Contacts of the strand formed by residues 230 - 237 (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 THR 230 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129F GLY* 3.2 4.3 - - - -
130F ARG* 3.0 46.7 + - - +
132F ILE* 5.5 3.4 - - + -
153F VAL* 3.7 38.4 - - + -
222F ILE* 4.4 12.3 - - + -
223F TRP 3.1 9.0 - - - +
224F VAL* 4.8 1.6 - - + -
228F ASP* 3.9 3.9 - - - +
229F HIS* 1.3 87.5 - - + +
231F ARG* 1.3 66.9 + - - +
232F VAL* 4.1 8.9 - - - +
266F PHE* 5.6 0.8 - - + -
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Residues in contact with ARG 231 (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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127F ARG* 3.7 41.0 - - + +
128F THR 3.3 9.1 + - - +
129F GLY* 4.2 3.6 - - - -
221F LEU 3.8 0.9 - - - +
222F ILE* 3.3 5.5 - - - +
223F TRP* 2.9 50.3 + - + +
226F GLU* 4.2 18.4 + - + +
227F GLU* 3.6 36.7 + - + +
228F ASP* 2.5 44.4 + - + +
230F THR* 1.3 80.9 - - - +
232F VAL* 1.3 61.9 + - - +
233F ILE* 4.1 10.3 + - + +
276F LEU* 5.2 2.5 - - - +
281F ASN* 4.0 16.0 - - - +
400F PO4 4.4 9.7 + - - -
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Residues in contact with VAL 232 (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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126F VAL 3.9 0.9 - - - +
127F ARG* 3.4 3.5 - - - -
128F THR* 2.8 45.4 + - + +
130F ARG* 5.1 4.3 - - + -
220F PHE* 3.7 33.4 - - + -
221F LEU 3.7 2.7 - - - -
222F ILE* 4.2 19.1 - - + -
230F THR* 4.3 16.6 - - - +
231F ARG* 1.3 74.3 - - - +
233F ILE* 1.3 65.8 + - - +
248F PHE* 4.0 7.4 - - + -
252F LEU* 4.1 28.0 - - + -
255F VAL* 6.5 1.6 - - + -
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Residues in contact with ILE 233 (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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125F ARG* 3.7 39.9 - - - +
126F VAL 3.5 7.9 - - - +
127F ARG* 4.1 17.0 - - + -
219F SER 4.1 0.2 - - - +
220F PHE* 3.4 9.3 - - - -
221F LEU* 2.8 65.6 + - + +
223F TRP* 4.8 21.1 - - + -
231F ARG* 4.6 9.2 - - + +
232F VAL* 1.3 83.8 - - - +
234F SER* 1.3 70.9 + - - +
235F MET* 4.3 14.0 + - - +
400F PO4 5.6 1.6 - - - +
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Residues in contact with SER 234 (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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125F ARG* 3.2 5.0 - - - +
126F VAL 2.9 34.2 + - - -
219F SER 3.5 5.4 - - - -
220F PHE* 4.2 4.5 - - - -
233F ILE* 1.3 73.0 - - - +
235F MET* 1.3 59.9 + - - +
244F VAL* 2.8 35.6 + - - +
247F ARG* 3.5 20.3 + - - -
248F PHE* 3.8 24.9 + - - -
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Residues in contact with MET 235 (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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124F SER 3.4 6.3 - - - +
125F ARG* 3.8 31.2 - - + +
185F ASP 6.0 0.7 - - - +
186F HIS* 5.6 5.6 - - + +
187F PHE* 3.8 30.1 - - + -
218F LYS 4.5 6.6 - - - +
219F SER* 3.1 23.5 + - - +
221F LEU* 4.9 12.6 - - + -
233F ILE* 4.4 12.6 - - + -
234F SER* 1.3 75.7 + - - +
236F GLU* 1.3 63.4 + - - +
244F VAL* 4.4 1.8 - - - -
247F ARG* 3.3 15.3 + - - -
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Residues in contact with GLU 236 (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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123F SER* 3.4 5.1 - - - -
124F SER* 3.0 30.3 + - - +
219F SER* 4.9 3.8 - - - -
235F MET* 1.3 83.2 - - - +
237F LYS* 1.3 69.7 + - - +
238F GLY 5.9 0.4 - - - -
240F ASN* 3.8 14.5 + - - +
243F ARG* 2.7 49.3 + - - +
244F VAL* 3.7 15.6 - - + +
247F ARG* 3.1 28.4 + - - +
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Residues in contact with LYS 237 (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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122F LEU 3.7 8.5 - - - +
123F SER* 4.2 4.7 - - - +
236F GLU* 1.3 87.6 - - - +
238F GLY* 1.3 61.6 + - - +
240F ASN 5.3 0.5 + - - -
243F ARG* 5.5 1.0 + - - -
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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