Contacts of the strand formed by residues 121 - 130 (chain C) 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 VAL 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C PHE* 3.6 30.7 - - + -
117C ASP 3.2 7.7 + - - +
118C GLU* 3.9 18.7 - - - +
120C TYR* 1.3 78.1 - - - +
122C LEU* 1.3 62.9 + - - +
123C SER 3.7 14.4 - - - +
124C SER* 4.0 4.0 - - - +
238C GLY* 3.4 26.2 - - - +
239C GLY* 3.8 11.0 - - - -
290C VAL* 4.0 13.0 - - + -
291C HIS 3.5 2.7 - - - -
292C ILE* 4.0 21.1 - - + -
352C VAL* 4.3 7.2 - - + -
356C ILE* 4.3 3.8 - - + -
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C GLU 5.4 4.7 - - - +
119C ARG 6.0 0.4 - - - +
120C TYR 4.3 5.6 - - - +
121C VAL* 1.3 75.5 - - - +
123C SER* 1.3 57.2 + - - +
237C LYS* 3.6 6.8 - - - +
238C GLY* 2.7 23.5 + - - -
291C HIS* 2.8 23.7 + - + +
293C LYS* 4.0 27.4 - - + -
322C THR* 4.5 11.9 - - + -
328C VAL* 4.0 29.8 - - + -
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Residues in contact with SER 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C VAL* 3.7 0.7 - - - +
122C LEU* 1.3 81.2 - - - +
124C SER* 1.3 61.8 + - - +
236C GLU 3.4 12.3 - - - -
237C LYS* 4.2 6.7 - - - -
238C GLY 3.2 11.1 + - - -
290C VAL* 3.2 8.7 - - - +
291C HIS* 3.1 50.9 + - - +
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Residues in contact with SER 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C PHE* 4.2 1.7 - - - -
121C VAL* 4.0 0.2 - - - +
123C SER* 1.3 75.7 + - - +
125C ARG* 1.3 63.8 + - - +
235C MET* 3.4 1.9 - - - +
236C GLU* 3.0 31.9 + - - +
238C GLY 3.1 15.2 + - - -
239C GLY* 3.5 15.8 - - - -
240C ASN 4.8 0.4 - - - -
241C MET* 4.2 20.8 + - - -
244C VAL* 4.0 19.6 - - - +
289C GLY 3.6 5.4 - - - -
290C VAL* 3.8 10.0 - - - +
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Residues in contact with ARG 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C SER* 6.4 0.2 - - - -
124C SER* 1.3 77.1 - - - +
126C VAL* 1.3 63.7 + - - +
127C ARG* 3.7 21.1 - - - +
221C LEU* 6.1 0.2 - - - +
223C TRP* 6.3 0.4 - - - -
233C ILE* 3.7 30.5 - - - +
234C SER 3.2 11.7 - - - +
235C MET* 3.8 23.5 - - + +
241C MET* 4.2 1.7 - - - +
244C VAL* 4.2 1.8 - - - -
287C ARG* 3.7 13.8 + - - +
288C ALA* 3.4 2.1 - - - -
289C GLY* 2.9 42.1 + - - +
400C PO4 2.8 50.1 + - - -
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ARG* 1.3 79.5 - - - +
127C ARG* 1.3 62.4 + - - +
233C ILE* 3.5 3.7 - - - +
234C SER 2.9 31.5 + - - +
241C MET* 3.8 23.3 - - - -
244C VAL* 3.9 12.1 - - + -
245C PHE* 4.4 16.6 - - + -
248C PHE* 3.6 35.7 - - + -
286C LEU* 3.7 25.8 - - + -
287C ARG 3.4 3.8 - - - +
288C ALA* 4.1 10.3 - - + -
345C VAL* 4.9 0.9 - - + -
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Residues in contact with ARG 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ARG* 3.7 19.1 - - - +
126C VAL* 1.3 75.5 - - - +
128C THR* 1.3 72.2 + - - +
231C ARG* 3.7 25.5 - - + +
232C VAL 3.4 8.5 - - - +
233C ILE* 4.1 13.2 - - + -
248C PHE* 4.2 2.5 - - - -
276C LEU* 5.8 0.6 - - - +
281C ASN* 2.8 32.1 + - - -
285C GLY 2.9 28.4 + - - +
286C LEU* 3.2 9.5 - - - +
287C ARG* 2.9 52.9 + - - +
336C ARG* 4.1 8.5 - - - +
400C PO4 2.9 45.2 + - - +
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Residues in contact with THR 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ARG* 1.3 86.5 - - - +
129C GLY* 1.3 65.7 + - - +
130C ARG* 3.0 22.4 + - - +
231C ARG* 3.3 7.3 - - - +
232C VAL* 2.8 37.8 + - + +
248C PHE* 3.5 29.8 - - + -
252C LEU* 4.1 10.5 - - + -
284C THR 2.7 27.1 + - - -
285C GLY* 3.3 10.4 + - - -
286C LEU* 4.6 1.3 - - - -
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Residues in contact with GLY 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C THR* 1.3 79.8 + - - +
130C ARG* 1.3 83.8 + - - -
230C THR 3.2 13.5 - - - -
231C ARG* 4.3 6.9 - - - -
232C VAL* 4.6 1.3 - - - -
274C TYR* 4.7 2.6 - - - +
276C LEU* 3.5 29.4 - - - +
285C GLY 4.2 2.6 + - - -
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Residues in contact with ARG 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU* 4.4 10.5 - - - +
128C THR* 3.0 25.7 + - - +
129C GLY* 1.3 99.0 + - - +
131C SER* 1.3 63.1 + - - +
132C ILE* 5.5 1.3 - - + +
229C HIS* 3.4 5.2 + - - +
230C THR* 2.9 43.6 + - - +
232C VAL* 5.0 4.3 - - + -
248C PHE* 5.5 0.8 - - - -
252C LEU* 3.6 34.9 - - + +
266C PHE* 3.8 44.8 - - + -
274C TYR* 3.4 61.2 + - - +
276C LEU* 3.6 4.1 - - - +
284C THR 4.2 1.8 + - - -
341C GLU* 4.6 6.7 + - - -
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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