Contacts of the helix formed by residues 112 - 136 (chain L) in PDB entry 6PST
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 112 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L LEU 5.3 2.5 - - - +
111L LEU* 1.3 82.0 - - - +
113L ARG* 1.3 56.2 + - - +
114L GLU* 3.9 11.4 - - - +
115L GLY* 3.0 14.6 + - - -
116L GLU* 2.8 38.9 + - - +
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Residues in contact with ARG 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L THR* 1.3 73.6 - - - +
114L GLU* 1.3 64.7 + - - +
116L GLU* 3.0 15.3 + - - +
117L ILE* 3.0 37.7 + - + +
424L GLY 3.3 20.0 + - - -
425L TYR 4.3 1.4 + - - -
426L LYS* 3.8 40.6 - - - +
52O A 2.9 29.6 + - - -
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Residues in contact with GLU 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L THR* 3.9 11.7 - - - +
113L ARG* 1.3 79.7 - - - +
115L GLY* 1.3 57.9 + - - +
117L ILE* 3.1 11.8 + - + +
118L ASP* 2.7 50.0 + - - +
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Residues in contact with GLY 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L LEU* 4.3 15.7 - - - -
112L THR* 3.0 15.1 + - - -
114L GLU* 1.3 85.7 - - - +
116L GLU* 1.3 57.8 + - - +
118L ASP* 3.2 11.2 + - - +
119L ILE* 2.9 32.4 + - - +
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Residues in contact with GLU 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L LEU* 3.8 25.7 - - + +
112L THR 2.8 19.1 + - - +
113L ARG* 3.0 25.6 + - - +
115L GLY* 1.3 69.5 - - - +
117L ILE* 1.3 65.0 + - + +
119L ILE* 3.8 3.6 - - - +
120L ALA* 2.9 31.6 + - - +
379L MET* 4.3 9.1 - - + +
383L ASN* 4.0 15.5 + - - +
419L PHE* 4.9 6.8 - - + -
426L LYS* 4.6 6.2 - - - +
427L PHE* 3.5 41.5 + - + +
428L SER* 4.9 5.4 + - - -
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Residues in contact with ILE 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L ARG* 3.0 43.5 + - + +
114L GLU* 3.1 13.7 + - + +
116L GLU* 1.3 80.4 - - + +
118L ASP* 1.3 60.7 + - - +
120L ALA* 3.3 1.9 + - - +
121L LYS* 2.9 51.7 + - - +
419L PHE* 5.8 2.5 - - + -
421L TYR* 3.8 37.3 - - + +
424L GLY* 5.9 6.3 - - - +
425L TYR 5.6 5.6 - - - +
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Residues in contact with ASP 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L GLU* 2.7 38.9 + - - +
115L GLY* 3.2 10.8 + - - +
117L ILE* 1.3 77.9 - - - +
119L ILE* 1.3 59.3 + - + +
121L LYS* 2.9 25.8 + - + +
122L ARG* 2.9 31.1 + - - +
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Residues in contact with ILE 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L LEU* 3.4 38.4 - - + -
115L GLY 2.9 16.7 + - - +
116L GLU* 3.9 3.6 - - - +
117L ILE 3.3 0.2 - - - -
118L ASP* 1.3 77.9 - - + +
120L ALA* 1.3 57.7 + - - +
122L ARG* 3.2 19.5 + - - +
123L ILE* 2.9 29.7 + - + +
375L ALA* 3.5 25.4 - - + +
378L GLU* 4.2 13.0 - - + +
379L MET* 3.5 37.5 - - + +
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Residues in contact with ALA 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116L GLU 2.9 18.3 + - - +
117L ILE 3.8 0.7 - - - +
119L ILE* 1.3 77.4 - - - +
121L LYS* 1.3 57.5 + - - +
123L ILE* 3.3 8.6 + - - +
124L GLU* 2.9 27.2 + - - +
379L MET* 4.2 7.2 - - + +
419L PHE* 3.9 26.7 - - + +
421L TYR* 3.3 27.7 - - + +
