Contacts of the helix formed by residues 117 - 139 (chain F) in PDB entry 2Q7M
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 ARG 117 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B PHE* 4.6 13.3 - - - +
139B PHE* 3.8 35.2 - - + -
142B ASP* 2.3 51.3 + - - -
115F GLY* 2.8 3.7 + - - +
116F LYS* 1.3 79.0 - - - +
118F ILE* 1.3 64.4 + - + +
120F LEU* 3.1 7.6 - - - +
121F PHE* 2.8 29.7 + - + +
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Residues in contact with ILE 118 (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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86F ALA* 2.8 36.1 - - + +
89F MET* 3.5 22.0 - - + -
90F TYR* 3.2 41.5 - - + +
93F VAL* 4.9 6.7 - - + -
115F GLY* 2.7 16.3 + - - +
117F ARG* 1.3 80.3 - - + +
119F ILE* 1.3 60.4 + - + +
121F PHE* 2.8 11.7 + - + +
122F LEU* 2.7 41.2 + - + +
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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
----------------------------------------------------------
504D 2CS 3.0 39.9 - - + +
66F THR 4.3 3.8 - - - +
67F PHE* 4.0 24.2 - - + -
70F VAL* 4.0 21.0 - - + +
90F TYR* 3.8 25.1 - - + -
114F PHE 3.8 1.6 - - - +
115F GLY 2.8 24.5 - - - +
116F LYS* 2.8 23.8 - - - +
118F ILE* 1.3 76.3 - - + +
120F LEU* 1.3 57.2 + - - +
122F LEU* 3.9 0.3 - - - +
123F PHE* 2.7 33.5 + - - +
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Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE* 3.0 38.4 - - + -
504D 2CS 3.3 56.5 - - + -
116F LYS 2.8 23.3 + - - +
117F ARG* 3.1 7.6 - - - +
119F ILE* 1.3 80.8 - - - +
121F PHE* 1.3 61.9 + - - +
123F PHE* 3.2 1.0 + - - +
124F LEU* 3.0 43.8 + - + +
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Residues in contact with PHE 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.7 17.0 - - + -
139B PHE* 3.0 59.0 - + + -
82F PRO* 4.4 12.1 - - + -
86F ALA* 3.4 34.1 - - + -
117F ARG* 2.8 15.2 + - + +
118F ILE* 2.8 10.2 + - + +
120F LEU* 1.3 71.0 - - - +
122F LEU* 1.3 59.9 + - + +
124F LEU* 2.7 22.5 + - - +
125F MET* 3.2 40.5 + - + -
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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
----------------------------------------------------------
67F PHE* 5.4 2.9 - - + -
70F VAL* 3.3 39.5 - - + +
71F LEU* 4.4 7.0 - - + -
74F ALA* 2.8 24.3 - - + +
83F ALA* 3.8 24.9 - - - +
86F ALA* 3.4 35.9 - - + -
87F GLY* 3.8 16.2 - - - +
118F ILE* 2.7 28.0 + - + +
121F PHE* 1.3 81.9 - - + +
123F PHE* 1.3 61.8 + - - +
125F MET* 3.0 13.9 + - + -
126F SER* 3.1 2.3 + - - -
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Residues in contact with PHE 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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17D LEU* 3.3 43.1 - - + -
20D VAL* 3.9 20.2 - - + -
21D VAL* 4.6 8.5 - - + -
504D 2CS 3.9 23.6 - - + -
70F VAL* 3.9 11.8 - - + +
119F ILE 2.7 19.7 + - - +
120F LEU 3.3 4.3 - - - +
122F LEU* 1.3 76.6 - - - +
124F LEU* 1.3 75.9 + - + +
125F MET 3.4 0.2 - - - -
126F SER* 3.6 8.2 - - - -
127F VAL* 3.0 37.7 + - + +
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Residues in contact with LEU 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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131B PHE* 4.7 11.0 - - + -
135B LEU* 4.2 26.6 - - + +
139B PHE* 3.6 10.8 - - + -
