Contacts of the helix formed by residues 112 - 134 (chain F) in PDB entry 7C17
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701 T 4.3 3.6 - - - +
110F LEU* 5.4 5.6 - - + -
111F LEU* 1.3 79.6 - - - +
113F ARG* 1.3 63.0 + - - +
114F GLU* 2.6 35.1 + - - +
115F GLY* 3.6 3.8 + - - +
116F GLU* 2.9 26.2 + - - +
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Residues in contact with ARG 113 (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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681 A 5.2 2.6 + - - -
112F THR* 1.3 73.6 - - - +
114F GLU* 1.3 62.9 + - - +
116F GLU* 3.2 18.6 + - - +
117F ILE* 3.0 43.9 + - + +
424F GLY 4.7 12.3 + - - -
425F TYR 6.0 1.2 - - - -
426F LYS* 3.5 41.4 - - - +
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Residues in contact with GLU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F THR* 2.6 23.2 + - - +
113F ARG* 1.3 78.8 - - - +
115F GLY* 1.3 68.5 + - - +
117F ILE* 3.3 17.4 - - + +
118F ASP* 2.9 31.0 + - - +
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Residues in contact with GLY 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F LEU* 3.6 20.4 - - - -
112F THR* 3.6 8.6 + - - -
113F ARG 3.3 0.4 - - - -
114F GLU* 1.3 90.9 - - - +
116F GLU* 1.3 58.2 - - - +
118F ASP* 3.6 6.4 - - - +
119F ILE* 2.9 35.3 + - - +
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Residues in contact with GLU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701 T 4.4 17.7 - - - +
111F LEU* 3.9 15.8 - - + +
112F THR 2.9 17.4 + - - +
113F ARG* 3.4 24.1 - - - +
115F GLY* 1.3 74.9 - - - +
117F ILE* 1.3 60.9 + - + +
119F ILE* 3.4 3.1 + - - +
120F ALA* 2.9 26.2 + - - +
379F MET* 5.1 6.1 - - - +
419F PHE* 5.8 3.8 - - + -
425F TYR 5.5 0.4 - - - -
426F LYS* 3.3 16.8 - - - +
427F PHE* 2.4 47.1 + - + +
428F SER* 4.0 2.4 + - - -
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Residues in contact with ILE 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F ARG* 3.0 32.1 + - + +
114F GLU* 3.3 24.9 - - + +
116F GLU* 1.3 78.6 - - + +
118F ASP* 1.3 58.1 + - - +
120F ALA* 3.6 7.9 - - + +
121F LYS* 2.9 53.5 + - - +
421F TYR* 5.1 6.2 - - + -
425F TYR 6.0 1.6 - - - +
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Residues in contact with ASP 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F GLU* 2.9 21.7 + - - +
115F GLY* 3.6 8.5 - - - +
116F GLU 3.2 0.4 - - - -
117F ILE* 1.3 75.6 - - - +
119F ILE* 1.3 65.1 + - + +
121F LYS* 3.3 10.7 + - - +
122F ARG* 2.9 33.4 + - + +
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Residues in contact with ILE 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F LEU* 3.7 24.9 - - + -
115F GLY 2.9 21.1 + - - +
116F GLU 4.0 3.6 - - - +
118F ASP* 1.3 75.1 - - + +
120F ALA* 1.3 59.5 + - - +
122F ARG* 3.3 15.2 + - - +
123F ILE* 2.9 28.1 + - + +
375F ALA* 4.0 10.1 - - - +
378F GLU* 3.4 34.5 - - + +
379F MET* 3.8 41.5 - - + -
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Residues in contact with ALA 120 (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 GLU* 2.9 18.7 + - + +
117F ILE* 3.6 8.7 - - + +
119F ILE* 1.3 76.9 - - - +
121F LYS* 1.3 56.6 + - - +
123F ILE* 3.3 5.7 + - - +
124F GLU 2.9 22.2 + - - -
379F MET* 4.1 10.6 - - + +
419F PHE* 4.5 12.6 - - + -
421F TYR* 3.5 43.5 - - + -
