Contacts of the strand formed by residues 220 - 224 (chain F) in PDB entry 1QK1
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 PHE 220 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F LEU* 5.1 2.5 - - + -
164F LEU* 4.1 14.6 - - + -
187F PHE* 6.1 0.7 - - - -
213F TRP* 3.5 26.5 - + - -
214F HIS* 3.2 7.8 - - - +
215F ASN* 3.1 39.8 + - - +
218F LYS 3.7 0.8 - - - -
219F SER* 1.3 79.3 - - - +
221F LEU* 1.3 58.7 + - - +
222F ILE* 4.2 16.2 - - + -
232F VAL* 3.7 29.6 - - + -
233F ILE 3.4 13.2 - - - -
234F SER* 4.2 10.3 - - - -
247F ARG* 4.2 18.6 - - + -
248F PHE* 4.3 10.1 - + - -
251F GLY* 3.7 33.9 - - - -
252F LEU* 4.3 1.3 - - - -
255F VAL* 5.0 4.9 - - + -
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Residues in contact with LEU 221 (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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186F HIS 4.8 1.6 - - - +
187F PHE* 3.8 41.1 - - + -
212F ILE* 3.7 16.6 - - + -
213F TRP 3.3 11.9 - - - +
214F HIS* 4.3 4.0 - - + -
219F SER 4.3 0.4 - - - -
220F PHE* 1.3 73.9 - - - +
222F ILE* 1.3 75.9 + - - +
223F TRP* 3.5 39.0 - - + +
231F ARG 3.8 0.7 - - - +
232F VAL* 4.5 0.3 - - - +
233F ILE* 2.8 63.2 + - + +
235F MET* 4.9 11.4 - - + -
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Residues in contact with ILE 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F VAL* 4.9 2.0 - - + -
157F LEU* 3.7 33.0 - - + -
211F GLY 4.2 0.2 - - - +
212F ILE* 3.7 1.7 - - - -
213F TRP* 2.7 60.0 + - + +
220F PHE* 4.2 14.4 - - + -
221F LEU* 1.3 80.9 - - - +
223F TRP* 1.3 75.0 + - - +
224F VAL* 4.0 13.0 + - + +
230F THR* 4.4 14.8 - - + -
231F ARG 3.3 6.5 - - - +
232F VAL* 4.2 22.7 - - + -
255F VAL* 4.7 8.7 - - + -
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Residues in contact with TRP 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F ARG* 6.3 0.9 - - - -
186F HIS 5.1 3.1 - - - -
187F PHE* 2.9 31.4 + - - -
188F LEU 3.9 7.4 - - - -
189F PHE* 3.4 42.1 - + + -
211F GLY 3.9 1.8 - - - -
212F ILE* 4.2 4.3 - - + -
221F LEU* 3.5 26.7 - - + +
222F ILE* 1.3 79.7 - - - +
224F VAL* 1.3 63.0 + - - +
225F ASN 3.9 0.2 + - - -
226F GLU* 3.6 35.5 + - + -
228F ASP 4.9 0.5 - - - +
229F HIS 3.7 0.3 - - - +
230F THR* 3.1 7.6 - - - -
231F ARG* 2.9 49.1 + - + +
233F ILE* 4.8 13.7 - - + -
400F PO4 5.7 5.2 - - - -
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Residues in contact with VAL 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F VAL* 4.6 3.8 - - + -
150F GLU* 4.1 22.9 - - + +
153F VAL* 4.0 25.8 - - + -
154F VAL* 5.5 0.4 - - + -
157F LEU* 5.2 1.6 - - + -
168F TYR* 4.1 20.4 - - + +
189F PHE* 4.2 2.3 - - - -
209F ALA 4.2 4.0 - - - +
210F ARG* 3.3 4.9 - - - +
211F GLY 2.9 34.9 + - - +
222F ILE* 4.3 12.6 - - + +
223F TRP* 1.3 74.9 - - - +
225F ASN* 1.3 89.2 + - - +
226F GLU* 3.4 2.6 + - - -
229F HIS 3.5 7.9 - - - +
230F THR* 4.8 0.2 - - + -
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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
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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