Contacts of the strand formed by residues 239 - 246 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A SER* 3.9 7.4 - - - +
211A VAL* 4.0 16.4 - - + -
230A VAL* 4.6 5.2 - - + -
231A ILE* 4.7 12.3 - - + -
234A THR* 4.1 25.8 - - + +
235A PRO 3.6 3.7 + - - +
236A ARG* 3.3 19.1 + - - +
237A LYS 4.6 2.4 - - - +
238A TYR* 1.3 74.2 - - - +
240A ALA* 1.3 65.7 + - - +
241A GLU 3.5 20.6 - - - +
242A ILE* 3.8 23.1 - - + -
268A LEU* 3.4 38.7 - - + +
311A TYR* 6.3 0.2 - - + -
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A THR* 4.4 7.6 - - - -
209A SER 2.8 24.6 + - - +
210A SER* 4.3 0.2 - - - +
237A LYS 5.4 1.1 - - - -
238A TYR 3.3 1.2 + - - -
239A LEU* 1.3 75.0 - - - +
241A GLU* 1.3 61.7 + - - +
268A LEU* 4.0 10.5 - - - +
270A LYS* 4.8 0.3 + - - -
293A LEU* 4.0 18.0 - - + +
294A GLY* 3.9 27.6 - - - +
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Residues in contact with GLU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A SER 3.7 0.4 + - - -
210A SER* 3.1 21.8 + - - +
211A VAL 3.2 20.6 + - - -
239A LEU* 3.5 9.5 - - - +
240A ALA* 1.3 76.9 - - - +
242A ILE* 1.3 64.4 + - - +
243A VAL* 3.5 17.2 - - + +
268A LEU* 3.5 12.3 - - - +
270A LYS* 2.8 50.0 + - + +
290A LYS 4.7 1.4 - - - +
291A ALA* 3.2 3.8 - - - -
292A LYS 3.0 28.6 + - - -
293A LEU* 3.0 21.6 + - + +
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A VAL* 3.4 26.9 - - + +
213A ILE* 4.2 7.6 - - + -
227A VAL* 4.3 11.4 - - + -
230A VAL* 3.8 17.3 - - + -
231A ILE* 3.7 33.4 - - + -
239A LEU* 3.8 21.8 - - + -
241A GLU* 1.3 77.7 - - - +
243A VAL* 1.3 60.9 + - - +
244A LEU* 4.0 21.3 - - + -
268A LEU* 3.1 7.3 + - + -
269A VAL* 3.4 16.5 - - + +
270A LYS* 3.0 25.7 + - - +
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A VAL 2.8 12.5 + - - +
212A VAL* 3.2 7.0 - - + +
213A ILE 3.0 24.3 + - - +
241A GLU* 3.5 37.2 - - + +
242A ILE* 1.3 70.3 - - - +
244A LEU* 1.3 64.2 + - - +
245A ILE* 3.7 28.3 + - + +
270A LYS* 3.5 13.2 - - + +
272A PHE* 3.8 16.8 - - + -
287A GLY 4.7 1.8 - - - +
290A LYS* 4.2 5.2 - - + +
291A ALA* 3.6 25.1 - - + -
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ILE* 3.4 40.8 - - + +
215A PHE* 4.0 14.8 - - + -
223A LEU* 4.6 10.5 - - + -
224A MET* 5.4 0.9 - - + -
227A VAL* 4.0 12.6 - - + -
242A ILE* 4.0 9.6 - - + -
243A VAL* 1.3 75.4 - - - +
245A ILE* 1.3 63.6 + - - +
246A ASP 3.9 0.2 - - - -
258A LEU* 4.7 13.2 - - + -
262A ILE* 4.8 9.6 - - + -
269A VAL* 4.1 19.7 - - + -
270A LYS 2.8 15.2 + - - +
271A VAL* 3.2 18.0 - - + +
272A PHE 3.0 26.3 + - - -
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Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A VAL* 5.2 2.5 - - + -
213A ILE 2.9 9.8 + - - +
214A VAL* 3.5 22.5 - - + +
215A PHE* 2.9 29.7 + - - -
243A VAL* 3.7 22.7 - - + +
244A LEU* 1.3 78.4 - - - +
246A ASP* 1.3 62.5 + - - +
247A ASP 3.3 0.9 + - - -
272A PHE* 3.6 21.3 - - + +
274A ASN* 3.6 28.0 - - - +
283A ALA 3.9 15.0 - - - +
286A ILE* 4.7 2.5 - - + -
287A GLY* 3.8 26.9 - - - +
290A LYS* 4.4 9.0 - - + -
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Residues in contact with ASP 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PHE* 3.5 22.5 - - + -
244A LEU 3.9 1.4 + - - -
245A ILE* 1.3 71.6 - - - +
247A ASP* 1.3 57.2 + - - +
248A PHE* 2.8 8.9 + - - -
249A SER* 2.2 43.0 + - - +
254A LEU 4.4 2.1 - - - +
255A LYS* 5.9 0.5 - - - +
271A VAL* 4.3 2.0 - - + -
272A PHE 3.0 13.3 + - - +
273A ARG* 2.9 41.8 + - - +
274A ASN* 3.1 21.7 + - - +
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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