Contacts of the helix formed by residues 116 - 137 (chain F) in PDB entry 7KHC
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 GLU 116 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115F GLY* 1.3 76.6 - - - +
117F ILE* 1.3 58.5 + - - +
119F ILE* 3.2 20.2 - - - +
120F ALA* 2.8 30.8 + - - +
376F LYS* 4.9 5.5 + - - -
379F MET* 3.4 5.6 - - - +
413F MET* 4.7 7.3 - - - +
416F VAL* 3.2 43.2 - - + +
417F ASP* 3.8 21.3 + - - +
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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
----------------------------------------------------------
115F GLY 5.1 4.7 - - - +
116F GLU* 1.3 76.9 - - - +
118F ASP* 1.3 67.0 + - + +
120F ALA* 3.4 8.5 + - + -
121F LYS* 2.9 33.3 + - + +
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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
----------------------------------------------------------
115F GLY* 3.1 18.3 + - - +
117F ILE* 1.3 85.1 - - + +
119F ILE* 1.3 60.3 + - + +
121F LYS* 3.1 7.7 + - - +
122F ARG* 2.9 45.5 + - - +
375F ALA* 4.5 3.8 - - - +
378F GLU* 6.0 1.3 - - - -
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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
----------------------------------------------------------
115F GLY* 2.5 34.7 + - - +
116F GLU* 3.2 21.1 - - - +
118F ASP* 1.3 75.5 - - + +
120F ALA* 1.3 61.0 + - + +
122F ARG* 3.7 1.4 - - - +
123F ILE* 2.7 36.8 + - + +
375F ALA* 2.9 44.6 - - + +
376F LYS* 3.8 23.6 - - + +
378F GLU* 4.9 2.5 - - - +
379F MET* 3.3 39.9 - - + +
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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
----------------------------------------------------------
116F GLU* 2.8 21.4 + - - +
117F ILE* 3.7 12.8 - - + +
119F ILE* 1.3 78.6 - - + +
121F LYS* 1.3 57.2 + - - +
123F ILE* 3.3 9.4 + - - +
124F GLU* 2.9 30.2 + - - +
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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
----------------------------------------------------------
117F ILE* 2.9 19.5 + - + +
118F ASP* 3.1 11.0 + - - +
120F ALA* 1.3 76.8 - - - +
122F ARG* 1.3 57.1 + - + +
124F GLU* 2.9 22.0 - - + +
125F ASP* 2.4 44.1 + - - +
164F GLY* 3.1 13.9 - - - -
165F PHE* 3.0 37.8 + - - +
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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 26.7 + - - +
119F ILE 3.8 0.2 - - - +
120F ALA 3.3 0.2 - - - -
121F LYS* 1.3 76.5 - - - +
123F ILE* 1.3 57.9 + - - +
125F ASP* 3.1 16.9 + - - +
126F GLY 2.8 24.1 + - - -
371F LYS* 3.5 42.4 + - - +
372F ALA* 3.2 14.9 + - - +
374F ARG* 5.3 5.1 - - - +
375F ALA* 3.2 41.2 - - + +
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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
----------------------------------------------------------
119F ILE* 2.7 33.5 + - + +
120F ALA* 3.3 8.9 + - - +
122F ARG* 1.3 72.8 - - - +
124F GLU* 1.3 65.2 + - - +
126F GLY* 3.1 2.6 + - - -
127F ILE* 3.0 40.2 + - + +
260F ARG* 4.7 4.9 - - - +
372F ALA* 3.7 28.6 - - + +
376F LYS* 4.9 13.7 - - + -