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Residues in contact with LYS 121 (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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117F ILE* 2.9 43.7 + - - +
118F ASP* 3.3 8.9 + - - +
120F ALA* 1.3 72.6 - - - +
122F ARG* 1.3 60.9 + - + +
124F GLU* 3.3 3.4 + - - +
125F ASP* 2.9 38.0 + - - +
421F TYR* 3.7 26.5 - - + +
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Residues in contact with ARG 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 ASP* 2.9 19.8 + - + +
119F ILE* 3.3 18.2 + - - +
121F LYS* 1.3 74.3 - - - +
123F ILE* 1.3 59.4 + - - +
125F ASP* 3.3 11.2 + - - +
126F GLY* 2.9 25.5 + - - -
371F LYS* 4.4 35.0 + - - +
374F ARG* 5.0 11.7 - - - +
375F ALA* 4.2 16.1 - - + +
378F GLU* 3.1 33.9 + - - -
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Residues in contact with ILE 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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119F ILE 2.9 17.1 + - - +
120F ALA* 3.5 11.0 - - - +
122F ARG* 1.3 77.0 - - - +
124F GLU* 1.3 58.0 + - - +
126F GLY* 3.3 1.7 + - - -
127F ILE* 2.9 46.8 + - + +
372F ALA* 4.3 4.7 - - + +
375F ALA* 3.8 11.7 - - + +
376F LYS* 3.7 48.5 - - + +
379F MET* 3.9 19.1 - - + -
416F VAL* 4.1 20.6 - - + +
417F ASP* 6.4 0.2 - - - -
419F PHE* 6.6 0.2 - - + -
421F TYR* 5.9 3.4 - - + -
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Residues in contact with GLU 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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120F ALA 2.9 10.2 + - - +
121F LYS* 3.5 7.7 - - - +
123F ILE* 1.3 78.2 - - - +
125F ASP* 1.3 77.6 + - - +
127F ILE* 3.4 6.3 + - - +
128F ASN* 2.9 56.0 + - - +
421F TYR* 3.3 35.8 + - + +
422F ARG* 2.8 33.1 + - - +
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Residues in contact with ASP 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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121F LYS* 2.9 22.3 + - - +
122F ARG* 3.7 9.8 - - - +
123F ILE 3.3 0.2 - - - -
124F GLU* 1.3 97.5 - - - +
126F GLY* 1.3 56.7 + - - +
128F ASN* 3.8 4.2 - - - +
129F GLN* 2.9 32.6 + - - +
371F LYS* 5.7 10.3 - - + +
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Residues in contact with GLY 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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122F ARG 2.9 15.1 + - - -
123F ILE 3.3 3.3 + - - -
125F ASP* 1.3 76.2 - - - +
127F ILE* 1.3 61.7 + - - +
129F GLN* 4.2 4.2 - - - +
130F VAL* 3.4 23.9 + - - +
368F GLY 3.9 9.4 - - - +
371F LYS* 5.0 8.6 - - - +
372F ALA* 4.0 26.6 - - - +
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Residues in contact with ILE 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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123F ILE* 2.9 36.9 + - + +
124F GLU* 3.8 6.5 - - - +
125F ASP 3.2 0.2 - - - -
126F GLY* 1.3 77.3 - - - +
128F ASN* 1.3 62.2 + - - +
130F VAL* 3.3 8.4 + - - +
131F GLN* 2.9 38.4 + - + +
261F LEU* 5.3 11.7 - - + -
266F PHE* 5.4 12.1 - - + -
372F ALA* 5.6 1.8 - - + -
376F LYS* 5.2 11.0 - - - +
416F VAL 6.1 0.2 - - - +
417F ASP* 6.0 7.2 - - + +
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Residues in contact with ASN 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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124F GLU* 2.9 47.9 + - - +
