Contacts of the strand formed by residues 210 - 215 (chain F) in PDB entry 5IJ7
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 THR 210 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F TRP* 3.4 8.3 - - - +
205F ASN* 2.8 38.5 + - - +
208F THR* 2.8 30.4 + - - +
209F ASP* 1.3 77.2 - - - +
211F LEU* 1.3 58.9 + - - +
212F VAL 3.6 0.2 + - - -
263F SER* 3.4 10.0 - - - +
266F TYR* 3.6 34.5 - - + -
275F PHE* 3.8 28.5 - - + -
572T LEU* 6.3 0.2 - - - -
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Residues in contact with LEU 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F ARG* 3.6 47.6 - - + +
203F LEU 3.4 17.5 - - - +
204F TRP* 4.0 17.3 - - + -
210F THR* 1.3 72.5 - - - +
212F VAL* 1.3 61.5 + - - +
213F ALA 3.5 16.2 - - - +
214F ILE* 3.8 21.1 - - + -
275F PHE* 3.5 11.4 - - - +
277F SER* 2.7 39.6 + - - +
570T THR* 4.0 11.9 - - - -
572T LEU* 4.0 18.7 - - + +
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Residues in contact with VAL 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191F LEU* 4.5 9.9 - - + -
203F LEU* 2.8 28.4 + - + +
204F TRP 4.2 2.7 - - - -
205F ASN* 3.9 19.7 - - + +
210F THR 3.6 0.2 + - - -
211F LEU* 1.3 73.0 - - - +
213F ALA* 1.3 56.9 + - - +
256F MET* 4.1 4.0 - - + -
259F ALA* 3.8 34.5 - - + +
260F ILE* 3.8 14.4 - - + +
263F SER* 3.6 26.5 - - - +
275F PHE* 4.2 8.0 - - - -
277F SER* 3.7 1.4 - - - -
278F GLN* 3.1 24.1 + - - +
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Residues in contact with ALA 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202F ARG* 3.6 0.7 - - - -
203F LEU* 3.0 26.6 + - + -
211F LEU* 3.5 11.4 - - - +
212F VAL* 1.3 81.0 - - - +
214F ILE* 1.3 63.0 - - - +
215F PHE* 3.9 15.9 - - + -
256F MET* 3.9 31.6 - - + -
277F SER* 4.8 0.4 - - - -
278F GLN* 3.3 16.4 - - + +
280F ILE* 4.2 4.5 - - + -
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Residues in contact with ILE 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B SER* 5.6 1.6 - - - +
200F ALA* 3.9 24.7 - - + -
201F LEU 3.5 4.9 - - - +
202F ARG* 4.2 15.3 - - + +
211F LEU* 3.8 28.0 - - + -
213F ALA* 1.3 74.2 - - - +
215F PHE* 1.3 62.2 + - - +
216F GLY* 3.5 10.7 + - - +
277F SER* 4.8 1.6 - - - -
278F GLN 2.8 11.6 + - - +
279F LYS* 3.8 22.0 - - + -
280F ILE 2.9 25.8 + - - -
569T ASP 3.4 26.0 - - - +
570T THR* 4.1 10.8 - - + -
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Residues in contact with PHE 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F LEU* 4.4 4.5 - - + -
199F HIS 4.4 0.5 - - - +
200F ALA* 3.4 2.3 - - - -
201F LEU* 2.8 65.8 + - + +
203F LEU* 3.8 24.7 - - + -
213F ALA* 3.9 7.6 - - + -
214F ILE* 1.3 68.7 - - - +
216F GLY* 1.3 56.2 + - - +
221F HIS 5.8 0.2 + - - -
237F ILE* 4.3 11.9 - - + -
249F TRP* 3.6 52.4 - + + -
250F ARG 5.0 1.8 - - - -
251F ILE* 3.9 17.9 - - + -
256F MET* 3.9 28.0 - - + -
280F ILE* 3.6 30.1 - - + -
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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