Contacts of the strand formed by residues 121 - 130 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116G PHE* 3.6 31.4 - - + -
117G ASP 3.2 7.7 + - - +
118G GLU* 3.9 18.5 - - - +
120G TYR* 1.3 76.6 - - - +
122G LEU* 1.3 64.6 + - - +
123G SER 3.7 14.6 - - - +
124G SER* 3.9 4.0 - - - +
238G GLY* 3.4 26.1 - - - +
239G GLY* 3.8 10.8 - - - -
290G VAL* 4.0 12.6 - - + -
291G HIS 3.5 3.1 - - - -
292G ILE* 4.0 20.0 - - + -
352G VAL* 4.3 4.5 - - + -
356G ILE* 4.3 6.3 - - + -
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Residues in contact with LEU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G GLU 5.4 4.0 - - - +
120G TYR 4.3 0.4 - - - +
121G VAL* 1.3 75.4 - - - +
123G SER* 1.3 54.8 + - - +
237G LYS* 3.6 6.8 - - - +
238G GLY* 2.7 24.6 + - - -
291G HIS* 2.7 23.9 + - + +
293G LYS* 3.7 44.6 - - + +
328G VAL* 3.9 29.6 - - + -
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Residues in contact with SER 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G VAL* 3.7 0.7 - - - +
122G LEU* 1.3 81.4 - - - +
124G SER* 1.3 61.0 + - - +
236G GLU 3.4 11.7 - - - -
237G LYS* 4.2 7.0 - - - -
238G GLY 3.2 12.0 + - - -
290G VAL* 3.2 9.4 - - - +
291G HIS* 3.0 51.7 + - - +
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Residues in contact with SER 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G PHE* 4.2 1.4 - - - -
123G SER* 1.3 75.0 + - - +
125G ARG* 1.3 63.5 + - - +
235G MET* 3.4 2.1 - - - +
236G GLU* 3.0 32.1 + - - +
238G GLY 3.1 15.4 + - - -
239G GLY* 3.5 15.8 - - - -
240G ASN 4.9 0.4 - - - -
241G MET* 4.2 21.4 + - - -
244G VAL* 4.0 19.2 - - - +
289G GLY 3.5 5.4 - - - -
290G VAL* 3.9 10.0 - - - +
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Residues in contact with ARG 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G SER* 1.3 78.7 - - - +
126G VAL* 1.3 64.8 + - - +
127G ARG* 3.7 21.9 - - - +
223G TRP* 6.3 1.0 - - - -
233G ILE* 3.7 29.4 - - - +
234G SER 3.2 12.8 - - - +
235G MET* 3.8 23.1 - - + +
241G MET* 4.2 1.9 - - - +
244G VAL* 4.2 1.6 - - - -
287G ARG* 3.7 15.4 + - - +
288G ALA* 3.5 1.9 - - - -
289G GLY* 2.9 41.7 + - - +
400G PO4 2.4 47.3 + - - -
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Residues in contact with VAL 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G ARG* 1.3 79.5 - - - +
127G ARG* 1.3 63.0 + - - +
233G ILE* 3.5 4.2 - - - +
234G SER 2.9 32.6 + - - +
241G MET* 3.9 22.7 - - - -
244G VAL* 3.9 13.5 - - + -
245G PHE* 4.4 16.4 - - + -
248G PHE* 3.6 34.3 - - + -
286G LEU* 3.7 26.0 - - + -
287G ARG 3.5 3.6 - - - +
288G ALA* 4.1 10.5 - - + -
345G VAL* 4.9 0.9 - - + -
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Residues in contact with ARG 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G ARG* 3.7 19.1 - - - +
126G VAL* 1.3 75.8 - - - +
128G THR* 1.3 73.2 + - - +
231G ARG* 3.6 25.0 - - + +
232G VAL 3.4 8.5 - - - +
233G ILE* 4.0 14.4 - - + -
248G PHE* 4.2 2.2 - - - -
276G LEU* 5.9 0.4 - - - +
281G ASN* 2.8 32.3 + - - +
285G GLY* 3.0 29.9 + - - +
286G LEU* 3.2 9.2 - - - +
287G ARG* 2.9 52.5 + - - +
336G ARG* 4.2 8.3 - - - +
400G PO4 3.0 44.8 + - - +
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Residues in contact with THR 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G ARG* 1.3 84.6 - - - +
129G GLY* 1.3 66.1 + - - +
130G ARG* 3.0 22.2 + - - +
231G ARG* 3.4 7.1 - - - +
232G VAL* 2.8 39.2 + - + +
248G PHE* 3.5 28.9 - - + -
252G LEU* 4.0 11.0 - - + -
284G THR 2.7 26.3 + - - -
285G GLY* 3.3 10.1 + - - -
286G LEU* 4.6 1.3 - - - -
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Residues in contact with GLY 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G THR* 1.3 79.6 + - - +
130G ARG* 1.3 82.7 + - - -
230G THR 3.2 13.7 - - - -
231G ARG* 4.3 7.4 - - - -
232G VAL* 4.6 1.1 - - - -
274G TYR* 4.6 2.4 - - - +
276G LEU* 3.5 31.3 - - - +
285G GLY 4.2 0.4 + - - -
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Residues in contact with ARG 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G LEU* 4.4 9.9 - - - +
128G THR* 3.0 26.5 + - - +
129G GLY* 1.3 97.9 + - - +
131G SER* 1.3 62.2 + - - +
132G ILE* 5.5 1.7 - - + +
229G HIS* 3.4 5.5 + - - +
230G THR* 2.9 43.7 + - - +
232G VAL* 5.0 4.5 - - + -
248G PHE* 5.4 0.6 - - - -
252G LEU* 3.6 34.4 - - + +
266G PHE* 3.7 44.4 - - + -
274G TYR* 3.3 62.0 + - - +
276G LEU* 3.6 4.5 - - - +
284G THR 4.2 1.8 + - - -
341G GLU* 4.6 6.9 + - - -
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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