Contacts of the strand formed by residues 121 - 130 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116F PHE* 3.6 30.5 - - + -
117F ASP 3.2 5.2 + - - +
118F GLU* 3.8 19.0 - - - +
120F TYR* 1.3 76.8 - - - +
122F LEU* 1.3 62.9 + - - +
123F SER 3.7 13.7 - - - +
124F SER* 4.0 3.8 - - - +
238F GLY* 3.4 25.3 - - - +
239F GLY* 3.8 12.1 - - - -
290F VAL* 4.0 12.6 - - + -
291F HIS 3.5 2.7 - - - -
292F ILE* 4.0 21.3 - - + -
352F VAL* 4.3 4.7 - - + -
356F ILE* 4.1 8.7 - - + -
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Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F GLU 5.4 3.4 - - - +
120F TYR 4.3 4.0 - - - +
121F VAL* 1.3 75.2 - - - +
123F SER* 1.3 56.1 + - - +
237F LYS* 3.6 6.8 - - - +
238F GLY* 2.7 23.5 + - - -
291F HIS* 2.7 24.8 + - + +
293F LYS* 3.8 32.3 - - + +
328F VAL* 3.9 34.8 - - + -
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Residues in contact with SER 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F VAL* 3.7 0.9 - - - +
122F LEU* 1.3 81.5 - - - +
124F SER* 1.3 59.9 + - - +
236F GLU 3.4 12.3 - - - -
237F LYS* 4.2 6.5 - - - -
238F GLY 3.2 12.2 + - - -
290F VAL* 3.2 8.7 - - - +
291F HIS* 3.0 51.8 + - - +
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Residues in contact with SER 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F PHE* 4.2 1.6 - - - -
121F VAL* 4.0 0.2 - - - +
123F SER* 1.3 75.4 + - - +
125F ARG* 1.3 63.2 + - - +
235F MET* 3.4 1.9 - - - +
236F GLU* 3.0 32.9 + - - +
238F GLY 3.1 15.5 + - - -
239F GLY* 3.4 15.5 - - - -
240F ASN 4.8 0.4 - - - -
241F MET* 4.1 21.1 + - - -
244F VAL* 3.9 19.1 - - - +
289F GLY 3.6 4.9 - - - -
290F VAL* 3.8 9.7 - - - +
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Residues in contact with ARG 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F SER* 1.3 79.1 - - - +
126F VAL* 1.3 63.6 + - - +
127F ARG* 3.7 20.1 - - - +
223F TRP* 6.3 0.6 - - - -
233F ILE* 3.7 31.9 - - - +
234F SER 3.2 11.4 - - - +
235F MET* 3.8 23.1 - - + +
241F MET* 4.2 1.1 - - - +
244F VAL* 4.2 2.0 - - - +
287F ARG* 3.7 13.5 + - - +
288F ALA* 3.4 1.7 - - - -
289F GLY 2.9 41.2 + - - +
400F PO4 2.7 47.9 + - - -
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Residues in contact with VAL 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ARG* 1.3 80.7 - - - +
127F ARG* 1.3 63.3 + - - +
233F ILE* 3.5 4.1 - - - +
234F SER 2.9 31.5 + - - -
241F MET* 3.8 23.3 - - - -
244F VAL* 3.9 13.2 - - + -
245F PHE* 4.4 16.6 - - + -
248F PHE* 3.7 29.9 - - + -
286F LEU* 3.7 31.6 - - + -
287F ARG 3.4 3.6 - - - +
288F ALA* 4.1 9.9 - - + -
345F VAL* 4.9 1.1 - - + -
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Residues in contact with ARG 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ARG* 3.7 18.8 - - - +
126F VAL* 1.3 76.7 - - - +
128F THR* 1.3 72.7 + - - +
231F ARG* 3.7 25.0 - - + +
232F VAL 3.4 5.4 - - - +
233F ILE* 4.1 15.9 - - + -
248F PHE* 4.2 2.2 - - - -
276F LEU* 5.9 0.6 - - - +
281F ASN* 2.8 31.5 + - - +
285F GLY 3.0 28.2 + - - +
286F LEU* 3.2 8.8 - - - +
287F ARG* 2.9 54.1 + - - +
336F ARG* 4.2 8.9 - - - +
400F PO4 2.9 47.5 + - - +
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Residues in contact with THR 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F ARG* 1.3 86.7 - - - +
129F GLY* 1.3 65.9 + - - +
130F ARG* 3.0 22.2 + - - +
231F ARG* 3.3 7.6 - - - +
232F VAL* 2.8 37.9 + - + -
248F PHE* 3.5 28.7 - - + -
252F LEU* 4.1 11.7 - - + -
284F THR 2.7 27.1 + - - -
285F GLY* 3.3 10.0 + - - -
286F LEU* 4.6 1.3 - - - -
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Residues in contact with GLY 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F ARG* 5.7 0.2 - - - +
128F THR* 1.3 77.9 + - - +
130F ARG* 1.3 87.6 + - - -
230F THR 3.2 13.0 - - - -
231F ARG* 4.2 7.4 - - - +
232F VAL 4.6 0.9 - - - -
274F TYR* 4.7 1.9 - - - +
276F LEU* 3.4 32.2 - - - +
285F GLY 4.2 0.8 + - - -
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Residues in contact with ARG 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 4.4 9.7 - - - +
128F THR* 3.0 24.9 + - + +
129F GLY* 1.3 99.6 + - - +
131F SER* 1.3 62.0 + - - +
132F ILE* 5.6 1.1 - - + +
229F HIS* 3.4 5.4 + - - +
230F THR* 3.0 42.2 + - - +
232F VAL* 5.1 4.0 - - + -
248F PHE* 5.5 0.8 - - - -
252F LEU* 3.7 34.7 - - + +
266F PHE* 3.8 44.9 - - + -
274F TYR* 3.3 61.3 + - - +
276F LEU* 3.6 4.7 - - - +
284F THR 4.2 2.6 + - - -
341F 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