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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 15.1 + - - +
121F LYS* 2.9 31.0 - - + +
123F ILE* 1.3 77.7 - - + +
125F ASP* 1.3 68.7 + - - +
127F ILE 3.7 0.2 - - - -
128F ASN* 2.2 70.4 + - - +
163F THR* 3.0 22.2 - - - +
164F GLY* 2.5 18.0 - - - +
165F PHE 3.1 19.6 - - - +
260F ARG* 4.0 21.3 - - - +
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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* 2.4 40.8 + - - +
122F ARG* 3.1 21.9 + - - +
124F GLU* 1.3 84.1 - - - +
126F GLY* 1.3 57.5 + - - +
128F ASN* 3.8 4.7 - - - -
129F GLN* 2.8 25.8 + - - +
165F PHE 4.0 1.0 - - - +
166F VAL* 2.9 30.5 - - - +
257F LYS* 3.0 12.2 + - - +
368F GLY* 4.9 1.0 - - - -
371F LYS* 6.0 3.8 - - + -
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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 2.8 13.4 + - - -
123F ILE 3.1 3.1 + - - -
125F ASP* 1.3 74.8 - - - +
127F ILE* 1.3 64.7 + - - +
129F GLN* 3.0 6.2 + - - +
130F VAL 3.0 15.4 + - - -
365F MET 4.9 0.2 - - - +
368F GLY* 3.4 29.7 + - - -
369F GLU* 2.9 21.3 - - - +
371F LYS* 5.8 0.2 - - - +
372F ALA* 4.3 1.6 - - - -
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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* 3.0 23.6 + - + +
126F GLY* 1.3 74.9 - - - +
128F ASN* 1.3 57.4 + - - +
130F VAL* 2.7 35.9 - - + +
131F GLN* 2.9 23.8 + - - +
260F ARG* 3.3 39.0 - - + +
266F PHE* 6.5 0.2 - - + -
369F GLU* 3.5 22.9 - - - +
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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* 2.2 55.9 + - - +
125F ASP 3.3 0.9 - - - +
127F ILE* 1.3 74.5 - - - +
129F GLN* 1.3 55.2 + - - +
131F GLN* 3.0 5.4 + - - +
132F CYS 2.8 18.7 + - - -
164F GLY 3.1 10.1 + - - -
166F VAL* 3.5 10.3 - - - +
257F LYS* 2.7 55.5 + - - +
258F GLN 3.0 6.8 + - - +
260F ARG* 2.9 24.8 - - - +
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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 2.8 10.8 + - - +
126F GLY 3.0 10.3 + - - +
128F ASN* 1.3 73.6 - - - +
130F VAL* 1.3 60.3 + - - +
132F CYS* 3.2 15.5 + - - +
133F SER* 2.9 22.1 + - - -
254F GLU* 5.0 4.4 + - - -
257F LYS* 3.5 21.8 - - - +
364F ARG* 2.7 53.5 + - - +
365F MET* 4.1 1.3 - - - +
367F ILE* 5.5 4.6 - - - +
368F GLY* 3.6 21.9 - - - +
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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 3.0 9.6 + - - +
127F ILE* 2.7 44.2 - - + +
129F GLN* 1.3 72.5 - - - +
131F GLN* 1.3 56.1 + - - +
133F SER* 2.2 25.0 + - - -
134F VAL* 2.9 16.5 + - - +
266F PHE* 3.9 21.1 - - + -
270F VAL* 5.2 7.4 - - + -
365F MET* 3.5 38.9 - - + +
369F GLU* 4.3 8.5 - - + +
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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 34.4 + - - +
128F ASN* 3.0 14.3 + - - +
130F VAL* 1.3 75.9 - - - +
132F CYS* 1.3 53.5 + - - +
134F VAL* 3.3 2.9 + - - +
135F ALA 2.9 23.0 + - - -
256F PHE* 3.2 30.3 - - + -
257F LYS 4.1 2.2 - - - +
259F PHE 2.9 19.9 - - - +
260F ARG* 3.2 19.6 - - + +
261F LEU 3.1 18.1 + - - +
266F PHE* 2.7 54.5 - - - -