120F LEU* 3.0 39.5 - - + +
121F PHE* 2.7 12.7 + - - +
123F PHE* 1.3 107.1 - - + +
125F MET* 1.3 57.7 + - - -
126F SER 3.3 0.2 - - - -
127F VAL* 3.1 12.2 - - + +
128F ALA* 2.9 26.0 + - - +
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Residues in contact with MET 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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135B LEU* 5.8 0.4 - - + -
74F ALA* 2.9 40.2 - - + +
77F LEU 3.7 0.2 - - - +
78F CYS* 3.1 32.4 - - + +
79F SER* 3.7 6.3 - - - +
82F PRO* 3.7 12.3 - - - -
83F ALA* 3.0 37.0 - - + +
121F PHE* 3.5 43.1 - - + +
122F LEU* 3.0 4.9 + - + +
124F LEU* 1.3 74.7 - - - +
126F SER* 1.3 64.2 + - - +
128F ALA* 3.0 22.9 - - - +
129F GLY 3.1 7.3 + - - -
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Residues in contact with SER 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 3.1 26.9 - - - -
70F VAL* 3.8 4.0 + - - -
73F SER* 2.8 24.4 - - - -
74F ALA* 2.7 29.5 + - - +
77F LEU* 4.0 5.6 - - - +
122F LEU 3.1 4.3 + - - -
123F PHE* 3.6 8.1 - - - -
125F MET* 1.3 76.6 - - - +
127F VAL* 1.3 57.2 + - - +
128F ALA 3.0 4.3 - - - -
130F ILE* 3.0 31.4 + - - +
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Residues in contact with VAL 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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131B PHE* 5.9 3.8 - - + -
17D LEU* 4.0 5.3 - - + +
123F PHE* 3.0 36.7 + - + +
124F LEU* 3.1 30.7 - - + +
126F SER* 1.3 73.3 - - - +
128F ALA* 1.3 65.7 + - - +
130F ILE* 3.5 20.9 - - + +
131F PHE* 3.5 9.8 + - + +
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Residues in contact with ALA 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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131B PHE* 4.7 19.1 - - + -
78F CYS* 4.5 7.4 - - - -
124F LEU 2.9 20.4 + - - +
125F MET* 3.0 13.0 - - - +
126F SER 3.0 0.2 - - - -
127F VAL* 1.3 76.0 - - - +
129F GLY* 1.3 62.8 + - - +
131F PHE* 2.9 13.7 + - - +
132F ASN* 2.9 26.1 + - - +
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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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6D VAL* 5.6 1.5 - - - +
77F LEU* 2.9 25.5 + - - -
78F CYS* 4.4 1.9 - - - +
125F MET 3.1 6.7 + - - -
128F ALA* 1.3 79.9 - - - +
130F ILE* 1.3 55.7 + - - +
132F ASN* 2.9 18.8 - - - +
133F TYR* 2.8 34.2 + - - +
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Residues in contact with ILE 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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6D VAL* 6.1 0.2 - - - -
10D VAL* 3.8 22.0 - - + +
13D ALA* 4.5 7.2 - - + -
14D ILE* 3.0 43.1 - - + +
17D LEU* 5.4 4.5 - - + -
77F LEU* 3.7 25.7 + - + +
126F SER 3.0 16.9 + - - +
127F VAL* 3.5 21.5 - - + +
128F ALA 3.1 0.2 - - - -
129F GLY* 1.3 76.4 - - - +
131F PHE* 1.3 68.6 + - + +
133F TYR* 3.8 6.6 - - - +
134F TYR* 3.7 18.6 - - + -
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Residues in contact with PHE 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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124B LEU* 4.8 13.7 - - + -
127B VAL* 5.6 2.9 - - + -
128B ALA* 4.9 14.6 - - + -
131B PHE* 5.8 10.8 - + - -
127F VAL* 3.6 11.2 - - + +
128F ALA* 2.9 13.9 + - - +
130F ILE* 1.3 81.9 - - + +
132F ASN* 1.3 75.8 + - + +
133F TYR 2.7 5.4 + - - -
134F TYR* 2.6 39.3 + - + +
