Contacts of the strand formed by residues 245 - 251 (chain E) in PDB entry 6F0X
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 ALA 245 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E TYR* 3.2 8.0 - - - -
206E TYR* 2.9 29.8 - - + +
207E GLY* 4.1 2.9 - - - -
208E GLN* 5.7 2.2 - - + -
239E LEU 5.5 3.6 - - - +
240E ILE 4.6 1.8 - - - +
242E ASP* 2.8 34.3 + - + +
243E LYS 3.1 1.6 - - - -
244E ASP* 1.3 73.4 - - - +
246E LEU* 1.3 59.8 + - - +
247E VAL* 5.1 1.6 - - + -
292E ASN* 2.5 34.3 + - - -
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Residues in contact with LEU 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E LEU* 4.6 7.6 - - + -
153E VAL* 5.6 4.7 - - + -
157E LEU* 6.0 1.1 - - + -
196E LEU* 4.7 9.6 - - + -
197E THR* 5.1 2.9 - - - +
200E LEU* 3.6 26.5 - - + -
204E TYR* 3.5 37.0 - - + +
206E TYR 3.0 9.4 + - - +
207E GLY* 3.0 3.9 - - - -
208E GLN* 2.9 26.5 + - - +
245E ALA* 1.3 74.8 - - - +
247E VAL* 1.3 68.8 + - - +
248E PHE* 3.5 33.0 - - + -
292E ASN* 3.7 17.9 - - + +
294E VAL* 5.8 7.0 - - + -
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Residues in contact with VAL 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E GLN* 4.2 9.9 - - + +
210E ILE* 5.6 5.2 - - + -
236E ILE* 4.8 2.5 - - + -
239E LEU 4.1 8.3 - - - +
240E ILE* 4.1 37.0 - - + +
245E ALA* 4.7 3.4 - - + +
246E LEU* 1.3 84.0 - - - +
248E PHE* 1.3 67.0 + - - +
249E VAL* 4.0 24.9 - - + +
292E ASN* 3.1 20.3 + - - +
293E VAL* 3.8 13.5 - - + -
294E VAL* 2.9 29.1 + - - +
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Residues in contact with PHE 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E LEU* 4.5 9.0 - - + -
192E LEU* 4.1 9.9 - - + -
193E ALA* 3.4 47.3 - - + -
196E LEU* 3.6 29.8 - - + -
197E THR* 4.7 0.2 - - - -
208E GLN 3.3 14.8 + - - +
209E LEU* 3.3 22.7 - - + +
210E ILE* 3.2 26.2 + - - +
246E LEU* 3.5 28.0 - - + -
247E VAL* 1.3 74.6 - - - +
249E VAL* 1.3 63.3 + - - +
250E LEU* 3.8 0.4 - - + -
294E VAL* 3.3 22.0 - - + -
296E LEU* 3.9 20.4 - - + -
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Residues in contact with VAL 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E ILE* 4.6 12.3 - - + -
232E MET* 5.0 2.2 - - + -
233E PHE* 4.9 3.1 - - + -
236E ILE* 3.8 46.0 - - + -
247E VAL* 4.0 12.1 - - + -
248E PHE* 1.3 73.0 - - - +
250E LEU* 1.3 61.4 + - - +
251E ILE* 4.1 20.2 - - + -
287E ILE* 5.6 0.7 - - + -
293E VAL* 5.2 2.2 - - + -
294E VAL 2.9 7.7 + - - -
295E ILE* 3.1 36.7 - - + +
296E LEU* 2.9 26.5 + - - -
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Residues in contact with LEU 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E THR* 3.7 30.5 - - + -
189E CYS* 3.4 37.9 - - + -
190E LYS* 4.1 17.9 - - + -
209E LEU* 4.0 14.4 - - + -
210E ILE* 3.2 26.6 + - - +
211E GLU* 3.6 11.4 - - + +
212E ILE 4.3 1.7 + - - -
213E ASN* 3.0 17.1 - - - +
248E PHE* 3.6 0.9 + - + -
249E VAL* 1.3 72.3 - - - +
251E ILE* 1.3 67.3 + - - +
252E ASP* 4.5 6.3 - - + +
296E LEU* 3.1 21.3 - - + +
297E THR* 4.6 0.9 - - - +
298E THR* 5.3 2.5 - - + -
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Residues in contact with ILE 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E ILE* 5.4 5.6 - - + -
213E ASN* 3.2 15.0 - - - +
232E MET* 4.3 20.9 - - + -
233E PHE* 4.3 11.4 - - + -
249E VAL* 4.0 21.7 + - + -
250E LEU* 1.3 76.8 - - - +
252E ASP* 1.3 62.6 + - - +
254E VAL* 3.2 26.4 - - + +
257E LEU* 3.7 30.5 - - + -
280E VAL* 5.2 7.9 - - + -
284E ILE* 6.2 1.8 - - + -
295E ILE* 4.8 3.6 - - + -
296E LEU 3.0 10.5 + - - -
297E THR* 3.3 25.9 - - + -
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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