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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 2.8 6.5 + - - -
129F GLN* 3.5 18.4 - - - +
131F GLN* 1.3 72.6 - - - +
133F SER* 1.3 67.6 + - - +
135F ALA 3.1 0.3 + - - -
136F GLU* 2.9 13.9 + - - +
250F LEU* 6.2 0.4 - - - -
253F SER* 2.0 67.8 + - - +
254F GLU* 3.2 35.0 - - - -
257F LYS* 3.6 15.6 - - + +
364F ARG* 6.4 1.1 - - - -
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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 11.1 + - - -
130F VAL* 2.2 40.5 + - - -
132F CYS* 1.3 75.1 - - - +
134F VAL* 1.3 58.2 + - - -
136F GLU* 2.8 32.6 - - - +
137F TYR* 3.3 4.5 + - - +
361F ILE* 3.1 29.5 - - - +
364F ARG* 4.8 1.6 - - - -
365F MET* 3.0 31.0 - - - +
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Residues in contact with VAL 134 (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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130F VAL 2.9 10.6 + - - +
131F GLN 3.7 0.2 - - - +
132F CYS 3.3 0.2 - - - -
133F SER* 1.3 76.7 + - - +
135F ALA* 1.3 61.8 + - - +
137F TYR* 3.0 16.4 + - - +
140F ALA* 3.1 32.3 - - + +
144F LEU* 6.0 4.3 - - + -
256F PHE* 5.9 0.9 - - + -
261F LEU* 6.0 0.4 - - + -
265F GLN* 5.1 3.6 - - - +
266F PHE* 3.1 46.0 - - + -
269F LEU* 3.1 36.6 - - + -
270F VAL* 5.9 1.8 - - + +
361F ILE* 4.8 0.7 - - - -
365F MET* 3.9 16.2 - - + -
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Residues in contact with ALA 135 (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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131F GLN 2.9 15.5 + - - +
132F CYS 3.1 0.2 + - - -
134F VAL* 1.3 76.7 - - - +
136F GLU* 1.3 58.6 + - - +
137F TYR 2.8 14.8 - - - +
140F ALA* 4.5 5.2 - - - -
141F ILE* 3.2 25.9 - - + +
144F LEU* 5.2 4.9 - - + -
249F ILE* 4.8 4.0 - - - +
252F LEU 5.1 0.2 - - - -
253F SER* 3.3 29.8 - - - +
256F PHE* 3.5 21.1 - - + -
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Residues in contact with GLU 136 (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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132F CYS* 2.9 13.8 + - - +
133F SER* 2.8 29.2 - - - +
135F ALA* 1.3 74.4 - - - +
137F TYR* 1.3 57.7 + - - +
138F PRO* 4.9 0.3 - - - +
249F ILE* 5.0 11.2 - - - +
250F LEU* 3.0 36.5 - - + +
253F SER* 3.0 16.4 + - - +
353F LEU* 5.5 4.7 - - - +
357F GLN* 4.8 4.2 - - - +
361F ILE* 3.2 29.3 - - + +
364F ARG* 2.3 44.4 + - - +
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Residues in contact with TYR 137 (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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133F SER 3.3 6.2 + - - +
134F VAL* 3.0 20.7 + - - +
135F ALA 2.8 15.1 - - - +
136F GLU* 1.3 76.3 - - - +
138F PRO* 1.3 83.1 - - + +
140F ALA* 3.5 6.5 - - + +
141F ILE* 3.6 3.5 - - - +
269F LEU* 4.0 29.6 - - + +
273F MET* 4.6 14.6 - - + +
276F MET* 4.9 5.0 - - - +
347F ILE* 4.8 5.7 - - - +
350F GLU* 4.1 9.2 + - - -
351F THR* 3.2 34.5 - - - +
354F THR 4.8 0.9 - - - -
357F GLN* 3.0 37.5 - - - -
358F VAL* 4.3 15.7 - - + -
361F ILE* 3.3 19.3 - - + -
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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