Contacts of the strand formed by residues 230 - 237 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D GLY* 3.2 4.2 - - - -
130D ARG* 3.0 45.9 + - - +
132D ILE* 5.5 2.7 - - + -
153D VAL* 3.6 38.4 - - + -
222D ILE* 4.4 11.4 - - + -
223D TRP 3.2 9.0 - - - +
224D VAL* 4.9 1.6 - - + -
228D ASP* 3.9 2.8 - - - +
229D HIS* 1.3 88.9 - - + +
231D ARG* 1.3 66.5 + - - +
232D VAL* 4.3 8.5 - - - +
266D PHE* 5.6 1.1 - - + -
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Residues in contact with ARG 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ARG* 3.6 42.8 - - + +
128D THR 3.4 8.0 + - - +
129D GLY* 4.3 4.2 - - - -
221D LEU 3.8 0.9 - - - +
222D ILE* 3.3 5.4 - - - +
223D TRP* 2.9 51.1 + - + +
226D GLU* 4.2 17.7 - - + +
227D GLU* 3.6 35.6 + - + +
228D ASP* 2.5 45.6 + - + +
230D THR* 1.3 80.4 - - - +
232D VAL* 1.3 61.4 + - - +
233D ILE* 4.5 9.6 - - + +
276D LEU* 5.2 2.1 - - - +
281D ASN* 4.0 14.7 - - - +
400D PO4 4.3 10.5 + - - -
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D VAL 3.9 0.5 - - - +
127D ARG* 3.4 3.1 - - - -
128D THR* 2.8 47.1 + - + +
130D ARG* 5.0 4.9 - - + -
220D PHE* 3.7 32.8 - - + -
221D LEU 3.7 2.2 - - - -
222D ILE* 4.2 19.5 - - + -
230D THR* 4.3 17.3 - - - +
231D ARG* 1.3 73.7 - - - +
233D ILE* 1.3 66.1 + - - +
248D PHE* 4.0 7.0 - - + -
252D LEU* 4.1 27.4 - - + -
255D VAL* 6.5 1.1 - - + -
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Residues in contact with ILE 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ARG* 3.7 40.4 - - - +
126D VAL 3.5 7.2 - - - +
127D ARG* 4.0 15.3 - - + -
219D SER 4.0 0.2 - - - +
220D PHE* 3.4 9.5 - - - -
221D LEU* 2.8 65.9 + - + +
223D TRP* 4.8 20.9 - - + -
231D ARG* 4.6 8.7 - - + +
232D VAL* 1.3 84.8 - - - +
234D SER* 1.3 70.8 + - - +
235D MET* 4.2 14.0 + - - +
248D PHE* 5.3 0.2 - - - -
400D PO4 5.0 2.9 - - - +
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Residues in contact with SER 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ARG* 3.2 4.5 - - - +
126D VAL* 2.9 35.4 + - - -
219D SER 3.5 5.2 - - - -
220D PHE* 4.3 4.5 - - - -
233D ILE* 1.3 73.3 - - - +
235D MET* 1.3 61.4 + - - +
244D VAL* 2.8 35.8 + - - +
247D ARG* 3.5 18.7 + - - +
248D PHE* 3.8 24.0 + - - -
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Residues in contact with MET 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D SER 3.4 6.1 - - - +
125D ARG* 3.8 30.7 - - + +
185D ASP 6.0 0.4 - - - +
186D HIS* 5.6 5.4 - - + +
187D PHE* 3.8 30.7 - - + -
218D LYS 4.6 9.8 - - - +
219D SER* 3.2 20.7 + - - +
221D LEU* 4.8 11.4 - - + -
233D ILE* 4.4 13.2 - - + +
234D SER* 1.3 76.7 + - - +
236D GLU* 1.3 64.1 + - - +
244D VAL* 4.3 1.1 - - - -
247D ARG* 3.2 15.7 + - - -
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Residues in contact with GLU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D SER* 3.4 5.6 - - - -
124D SER* 3.0 30.1 + - - +
219D SER* 5.0 3.6 - - - -
235D MET* 1.3 82.5 - - - +
237D LYS* 1.3 68.3 + - - +
238D GLY 5.9 0.4 - - - -
240D ASN* 3.8 14.8 + - - +
243D ARG* 2.8 49.0 + - - +
244D VAL* 3.7 16.4 - - + +
247D ARG* 3.1 28.0 + - - +
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Residues in contact with LYS 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D LEU 3.7 7.9 - - - +
123D SER* 4.2 6.1 - - - +
236D GLU* 1.3 86.6 - - - +
238D GLY* 1.3 60.7 + - - +
239D GLY 4.2 0.3 + - - -
243D ARG* 5.5 1.2 + - - -
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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