Contacts of the strand formed by residues 209 - 215 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C THR* 1.3 73.4 + - - +
210C SER* 1.3 62.4 + - - +
211C VAL* 4.1 3.1 - - - -
238C TYR 2.9 8.7 + - - +
239C LEU* 3.8 4.3 - - - +
240C ALA* 2.8 32.4 + - - +
241C GLU 3.8 1.9 + - - +
294C GLY* 4.0 0.9 - - - -
296C VAL* 3.1 22.8 - - - +
298C ILE* 2.8 34.8 - - - +
311C TYR* 3.4 20.0 + - - -
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Residues in contact with SER 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C SER* 1.3 72.5 + - - +
211C VAL* 1.3 63.4 + - - +
212C VAL* 3.8 1.4 + - - -
241C GLU* 3.1 32.4 + - - +
291C ALA* 3.9 18.1 + - - -
294C GLY* 2.6 34.0 + - - -
296C VAL 2.9 6.9 + - - +
297C LEU* 3.6 11.6 - - - +
298C ILE 2.9 22.7 + - - +
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Residues in contact with VAL 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C SER* 5.0 1.3 - - - -
210C SER* 1.3 76.5 - - - +
212C VAL* 1.3 59.4 + - - +
213C ILE* 4.5 12.8 - - + -
230C VAL* 4.3 17.9 - - + -
234C THR* 6.4 0.2 - - + -
239C LEU* 4.0 18.8 - - + -
241C GLU 3.2 5.5 + - - -
242C ILE* 3.5 33.6 - - + +
243C VAL* 2.8 26.0 + - - +
298C ILE* 3.1 37.9 - - + +
300C LEU* 4.5 7.4 - - + -
310C TRP* 4.5 4.5 - - + -
311C TYR* 6.1 0.2 - - + -
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Residues in contact with VAL 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C SER 4.3 7.6 - - - +
211C VAL* 1.3 77.7 - - - +
213C ILE* 1.3 60.9 + - - +
214C VAL* 4.0 6.0 + - + +
243C VAL* 3.2 12.8 - - + +
245C ILE* 5.2 1.8 - - + -
287C GLY* 4.1 18.8 - - - +
291C ALA* 3.9 27.1 - - + -
297C LEU* 4.4 9.2 - - + -
298C ILE 2.9 5.6 + - - +
299C TYR* 3.1 43.1 - - + +
300C LEU 3.0 23.9 + - - +
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Residues in contact with ILE 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C VAL* 4.5 9.6 - - + -
212C VAL* 1.3 76.0 - - - +
214C VAL* 1.3 62.4 + - - +
215C PHE* 3.9 2.0 + - + -
223C LEU* 4.2 12.3 - - + -
226C THR* 3.9 22.4 - - + -
227C VAL* 4.0 13.2 - - + +
230C VAL* 5.2 1.8 - - + -
242C ILE* 4.2 10.1 - - + -
243C VAL 3.0 4.9 + - - -
244C LEU* 3.4 24.9 - - + +
245C ILE* 2.9 21.7 + - - -
300C LEU* 3.3 26.0 - - + +
301C ASP 4.0 0.2 - - - +
302C ALA* 3.5 36.8 - - + -
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Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C VAL* 4.3 6.7 + - + +
213C ILE* 1.3 74.5 - - - +
215C PHE* 1.3 66.7 + - - +
245C ILE* 3.5 20.6 - - + +
247C ASP* 4.3 10.1 - - + -
280C LEU* 4.7 19.6 - - + +
283C ALA* 3.5 29.2 - - + +
284C ARG* 4.0 37.7 - - + +
287C GLY* 6.0 0.2 - - - -
299C TYR* 5.4 0.9 - - + -
300C LEU 4.1 3.7 + - - +
301C ASP* 5.1 1.0 - - - -
302C ALA* 3.3 19.4 + - - +
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Residues in contact with PHE 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ILE 4.3 6.3 - - - -
214C VAL* 1.3 80.2 - - - +
216C HIS* 1.3 63.3 + - - +
217C ASN 4.2 3.4 - - - -
218C GLU* 4.2 9.4 - - + -
223C LEU* 4.2 20.6 - - + -
244C LEU* 4.0 19.5 - - + -
245C ILE 2.9 12.0 + - - -
246C ASP* 3.4 36.6 - - + -
247C ASP* 2.9 28.8 + - - +
249C SER* 3.4 20.4 - - - -
254C LEU* 4.0 23.6 - - + -
258C LEU* 4.1 19.1 - - + -
271C VAL* 4.4 4.0 - - + -
302C ALA* 3.7 19.7 - - + -
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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