Contacts of the strand formed by residues 121 - 130 (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 VAL 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B PHE* 3.6 30.5 - - + -
117B ASP 3.2 5.5 + - - +
118B GLU* 3.8 19.4 - - - +
120B TYR* 1.3 77.9 - - - +
122B LEU* 1.3 63.8 + - - +
123B SER 3.7 14.1 - - - +
124B SER* 4.0 2.7 - - - +
238B GLY* 3.4 26.6 - - - +
239B GLY* 3.8 10.5 - - - -
290B VAL* 4.0 14.8 - - + -
291B HIS 3.5 2.7 - - - -
292B ILE* 4.0 13.0 - - + -
352B VAL* 4.3 4.3 - - + -
356B ILE* 4.0 16.8 - - + -
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Residues in contact with LEU 122 (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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118B GLU 5.3 3.8 - - - +
120B TYR 4.3 4.0 - - - +
121B VAL* 1.3 75.9 - - - +
123B SER* 1.3 58.1 + - - +
237B LYS* 3.6 6.9 - - - +
238B GLY* 2.7 23.6 + - - -
291B HIS* 2.7 22.9 + - + +
293B LYS* 4.1 35.2 - - + +
328B VAL* 3.9 30.5 - - + -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 3.7 0.7 - - - +
122B LEU* 1.3 81.3 - - - +
124B SER* 1.3 60.5 + - - +
236B GLU 3.5 11.9 - - - -
237B LYS* 4.2 6.7 - - - -
238B GLY 3.2 11.5 + - - -
290B VAL* 3.2 9.2 - - - +
291B HIS* 3.0 51.6 + - - +
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 4.2 1.4 - - - -
121B VAL* 4.0 0.2 - - - +
123B SER* 1.3 74.3 + - - +
125B ARG* 1.3 62.9 + - - +
235B MET* 3.4 2.1 - - - +
236B GLU* 3.0 32.4 + - - +
238B GLY 3.2 14.7 + - - -
239B GLY* 3.4 16.4 - - - -
240B ASN 4.8 0.4 - - - -
241B MET* 4.1 21.1 + - - -
244B VAL* 4.0 18.2 - - - +
289B GLY 3.6 5.6 - - - -
290B VAL* 3.9 9.9 - - - +
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Residues in contact with ARG 125 (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* 1.3 77.1 - - - +
126B VAL* 1.3 64.7 + - - +
127B ARG* 3.7 20.1 - - - +
223B TRP* 6.3 0.8 - - - -
233B ILE* 3.7 30.9 - - - +
234B SER 3.2 12.6 - - - +
235B MET* 3.9 23.9 - - + +
241B MET* 4.3 1.5 - - - +
244B VAL* 4.2 1.6 - - - -
287B ARG* 3.7 14.7 + - - +
288B ALA* 3.5 1.7 - - - -
289B GLY* 2.9 40.6 + - - +
400B PO4 2.9 46.4 + - - -
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Residues in contact with VAL 126 (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* 1.3 80.5 - - - +
127B ARG* 1.3 62.0 + - - +
233B ILE* 3.5 4.0 - - - +
234B SER 2.9 31.2 + - - +
241B MET* 3.8 22.9 - - - -
244B VAL* 3.9 13.9 - - + -
245B PHE* 4.4 15.7 - - + -
248B PHE* 3.7 35.6 - - + -
286B LEU* 3.7 25.8 - - + -
287B ARG 3.4 4.0 - - - +
288B ALA* 4.1 9.9 - - + -
345B VAL* 4.9 1.1 - - + -
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Residues in contact with ARG 127 (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 18.6 - - - +
126B VAL* 1.3 75.3 - - - +
128B THR* 1.3 72.7 + - - +
231B ARG* 3.7 23.4 - - + +
232B VAL 3.4 8.3 - - - +
233B ILE* 4.1 13.0 - - + -
248B PHE* 4.2 2.2 - - - -
276B LEU* 5.9 0.6 - - - +
281B ASN* 2.8 32.3 + - - -
285B GLY 3.0 28.7 + - - +
286B LEU* 3.2 8.7 - - - +
287B ARG* 2.9 52.4 + - - +
336B ARG* 4.1 8.7 - - - +
400B PO4 3.0 48.9 + - - +
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Residues in contact with THR 128 (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* 1.3 84.8 - - - +
129B GLY* 1.3 64.7 + - - +
130B ARG* 3.0 21.8 + - - +
231B ARG* 3.3 7.2 - - - +
232B VAL* 2.8 38.6 + - + +
248B PHE* 3.5 28.7 - - + -
252B LEU* 4.1 11.0 - - + -
284B THR 2.7 26.6 + - - -
285B GLY* 3.3 10.5 + - - -
286B LEU* 4.6 1.3 - - - -
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Residues in contact with GLY 129 (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* 5.7 0.2 - - - +
128B THR* 1.3 78.7 + - - +
130B ARG* 1.3 87.7 + - - -
230B THR 3.2 13.9 - - - -
231B ARG* 4.2 6.7 - - - -
232B VAL* 4.6 1.1 - - - -
274B TYR* 4.6 1.9 - - - +
276B LEU* 3.5 28.8 - - - +
285B GLY 4.2 2.6 + - - -
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Residues in contact with ARG 130 (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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106B LEU* 4.4 10.1 - - - +
128B THR* 3.0 25.4 + - + +
129B GLY* 1.3 98.4 + - - +
131B SER* 1.3 61.8 + - - +
132B ILE* 5.5 1.1 - - + +
229B HIS* 3.4 5.9 + - - +
230B THR* 3.0 43.4 + - - +
232B VAL* 5.0 4.0 - - + -
248B PHE* 5.5 0.6 - - - -
252B LEU* 3.7 35.3 - - + +
266B PHE* 3.8 43.5 - - + -
274B TYR* 3.3 61.1 + - - +
276B LEU* 3.6 5.0 - - - +
284B THR 4.1 2.2 + - - -
341B 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