 6.3 2.2 - - + -
183v ALA* 4.6 20.2 - - + -
235v LEU* 4.8 9.6 - - + -
236v ILE 3.3 10.1 - - - +
237v THR* 5.5 0.7 - - - -
238v VAL* 5.5 1.1 - - - -
247v GLY* 1.3 75.4 - - - +
249v LEU* 1.3 63.3 + - - +
250v ILE* 5.6 0.2 - - - +
257v THR 4.1 5.2 - - - +
258v TYR* 4.3 10.6 - - - +
259v LYS* 4.3 8.3 + - - +
260v ASN* 5.4 2.9 + - - +
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Residues in contact with LEU 249 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235v LEU* 3.2 9.5 - - - +
236v ILE* 2.9 47.9 + - + +
238v VAL* 5.6 1.7 - - + +
248v VAL* 1.3 74.6 - - - +
250v ILE* 1.3 61.0 + - - +
251v CYS 4.0 1.0 + - - -
256v ILE* 6.4 1.8 - - + -
257v THR 3.5 8.5 - - - +
258v TYR* 5.2 1.6 - - + +
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Residues in contact with ILE 250 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232v GLY* 5.9 3.4 - - - -
234v PHE 4.1 5.2 - - - +
235v LEU* 4.8 2.2 - - + +
248v VAL 4.2 0.4 - - - +
249v LEU* 1.3 72.4 - - - +
251v CYS* 1.3 63.7 + - - +
252v SER* 3.9 2.7 + - - -
255v TYR 4.6 0.2 - - - -
256v ILE* 3.5 4.9 - - - -
257v THR* 2.9 52.9 + - - +
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Residues in contact with CYS 251 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232v GLY* 3.3 5.5 - - - -
233v ASN* 3.2 26.3 + - + -
234v PHE* 3.3 20.3 + - + +
249v LEU 4.0 1.4 + - - -
250v ILE* 1.3 74.4 - - - +
252v SER* 1.3 59.3 + - - +
255v TYR 4.0 4.0 - - - +
256v ILE* 4.8 3.6 - - + +
286v ILE* 6.1 0.9 - - + -
287v PHE* 4.1 28.9 - - + +
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Residues in contact with SER 252 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230v GLU* 4.5 16.4 - - - -
231v HIS 3.4 20.6 - - - -
232v GLY* 3.9 5.4 - - - -
233v ASN* 4.9 1.8 - - - +
250v ILE* 4.9 3.8 - - - -
251v CYS* 1.3 77.3 - - - +
253v GLU* 1.3 61.6 + - - +
254v ASN 3.1 1.2 + - - -
255v TYR* 2.9 35.7 + - - +
257v THR* 6.2 2.0 - - - -
285v MET 3.4 7.1 - - - +
286v ILE* 4.3 9.9 - - - +
287v PHE 5.4 0.2 + - - -
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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