Contacts of the strand formed by residues 209 - 215 (chain B) 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 SER 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B THR* 1.3 73.8 + - - +
210B SER* 1.3 62.7 + - - +
211B VAL* 4.0 3.4 - - - -
238B TYR 2.8 7.0 + - - +
239B LEU* 3.7 6.4 - - - +
240B ALA* 2.7 30.9 + - - +
241B GLU 3.7 2.1 + - - +
294B GLY* 4.0 1.1 - - - -
296B VAL* 3.2 30.6 - - - +
298B ILE* 3.7 13.3 - - - +
311B TYR* 2.9 37.4 + - - -
315B VAL* 4.2 1.2 - - - +
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B SER* 1.3 74.5 - - - +
211B VAL* 1.3 62.7 + - - +
212B VAL* 3.8 1.2 + - - -
240B ALA* 4.0 0.2 - - - +
241B GLU* 3.1 32.5 + - - +
291B ALA* 4.0 17.6 + - - -
294B GLY* 2.7 34.6 + - - -
296B VAL 2.9 7.5 + - - +
297B LEU* 3.6 12.2 - - - +
298B ILE 2.9 22.9 + - - +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B SER* 5.0 2.7 - - - +
210B SER* 1.3 75.2 - - - +
212B VAL* 1.3 60.1 + - - +
213B ILE* 4.5 12.3 - - + -
230B VAL* 4.7 8.3 - - + -
239B LEU* 4.0 19.5 - - + -
241B GLU 3.2 5.9 + - - -
242B ILE* 3.5 35.4 - - + +
243B VAL* 2.8 26.9 + - - +
298B ILE* 3.1 26.9 - - + +
300B LEU* 4.7 11.2 - - + -
310B TRP* 4.5 16.6 - - + -
311B TYR* 6.1 0.4 - - + -
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B SER 4.3 7.9 - - - +
211B VAL* 1.3 78.1 - - - +
213B ILE* 1.3 61.8 + - - +
214B VAL* 4.0 5.8 + - + -
243B VAL* 3.2 12.1 - - + +
245B ILE* 5.2 2.2 - - + -
287B GLY* 4.1 19.1 - - - +
291B ALA* 4.0 27.6 - - + -
297B LEU* 4.4 9.6 - - + -
298B ILE 2.9 6.0 + - - +
299B TYR* 3.0 43.3 - - + -
300B LEU 3.1 24.8 + - - +
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B VAL* 4.5 9.9 - - + -
212B VAL* 1.3 77.3 - - - +
214B VAL* 1.3 61.3 + - - +
215B PHE* 3.9 2.1 + - + -
223B LEU* 4.2 13.2 - - + -
226B THR* 3.9 21.5 - - + -
227B VAL* 4.1 13.9 - - + -
230B VAL* 5.2 1.6 - - + -
242B ILE* 4.2 10.1 - - + -
243B VAL 3.0 4.6 + - - -
244B LEU* 3.4 25.9 - - + +
245B ILE* 2.9 22.0 + - - -
300B LEU* 3.6 22.4 - - + +
302B ALA* 3.4 38.4 - - + +
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B VAL* 4.0 7.4 + - + -
213B ILE* 1.3 75.4 - - - +
215B PHE* 1.3 70.8 + - - +
245B ILE* 3.6 20.4 - - + +
247B ASP* 4.5 6.1 - - + -
280B LEU* 4.7 20.3 - - + +
283B ALA* 3.5 29.4 - - + +
284B ARG* 4.0 37.2 - - + +
299B TYR* 5.4 0.7 - - + -
300B LEU 4.2 4.1 + - - +
301B ASP* 5.3 0.3 - - - -
302B ALA* 3.3 20.1 + - - +
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Residues in contact with PHE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ILE 4.3 6.7 - - - -
214B VAL* 1.3 79.6 - - - +
216B HIS* 1.3 64.5 + - - +
217B ASN 4.2 1.3 - - - -
218B GLU* 4.2 11.7 - - + -
223B LEU* 4.2 20.2 - - + -
244B LEU* 4.0 21.8 - - + -
245B ILE 3.0 12.4 + - - +
246B ASP* 3.4 41.3 - - + -
247B ASP* 3.0 27.0 + - - +
249B SER* 3.5 14.1 - - - -
254B LEU* 3.5 20.4 - - + -
258B LEU* 4.0 21.8 - - + -
271B VAL* 4.4 3.1 - - + -
302B ALA* 3.7 18.4 - - + -
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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