Contacts of the strand formed by residues 213 - 218 (chain L) in PDB entry 3IT8
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 ILE 213 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L TYR* 4.3 17.0 - - + +
100L THR* 4.1 19.3 - - + +
103L LEU* 3.5 35.0 - - + -
211L ASP* 6.2 0.2 - - + -
212L VAL* 1.3 86.2 - - - +
214L THR* 1.3 72.1 + - - +
215L LYS* 4.9 4.3 - - + -
245L PRO* 4.6 11.4 - - + +
246L GLY* 4.3 20.0 - - - +
252L TRP* 4.0 21.1 - - + +
283L VAL* 3.8 1.9 - - - -
284L PHE* 2.8 39.0 + - + +
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Residues in contact with THR 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202L CYS* 4.2 2.6 - - - +
204L VAL* 5.5 0.3 - - - +
212L VAL* 5.4 0.2 - - - -
213L ILE* 1.3 81.2 - - - +
215L LYS* 1.3 63.6 + - - +
216L TRP* 3.8 10.9 - - + +
239L ARG* 5.5 4.2 - - - +
252L TRP* 3.5 28.2 - - + -
265L LEU* 5.1 10.0 - - - +
267L ASP* 2.9 33.8 - - + +
281L CYS* 3.3 27.2 - - - -
282L VAL 3.4 4.0 + - - -
283L VAL* 4.1 6.9 - - - +
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Residues in contact with LYS 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L LEU* 4.2 23.5 - - - +
213L ILE* 4.9 3.8 - - + -
214L THR* 1.3 78.7 - - - +
216L TRP* 1.3 63.1 + - - +
217L ILE* 3.9 9.9 - - + -
228L TYR* 3.9 20.6 + - + +
236L GLU* 3.1 44.4 + - + +
281L CYS* 3.8 0.9 - - - -
282L VAL* 2.8 46.1 + - + +
284L PHE* 3.4 33.0 - - + -
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Residues in contact with TRP 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188L VAL* 4.1 9.6 - - + -
200L LEU* 3.8 33.7 - - + -
202L CYS* 3.3 38.6 - - + -
214L THR* 3.8 9.0 - - + +
215L LYS* 1.3 73.7 - - - +
217L ILE* 1.3 60.4 + - - +
236L GLU 2.7 34.0 + - - +
237L TRP* 3.4 20.7 + - + +
239L ARG* 5.2 8.3 - - + -
267L ASP* 2.7 34.1 + - - -
269L VAL* 3.0 30.4 - - + +
279L PRO* 3.7 31.0 - - + -
280L VAL 3.6 13.5 - - - -
281L CYS* 3.8 20.0 - - + -
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Residues in contact with ILE 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215L LYS* 4.4 9.4 - - + +
216L TRP* 1.3 81.0 - - - +
218L GLU* 1.3 77.4 + - - +
221L HIS* 3.9 14.6 - - + -
222L PHE* 3.7 18.8 - - + -
228L TYR* 4.0 15.9 - - + -
234L TYR* 3.8 25.8 - - + -
235L PRO 3.5 23.1 - - - +
236L GLU* 4.2 8.1 - - + +
237L TRP* 5.7 0.4 - - - -
279L PRO* 3.8 3.6 - - - -
280L VAL* 2.8 39.7 + - + +
282L VAL* 3.9 22.0 - - + -
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Residues in contact with GLU 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217L ILE* 1.3 77.2 - - - +
219L SER* 1.3 65.6 + - - +
220L GLU* 3.0 23.3 + - + +
221L HIS* 3.1 34.6 + - + +
222L PHE* 4.0 1.2 - - - -
235L PRO 5.1 0.2 + - - -
237L TRP* 3.7 36.7 - - + +
275L MET* 3.8 21.8 - - + +
276L SER* 3.5 15.4 + - - -
277L SER* 3.5 15.4 + - - +
278L GLN 4.6 3.1 - - - +
279L PRO* 3.9 8.2 - - - +
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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
------------------------------------------------------------
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