125F ASP* 4.2 4.0 - - - +
127F ILE* 1.3 77.7 - - - +
129F GLN* 1.3 60.3 + - - +
131F GLN* 3.5 11.5 - - - +
132F CYS* 2.9 32.8 + - - +
257F LYS* 3.3 31.3 - - - +
422F ARG* 4.0 5.6 + - - +
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Residues in contact with GLN 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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125F ASP 2.9 19.1 + - - +
126F GLY* 4.2 6.3 - - - +
127F ILE 3.3 0.2 - - - -
128F ASN* 1.3 77.0 - - - +
130F VAL* 1.3 57.2 + - - +
132F CYS* 3.3 16.5 - - - -
133F SER* 2.9 36.1 + - - -
364F ARG* 4.5 26.0 + - - +
367F ILE* 5.7 4.7 - - + -
368F GLY* 4.1 22.9 - - - +
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Residues in contact with VAL 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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126F GLY 3.4 19.5 - - - +
127F ILE* 3.3 5.3 + - - +
129F GLN* 1.3 75.2 - - - +
131F GLN* 1.3 60.5 + - - +
133F SER* 3.3 5.8 + - - -
134F VAL* 3.0 31.7 + - + +
266F PHE* 4.6 21.3 - - + -
270F VAL* 5.1 9.4 - - + -
273F MET* 5.4 2.7 - - + -
364F ARG 5.7 0.9 - - - +
365F MET* 4.1 23.3 - - + +
368F GLY* 4.1 22.2 - - - +
369F GLU* 4.4 15.5 - - - +
372F ALA* 5.8 0.4 - - + -
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Residues in contact with GLN 131 (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 ILE* 2.9 32.8 + - + +
128F ASN* 3.6 20.8 - - - +
129F GLN 3.2 0.4 - - - -
130F VAL* 1.3 78.5 - - - +
132F CYS* 1.3 57.4 + - - +
134F VAL* 3.3 24.8 - - - +
135F ALA 3.9 0.7 + - - -
256F PHE* 3.5 31.1 - - + -
257F LYS* 4.3 11.1 + - - +
259F PHE* 4.2 16.4 - - - +
261F LEU* 3.9 25.9 - - + +
266F PHE* 3.3 29.6 - - + -
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Residues in contact with CYS 132 (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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128F ASN 2.9 24.8 + - - +
129F GLN* 3.3 28.7 - - - -
131F GLN* 1.3 75.7 - - - +
133F SER* 1.3 64.2 + - - +
134F VAL 3.3 0.4 - - - -
135F ALA* 3.4 19.9 + - - +
136F GLU* 4.0 12.6 - - - +
253F SER* 4.9 2.4 - - - +
256F PHE* 5.6 0.2 - - - -
257F LYS* 5.3 7.4 - - - +
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Residues in contact with SER 133 (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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129F GLN* 2.9 24.8 + - - -
130F VAL* 3.3 7.1 + - - -
131F GLN 3.5 0.2 - - - -
132F CYS* 1.3 78.9 - - - +
134F VAL* 1.3 60.8 + - - +
135F ALA 3.2 1.4 + - - -
136F GLU* 3.5 25.9 + - - +
137F TYR 4.1 2.1 + - - -
361F ILE* 4.4 5.6 - - - +
364F ARG* 4.5 20.4 - - - -
365F MET* 2.9 38.7 - - - +
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Residues in contact with VAL 134 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F VAL* 3.0 18.2 + - + +
131F GLN* 3.3 26.9 - - - +
133F SER* 1.3 74.5 + - - +
135F ALA* 1.3 63.4 + - - +
136F GLU 3.2 0.2 - - - -
137F TYR* 3.2 12.1 + - + +
140F ALA* 3.4 15.3 - - + +
256F PHE* 3.8 19.7 - - + -
266F PHE* 6.3 0.7 - - + -
269F LEU* 3.9 27.4 - - + -
273F MET* 3.7 32.1 - - + -
365F MET* 3.8 7.6 - - + -
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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