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Residues in contact with LYS 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L ILE* 2.9 39.5 + - - +
118L ASP* 2.9 37.6 + - + +
120L ALA* 1.3 76.9 - - - +
122L ARG* 1.3 57.4 + - + +
124L GLU* 3.3 5.8 + - - +
125L ASP* 2.9 27.7 + - - +
421L TYR* 3.0 34.1 + - + +
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Residues in contact with ARG 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118L ASP 2.9 18.5 + - - +
119L ILE* 3.7 19.8 - - - +
120L ALA 3.2 0.4 - - - -
121L LYS* 1.3 76.5 - - + +
123L ILE* 1.3 61.4 + - - +
125L ASP* 3.2 5.3 + - - +
126L GLY* 2.9 25.1 + - - -
371L LYS* 3.3 40.7 + - + +
372L ALA* 4.7 0.2 - - - -
374L ARG* 4.9 0.8 - - - +
375L ALA* 3.7 27.8 - - + +
378L GLU* 3.8 33.9 + - - +
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Residues in contact with ILE 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L ILE* 2.9 21.6 + - + +
120L ALA* 3.6 5.8 - - - +
122L ARG* 1.3 75.1 - - - +
124L GLU* 1.3 64.5 + - - +
126L GLY* 3.3 1.0 + - - -
127L ILE* 3.0 42.3 + - + +
372L ALA* 3.7 8.9 - - + +
375L ALA* 3.2 25.1 - - + +
376L LYS* 3.3 48.7 - - + +
379L MET* 4.8 4.9 - - + -
416L VAL* 4.4 17.3 - - + +
417L ASP* 6.5 0.2 - - - -
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Residues in contact with GLU 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L ALA 2.9 12.5 + - - +
121L LYS* 3.5 8.5 - - - +
122L ARG 3.2 0.2 - - - -
123L ILE* 1.3 78.5 - - - +
125L ASP* 1.3 55.6 + - - +
127L ILE* 3.2 16.4 - - + +
128L ASN* 2.9 34.1 + - + +
421L TYR* 3.4 22.5 + - - -
422L ARG* 3.4 37.2 + - - +
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Residues in contact with ASP 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L LYS 2.9 17.1 + - - +
122L ARG* 3.2 7.4 + - - +
124L GLU* 1.3 76.8 - - - +
126L GLY* 1.3 57.6 + - - +
128L ASN* 3.2 6.1 + - - +
129L GLN* 2.9 31.3 + - - +
371L LYS* 2.8 33.8 + - - +
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Residues in contact with GLY 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122L ARG 2.9 13.5 + - - -
123L ILE 3.3 2.4 + - - -
125L ASP* 1.3 77.0 - - - +
127L ILE* 1.3 61.8 + - - +
129L GLN* 3.2 2.2 + - - -
130L VAL* 3.0 18.5 + - - +
368L GLY* 3.4 35.2 - - - +
371L LYS* 4.3 8.3 - - - +
372L ALA* 3.8 10.1 - - - -
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Residues in contact with ILE 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L ILE* 3.0 25.4 + - + +
124L GLU* 3.2 22.4 - - + +
126L GLY* 1.3 73.8 - - - +
128L ASN* 1.3 60.5 + - + +
130L VAL* 3.3 10.4 + - - +
131L GLN* 2.8 64.8 + - + +
266L PHE* 5.4 2.3 - - + -
372L ALA* 3.9 13.2 - - + -
376L LYS* 5.3 7.2 - - - +
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Residues in contact with ASN 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L GLU* 2.9 22.1 + - + +
125L ASP* 3.6 8.7 - - - +
126L GLY 3.1 0.2 - - - -
127L ILE* 1.3 76.5 - - + +
129L GLN* 1.3 58.4 + - - +
131L GLN* 3.0 22.7 + - - +
132L CYS* 2.9 40.6 + - - -
257L LYS* 5.4 2.9 - - - -
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Residues in contact with GLN 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125L ASP* 2.9 22.3 + - - +
126L GLY* 3.6 6.6 - - - +
128L ASN* 1.3 73.9 - - - +
130L VAL* 1.3 64.5 + - - +
