Contacts of the strand formed by residues 239 - 246 (chain E) in PDB entry 6IWQ
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 LEU 239 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E SER* 3.9 7.6 - - - +
211E VAL* 4.0 16.4 - - + -
230E VAL* 4.6 3.8 - - + -
231E ILE* 4.7 8.1 - - + -
234E THR* 3.6 30.1 - - + +
235E PRO 3.7 4.8 + - - +
236E ARG* 3.5 16.6 + - - +
237E LYS 3.3 3.5 - - - +
238E TYR* 1.3 74.8 - - - +
240E ALA* 1.3 63.9 + - - +
241E GLU 3.5 21.3 - - - +
242E ILE* 3.8 22.0 - - + -
268E LEU* 3.4 38.1 - - + +
311E TYR* 5.9 2.5 - - + -
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Residues in contact with ALA 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E THR* 4.4 8.1 - - - -
209E SER 2.8 23.8 + - - +
210E SER* 4.3 0.2 - - - +
237E LYS 5.4 1.3 - - - -
238E TYR 3.2 2.2 + - - -
239E LEU* 1.3 75.0 - - - +
241E GLU* 1.3 60.0 + - - +
268E LEU* 4.0 10.7 - - - +
270E LYS* 5.5 0.2 + - - -
293E LEU* 4.1 18.9 - - + +
294E GLY* 3.7 29.4 - - - +
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Residues in contact with GLU 241 (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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209E SER 3.7 0.2 + - - -
210E SER* 3.1 27.3 + - - +
211E VAL 3.2 21.1 + - - -
239E LEU* 3.5 9.9 - - - +
240E ALA* 1.3 77.6 - - - +
242E ILE* 1.3 62.9 + - - +
243E VAL* 3.5 18.8 - - + +
268E LEU* 3.5 11.9 - - - +
270E LYS* 2.9 37.5 - - - +
290E LYS 4.7 1.9 - - - +
291E ALA* 3.1 26.3 - - - -
292E LYS 4.6 0.7 + - - -
293E LEU* 3.1 22.9 + - + +
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Residues in contact with ILE 242 (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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211E VAL* 3.4 26.9 - - + +
213E ILE* 4.2 7.0 - - + -
227E VAL* 4.3 9.4 - - + -
230E VAL* 3.8 16.4 - - + -
231E ILE* 3.7 33.4 - - + -
239E LEU* 3.8 20.9 - - + -
241E GLU* 1.3 76.0 - - - +
243E VAL* 1.3 60.5 + - - +
244E LEU* 4.0 22.0 - - + -
268E LEU* 3.1 8.5 + - + -
269E VAL* 3.4 19.9 - - + +
270E LYS* 3.1 26.1 + - - +
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Residues in contact with VAL 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E VAL 2.8 13.1 + - - +
212E VAL* 3.2 7.8 - - + +
213E ILE 3.0 24.4 + - - +
241E GLU* 3.5 36.6 - - + +
242E ILE* 1.3 71.5 - - - +
244E LEU* 1.3 63.5 + - - +
245E ILE* 3.7 17.8 + - + -
270E LYS* 3.7 11.9 - - + -
272E PHE* 3.7 26.5 - - + -
287E GLY 4.7 3.4 - - - +
290E LYS 4.2 4.3 - - - +
291E ALA* 3.7 23.6 - - + -
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Residues in contact with LEU 244 (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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213E ILE* 3.4 40.8 - - + +
215E PHE* 4.0 19.7 - - + -
223E LEU* 4.7 10.3 - - + -
224E MET* 5.1 1.3 - - + -
227E VAL* 4.0 12.1 - - + -
242E ILE* 4.0 8.7 - - + -
243E VAL* 1.3 75.3 - - - +
245E ILE* 1.3 64.2 + - - +
246E ASP 3.9 0.4 - - - -
258E LEU* 4.7 14.1 - - + -
262E ILE* 4.6 12.1 - - + -
269E VAL* 4.1 19.7 - - + -
270E LYS 2.9 17.1 + - - +
271E VAL* 3.4 8.9 - - + +
272E PHE 2.9 26.9 + - - +
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Residues in contact with ILE 245 (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 VAL* 5.2 3.1 - - + -
213E ILE 2.9 9.6 + - - +
214E VAL* 3.5 22.4 - - + +
215E PHE* 2.9 28.9 + - - -
243E VAL* 3.7 22.4 - - + +
244E LEU* 1.3 76.9 - - - +
246E ASP* 1.3 62.9 + - - +
247E ASP 3.2 1.4 + - - -
272E PHE* 3.7 21.1 - - + +
274E ASN* 3.8 28.3 - - - +
283E ALA* 3.9 15.0 - - + +
286E ILE* 4.7 9.4 - - + -
287E GLY* 3.8 27.1 - - - +
290E LYS* 4.7 1.8 - - + -
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Residues in contact with ASP 246 (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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215E PHE* 3.4 28.0 - - + -
244E LEU 3.8 1.6 + - - -
245E ILE* 1.3 71.3 - - - +
247E ASP* 1.3 58.0 + - - +
248E PHE* 2.9 7.8 + - - -
249E SER* 2.8 43.0 + - - -
254E LEU 4.3 2.8 - - - +
255E LYS* 5.7 2.1 - - - +
271E VAL* 4.3 1.3 - - + -
272E PHE 2.9 14.1 + - - +
273E ARG* 3.2 41.6 + - - +
274E ASN* 3.0 24.2 + - - +
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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