Contacts of the strand formed by residues 239 - 246 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D SER* 4.0 8.1 - - - +
211D VAL* 3.7 24.0 - - + -
230D VAL* 4.3 7.9 - - + +
231D ILE* 4.6 13.9 - - + -
234D THR* 3.9 20.4 - - + +
235D PRO 3.7 6.9 + - - +
236D ARG* 3.1 17.7 + - - +
237D LYS 4.6 1.7 - - - +
238D TYR* 1.3 75.7 - - - +
240D ALA* 1.3 65.2 + - - +
241D GLU 3.4 20.3 + - - +
242D ILE* 4.1 16.2 - - + -
268D LEU* 3.8 37.3 - - + +
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Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D THR* 2.8 29.6 - - + -
209D SER 3.0 11.9 + - - +
237D LYS 5.4 0.9 - - - -
238D TYR 3.3 3.2 + - - -
239D LEU* 1.3 74.8 - - - +
241D GLU* 1.3 64.7 - - - +
268D LEU* 3.8 10.6 - - - +
270D LYS* 4.8 0.3 + - - -
293D LEU* 4.0 17.6 - - + +
294D GLY* 3.6 18.4 - - - +
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Residues in contact with GLU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D SER 3.7 1.0 + - - -
210D SER* 2.2 34.9 + - - +
211D VAL 3.1 21.5 + - - -
239D LEU* 3.4 8.4 - - - +
240D ALA* 1.3 80.5 - - - +
242D ILE* 1.3 66.3 + - - +
243D VAL* 3.5 25.0 - - + +
268D LEU* 3.6 9.9 - - - -
270D LYS* 3.0 41.2 + - - +
290D LYS 4.7 0.7 - - - +
291D ALA* 3.5 10.1 - - - +
292D LYS 4.4 0.5 + - - -
293D LEU* 3.2 30.9 + - + +
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Residues in contact with ILE 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D VAL* 3.4 18.6 - - + +
213D ILE* 4.9 6.3 - - + -
227D VAL* 4.2 16.8 - - + -
230D VAL* 3.6 34.1 - - + -
231D ILE* 4.2 14.4 - - + -
239D LEU* 4.1 16.8 - - + -
241D GLU* 1.3 78.7 - - - +
243D VAL* 1.3 63.8 + - - +
244D LEU* 4.0 22.4 - - + -
268D LEU* 3.1 10.1 + - + -
269D VAL* 4.1 16.6 - - + -
270D LYS* 2.9 30.0 + - - +
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Residues in contact with VAL 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D VAL 2.8 11.4 + - - +
212D VAL* 3.4 8.1 - - + +
213D ILE 2.9 26.5 + - - +
241D GLU* 3.5 35.9 - - + +
242D ILE* 1.3 72.1 - - - +
244D LEU* 1.3 61.5 + - - +
245D ILE* 3.2 29.5 + - + -
270D LYS* 3.5 15.7 - - + -
272D PHE* 3.8 15.9 - - + -
287D GLY 4.7 0.4 - - - +
290D LYS* 4.2 5.2 - - + +
291D ALA* 3.6 22.9 - - + -
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Residues in contact with LEU 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ILE* 3.3 24.9 - - + +
215D PHE* 3.9 18.4 - - + -
223D LEU* 4.5 15.3 - - + -
224D MET* 4.8 1.6 - - + -
227D VAL* 3.9 25.1 - - + -
242D ILE* 4.0 9.9 - - + -
243D VAL* 1.3 73.9 - - - +
245D ILE* 1.3 64.4 + - - +
258D LEU* 4.7 8.3 - - + -
262D ILE* 4.7 13.7 - - + -
269D VAL* 4.3 18.4 - - + -
270D LYS 2.7 17.6 + - - +
271D VAL* 3.2 18.1 - - + +
272D PHE 2.9 26.0 + - - -
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Residues in contact with ILE 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D VAL* 4.1 13.5 - - + -
213D ILE 2.8 11.8 + - - +
214D VAL* 3.4 10.2 - - + +
215D PHE* 2.8 33.9 + - - +
243D VAL* 3.2 29.2 - - + -
244D LEU* 1.3 76.5 - - - +
246D ASP* 1.3 63.7 + - - +
272D PHE* 3.8 20.2 - - + +
274D ASN* 3.8 26.0 - - - +
283D ALA* 4.1 19.1 - - + +
286D ILE* 4.7 5.8 - - + -
287D GLY* 3.8 24.9 - - - +
290D LYS* 4.7 4.7 - - + -
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Residues in contact with ASP 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D PHE* 3.5 28.1 - - + -
244D LEU 4.1 0.4 + - - -
245D ILE* 1.3 71.8 - - - +
247D ASP* 1.3 60.6 + - - +
248D PHE* 3.2 2.7 + - - -
249D SER* 2.8 41.6 + - - +
254D LEU* 4.7 2.9 - - - +
255D LYS* 6.1 0.9 - - - +
271D VAL* 4.7 0.2 - - + -
272D PHE 3.2 13.0 + - - +
273D ARG* 3.2 39.5 + - - +
274D ASN* 2.9 32.0 + - - +
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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