Contacts of the strand formed by residues 230 - 237 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B GLY* 3.2 4.5 - - - -
130B ARG* 3.0 44.8 + - - +
132B ILE* 5.5 3.8 - - + -
153B VAL* 3.8 37.0 - - + -
222B ILE* 4.4 11.7 - - + -
223B TRP 3.2 8.5 - - - +
224B VAL* 4.9 1.3 - - + -
228B ASP* 3.8 3.4 - - - +
229B HIS* 1.3 87.4 - - + +
231B ARG* 1.3 67.4 + - - +
232B VAL* 4.1 9.5 - - - +
266B PHE* 5.6 0.8 - - + -
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Residues in contact with ARG 231 (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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127B ARG* 3.7 41.6 - - + +
128B THR 3.3 8.8 + - - +
129B GLY* 4.2 4.3 - - - -
221B LEU 3.8 0.9 - - - +
222B ILE* 3.4 5.4 - - - +
223B TRP* 2.9 50.1 + - + +
226B GLU* 4.2 18.4 - - + +
227B GLU* 3.6 33.3 + - + +
228B ASP* 2.5 44.2 + - + +
230B THR* 1.3 81.3 - - - +
232B VAL* 1.3 61.2 + - - +
233B ILE* 4.1 10.4 - - + +
276B LEU* 5.3 2.3 - - - +
281B ASN* 4.0 16.4 - - - +
400B PO4 4.2 10.3 + - - -
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Residues in contact with VAL 232 (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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126B VAL 3.9 0.7 - - - +
127B ARG* 3.4 1.7 - - - -
128B THR* 2.8 46.3 + - + +
130B ARG* 5.0 4.9 - - + -
220B PHE* 3.6 33.4 - - + -
221B LEU 3.7 2.7 - - - -
222B ILE* 4.2 19.3 - - + -
230B THR* 4.3 17.0 - - - +
231B ARG* 1.3 73.9 - - - +
233B ILE* 1.3 67.5 + - - +
248B PHE* 4.1 6.9 - - + -
252B LEU* 4.1 27.1 - - + -
255B VAL* 6.5 0.9 - - + -
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Residues in contact with ILE 233 (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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125B ARG* 3.7 39.3 - - - +
126B VAL 3.5 7.2 - - - +
127B ARG* 4.1 15.5 - - + -
220B PHE* 3.4 9.3 - - - -
221B LEU* 2.7 66.6 + - + +
223B TRP* 4.8 21.1 - - + -
231B ARG* 4.5 9.0 - - + +
232B VAL* 1.3 85.5 - - - +
234B SER* 1.3 71.1 + - - +
235B MET* 4.2 14.2 + - - +
248B PHE* 5.3 0.2 - - - -
400B PO4 5.3 2.9 - - - +
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Residues in contact with SER 234 (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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125B ARG* 3.2 4.7 - - - +
126B VAL* 2.9 35.8 + - - -
219B SER 3.5 4.7 - - - -
220B PHE* 4.3 4.9 - - - -
233B ILE* 1.3 73.0 - - - +
235B MET* 1.3 61.2 + - - +
244B VAL* 2.8 36.3 + - - +
247B ARG* 3.5 19.2 + - - +
248B PHE* 3.9 23.8 + - - -
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Residues in contact with MET 235 (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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124B SER 3.4 6.3 - - - +
125B ARG* 3.9 30.3 - - + +
185B ASP 6.0 0.4 - - - +
186B HIS* 5.6 5.2 - - + +
187B PHE* 3.8 30.1 - - + -
218B LYS 4.6 6.4 - - - +
219B SER* 3.1 23.9 + - - +
221B LEU* 4.9 11.4 - - + -
233B ILE* 4.5 13.0 - - + +
234B SER* 1.3 76.4 + - - +
236B GLU* 1.3 64.0 + - - +
244B VAL* 4.4 1.6 - - - -
247B ARG* 3.3 15.1 + - - -
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Residues in contact with GLU 236 (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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123B SER* 3.5 5.4 - - - -
124B SER* 3.0 30.4 + - - +
219B SER* 5.0 3.1 - - - -
235B MET* 1.3 74.1 - - - +
237B LYS* 1.3 69.1 + - - +
238B GLY 5.9 0.2 - - - -
240B ASN* 3.8 14.3 + - - +
243B ARG* 2.7 51.1 + - - +
244B VAL* 3.7 16.9 - - + +
247B ARG* 3.1 35.4 + - - +
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Residues in contact with LYS 237 (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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122B LEU 3.7 9.4 - - - +
123B SER* 4.2 4.5 - - - +
236B GLU* 1.3 86.7 - - - +
238B GLY* 1.3 60.6 + - - +
240B ASN 5.3 0.2 + - - -
243B ARG* 5.5 1.4 + - - -
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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