Contacts of the strand formed by residues 230 - 237 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H GLY* 3.1 5.0 - - - -
130H ARG* 3.0 46.4 + - - +
132H ILE* 5.5 4.0 - - + -
153H VAL* 3.8 35.4 - - + -
222H ILE* 4.4 12.8 - - + -
223H TRP 3.2 8.3 - - - +
224H VAL* 4.9 2.0 - - + -
228H ASP* 3.9 3.5 - - - +
229H HIS* 1.3 89.0 - - + +
231H ARG* 1.3 67.9 + - - +
232H VAL* 4.1 9.3 - - - +
266H PHE* 5.6 0.6 - - + -
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Residues in contact with ARG 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H ARG* 3.7 41.6 - - + +
128H THR 3.3 8.2 + - - +
129H GLY* 4.2 3.8 - - - -
221H LEU 3.7 0.9 - - - +
222H ILE* 3.3 6.1 - - - +
223H TRP* 2.9 49.9 + - + +
226H GLU* 4.2 17.7 + - + +
227H GLU* 3.6 35.6 + - + +
228H ASP* 2.5 44.0 + - + +
230H THR* 1.3 81.3 - - - +
232H VAL* 1.3 61.6 + - - +
233H ILE* 4.1 10.3 - - + +
276H LEU* 5.2 2.3 - - - +
281H ASN* 4.0 16.1 - - - +
400H PO4 4.2 10.5 + - - -
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Residues in contact with VAL 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H VAL 3.9 0.5 - - - +
127H ARG* 3.4 4.0 - - - -
128H THR* 2.7 47.2 + - + +
130H ARG* 5.0 4.3 - - + -
220H PHE* 3.6 33.7 - - + -
221H LEU 3.7 2.2 - - - -
222H ILE* 4.2 19.1 - - + -
230H THR* 4.3 17.3 - - - +
231H ARG* 1.3 74.4 - - - +
233H ILE* 1.3 66.5 + - - +
248H PHE* 4.1 7.0 - - + -
252H LEU* 4.1 28.3 - - + -
255H VAL* 6.5 0.9 - - + -
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Residues in contact with ILE 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H ARG* 3.7 39.5 - - - +
126H VAL 3.5 7.9 - - - +
127H ARG* 4.1 16.6 - - + -
219H SER 4.0 0.3 - - - +
220H PHE* 3.4 9.8 - - - -
221H LEU* 2.8 64.6 + - + +
223H TRP* 4.8 22.0 - - + -
231H ARG* 4.5 9.2 - - + +
232H VAL* 1.3 84.4 - - - +
234H SER* 1.3 70.3 + - - +
235H MET* 4.2 14.0 + - - +
400H PO4 5.1 2.2 - - - +
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Residues in contact with SER 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H ARG* 3.2 5.2 - - - +
126H VAL 2.9 34.9 + - - -
219H SER 3.5 4.5 - - - -
220H PHE* 4.3 4.5 - - - -
233H ILE* 1.3 73.6 - - - +
235H MET* 1.3 62.0 + - - +
244H VAL* 2.8 35.8 + - - +
247H ARG* 3.5 19.1 + - - -
248H PHE* 3.9 24.5 + - - -
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Residues in contact with MET 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H SER 3.4 6.1 - - - +
125H ARG* 3.9 31.6 - - + +
185H ASP 6.0 0.4 - - - +
186H HIS* 5.7 5.2 - - + +
187H PHE* 3.8 29.2 - - + -
218H LYS 4.6 6.2 - - - +
219H SER* 3.1 23.7 + - - +
221H LEU* 4.9 10.8 - - + -
233H ILE* 4.5 13.0 - - + +
234H SER* 1.3 77.3 + - - +
236H GLU* 1.3 64.5 + - - +
244H VAL* 4.4 1.6 - - - -
247H ARG* 3.2 15.8 + - - -
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Residues in contact with GLU 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H SER* 3.4 5.4 - - - -
124H SER* 3.0 30.6 + - - +
219H SER* 5.0 3.8 - - - -
235H MET* 1.3 82.5 - - - +
237H LYS* 1.3 69.7 + - - +
238H GLY 4.2 0.6 - - - +
240H ASN* 3.8 15.0 + - - +
243H ARG* 2.7 49.5 + - - +
244H VAL* 3.7 16.0 - - + +
247H ARG* 3.1 28.2 + - - +
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Residues in contact with LYS 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H LEU 3.6 9.6 - - - +
123H SER* 4.2 5.4 - - - +
236H GLU* 1.3 87.2 - - - +
238H GLY* 1.3 60.5 + - - +
240H ASN* 5.3 0.3 + - - +
243H 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