132L CYS* 3.3 8.3 + - + +
133L SER* 2.9 24.7 + - - +
364L ARG* 2.6 39.6 + - + +
367L ILE* 3.1 21.6 - - - +
368L GLY* 3.0 24.3 + - - +
371L LYS* 4.9 8.1 - - - +
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Residues in contact with VAL 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126L GLY 3.0 8.7 + - - +
127L ILE* 3.5 11.7 - - - +
129L GLN* 1.3 75.7 - - - +
131L GLN* 1.3 63.5 + - - +
133L SER* 3.8 1.4 - - - -
134L VAL* 2.9 24.0 + - + +
266L PHE* 3.6 28.3 - - + -
270L VAL* 5.0 3.6 - - + -
365L MET* 3.0 45.5 - - + +
368L GLY 3.6 2.2 - - - -
369L GLU* 3.1 32.3 - - + +
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Residues in contact with GLN 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127L ILE* 2.8 45.3 + - + +
128L ASN* 3.0 33.1 + - - +
130L VAL* 1.3 77.7 - - - +
132L CYS* 1.3 58.2 + - - +
134L VAL* 3.4 5.6 + - - +
135L ALA* 2.8 31.7 + - - +
256L PHE* 5.5 0.9 - - - -
257L LYS* 6.1 4.3 - - + -
266L PHE* 5.0 15.5 - - + -
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Residues in contact with CYS 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L ASN* 2.9 35.6 + - - +
129L GLN* 3.8 6.5 - - + +
131L GLN* 1.3 76.6 - - - +
133L SER* 1.3 63.4 + - - +
135L ALA* 3.7 6.2 - - - +
136L GLU* 2.9 39.0 + - + +
257L LYS* 4.5 26.9 - - + -
364L ARG* 5.5 3.1 - - - +
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Residues in contact with SER 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L GLN* 2.9 14.3 + - - +
130L VAL 3.8 0.4 - - - -
132L CYS* 1.3 78.7 - - - +
134L VAL* 1.3 61.4 + - - +
136L GLU* 3.4 13.3 + - - +
137L TYR* 3.9 0.7 + - - +
273L MET* 5.1 0.4 - - - -
361L ILE* 3.2 35.8 - - - +
364L ARG* 3.0 23.4 + - - +
365L MET* 2.8 44.6 + - - -
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Residues in contact with VAL 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L VAL 2.9 15.8 + - - +
131L GLN 3.8 3.8 - - - +
133L SER* 1.3 76.9 - - - +
135L ALA* 1.3 62.0 + - - +
137L TYR* 2.9 20.6 + - - +
140L ALA* 3.8 6.8 - - + +
141L ILE* 6.1 0.4 - - + -
256L PHE* 5.8 4.3 - - + -
266L PHE* 4.3 28.5 - - + -
269L LEU* 4.9 9.4 - - + -
270L VAL* 4.4 9.0 - - + +
273L MET* 3.0 48.6 - - + +
365L MET* 3.5 22.4 - - - -
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Residues in contact with ALA 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L GLN 2.8 19.9 + - - +
132L CYS* 3.2 6.7 + - - +
134L VAL* 1.3 78.8 - - - +
136L GLU* 1.3 53.5 + - - +
137L TYR 3.1 8.8 + - - +
138L PRO* 5.6 0.2 - - - +
141L ILE* 4.3 16.2 - - - +
249L ILE* 5.4 1.2 - - - +
253L SER* 2.3 33.3 + - - +
256L PHE* 3.9 28.9 - - + -
257L LYS* 4.7 8.3 - - + -
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Residues in contact with GLU 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132L CYS* 2.9 26.0 + - + +
133L SER* 3.7 5.0 - - - +
134L VAL 3.1 0.6 - - - -
135L ALA* 1.3 78.0 - - - +
137L TYR* 1.3 55.8 + - - +
138L PRO* 4.0 5.2 - - - +
249L ILE* 5.4 11.4 - - + +
250L LEU* 5.1 12.2 - - + +
253L SER* 3.9 9.6 - - - +
361L ILE* 3.0 38.5 - - + +
364L ARG* 2.8 35.9 + - - -
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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
------------------------------------------------------------
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