Contacts of the strand formed by residues 213 - 218 (chain B) in PDB entry 1F0K
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 VAL 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B PRO* 3.8 5.5 - - - +
184B VAL* 3.2 20.6 - - + +
186B VAL* 3.9 16.4 - - + -
206B ALA* 5.2 3.4 - - - -
209B LEU* 3.9 30.3 - - + -
210B GLY 3.4 14.4 + - - +
211B ASP* 3.2 4.0 - - - +
212B SER* 1.3 92.6 + - - +
214B THR* 1.3 61.0 + - - +
215B ILE* 4.0 24.7 - - + -
238B GLN* 5.3 0.9 + - - -
239B HIS* 3.4 13.3 - - + +
319B LEU* 5.3 5.4 - - + +
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Residues in contact with THR 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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214A THR* 5.0 7.8 + - - -
183B PRO* 3.9 17.5 - - + +
184B VAL 3.0 3.9 + - - +
185B ARG* 3.3 32.8 - - + +
186B VAL* 2.8 25.1 + - - +
213B VAL* 1.3 75.2 - - - +
215B ILE* 1.3 64.2 + - - +
239B HIS* 3.8 7.1 + - - -
254B TRP* 3.8 11.6 - - + +
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Residues in contact with ILE 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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186B VAL* 3.3 22.9 - - + +
188B VAL* 3.9 11.7 - - + -
202B MET* 4.5 15.5 - - + +
205B VAL* 5.7 0.9 - - + -
206B ALA* 3.8 29.8 - - + -
213B VAL* 4.0 15.7 - - + -
214B THR* 1.3 81.4 + - - +
216B TRP* 1.3 73.7 + - - +
217B HIS* 3.8 4.0 - - + +
231B TYR* 3.6 25.8 - - + +
239B HIS* 3.1 24.4 + - + +
240B LYS* 3.0 25.5 + - - +
254B TRP* 4.2 3.0 - - - -
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Residues in contact with TRP 216 (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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228A GLU* 5.8 0.2 - - - -
237A PRO* 4.2 24.9 - - + -
238A GLN* 4.1 25.4 - - + +
186B VAL 3.0 4.4 + - - -
187B LEU* 3.5 10.7 - - + +
188B VAL 2.9 23.4 + - - +
215B ILE* 1.3 75.3 - - - +
217B HIS* 1.3 67.2 + - - +
240B LYS* 3.3 39.4 - - + +
242B THR* 3.1 26.4 + - + -
244B PHE 5.5 0.2 - - - -
245B ILE* 3.7 29.6 - - + +
247B ASP 5.4 1.1 - - - -
250B ALA* 5.8 0.4 - - + -
251B ALA* 3.8 30.7 - - + -
254B TRP* 3.6 37.2 - + + -
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Residues in contact with HIS 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL* 3.8 21.9 - - + +
198B LEU 3.4 27.1 - - - -
199B ASN* 2.8 30.4 + - - -
202B MET* 3.8 4.4 - - + +
203B PRO* 4.7 0.2 - - + -
215B ILE* 4.0 4.0 - - + -
216B TRP* 1.3 76.4 - - - +
218B GLN* 1.3 75.2 + - - +
219B SER* 3.6 4.7 - - - -
227B VAL* 3.8 13.4 - - + +
231B TYR* 2.8 42.8 + + + +
240B LYS 2.7 12.3 + - - +
241B VAL* 3.2 7.6 - - + +
242B THR* 2.9 26.7 + - - +
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Residues in contact with GLN 218 (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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188B VAL* 2.8 16.8 + - - +
189B VAL* 3.5 12.9 - - - +
190B GLY* 2.9 38.3 + - - +
191B GLY* 2.8 33.6 - - - +
199B ASN* 4.4 0.9 - - - +
216B TRP* 4.1 0.6 + - - -
217B HIS* 1.3 77.2 + - - +
219B SER* 1.3 60.2 + - - +
220B GLY* 3.5 2.3 + - - -
242B THR* 3.2 4.9 - - - +
243B GLU 3.1 22.9 - - - +
244B PHE* 3.6 26.5 - - - -
245B ILE* 3.8 23.8 - - + +
248B MET* 4.6 3.5 - - - +
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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