135F LEU* 3.4 42.0 + - + -
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Residues in contact with ASN 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 ALA 2.9 14.0 + - - +
129F GLY* 2.9 19.8 - - - +
131F PHE* 1.3 93.6 - - + +
133F TYR* 1.3 65.4 + - - +
135F LEU* 3.3 9.7 + - - +
136F ILE* 2.7 47.4 + - - +
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Residues in contact with TYR 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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3D GLN* 2.9 56.2 + - - -
6D VAL* 4.0 18.2 - - + -
7D GLY* 2.9 29.3 + - - -
10D VAL* 3.8 13.9 - - + -
129F GLY 2.8 17.8 + - - +
130F ILE* 3.8 4.3 - - - +
131F PHE 2.7 0.6 + - - -
132F ASN* 1.3 75.3 + - - +
134F TYR* 1.3 106.1 + + - +
135F LEU 2.9 4.7 + - - -
136F ILE* 3.0 16.3 + - + +
137F PHE* 2.9 38.6 + + + +
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Residues in contact with TYR 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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10D VAL* 3.1 28.8 - - + +
11D LEU* 4.6 6.1 - - - +
14D ILE* 4.1 12.3 - - + +
130F ILE* 3.7 10.3 - - + -
131F PHE* 2.6 21.1 + - + +
133F TYR* 1.3 108.7 - + - +
135F LEU* 1.3 57.6 + - + +
137F PHE* 4.4 9.2 - + - -
138F PHE* 2.7 54.9 + + + +
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Residues in contact with LEU 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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121B PHE* 5.7 5.6 - - + -
124B LEU* 4.3 30.3 - - + +
125B MET* 5.9 1.6 - - + -
128B ALA* 5.7 1.6 - - + -
131F PHE* 3.5 48.5 - - + +
132F ASN* 3.3 12.1 - - - +
133F TYR 2.9 0.6 - - - -
134F TYR* 1.3 81.4 - - + +
136F ILE* 1.3 59.3 + - - +
137F PHE 2.9 4.0 + - - -
138F PHE* 4.6 3.8 - - + -
139F PHE* 2.7 51.6 + - + +
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Residues in contact with ILE 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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3D GLN* 2.9 37.9 + - + +
132F ASN* 2.7 31.6 - - - +
133F TYR* 3.0 23.3 - - + +
135F LEU* 1.3 73.4 - - - +
137F PHE* 1.3 59.3 + - - +
139F PHE 4.3 2.3 - - - +
140F GLY* 4.0 14.2 + - - -
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Residues in contact with PHE 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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3D GLN* 3.2 21.3 - - - +
133F TYR* 2.9 35.1 + + + +
134F TYR* 4.4 7.6 - + - -
135F LEU 2.9 0.4 + - - -
136F ILE* 1.3 79.0 - - - +
138F PHE* 1.3 98.8 + + - +
139F PHE 3.3 0.8 + - - -
140F GLY* 3.6 10.4 + - - -
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Residues in contact with PHE 138 (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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117B ARG* 3.5 21.8 + - - +
134F TYR* 2.7 39.2 + + + +
135F LEU* 4.2 4.0 - - + +
137F PHE* 1.3 114.6 - + - +
139F PHE* 1.3 81.4 + + + +
140F GLY 3.4 2.1 + - - -
141F SER* 4.5 2.9 + - - -
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Residues in contact with PHE 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ARG* 3.8 32.3 - - + +
120B LEU* 3.3 26.0 - - + -
121B PHE* 3.0 59.5 - + + -
124B LEU* 4.3 7.9 - - + -
135F LEU* 2.7 33.8 + - + +
136F ILE* 4.3 3.1 - - - +
138F PHE* 1.3 95.6 - + + +
140F GLY* 1.3 55.9 + - - +
141F SER* 3.2 8.7 - - - +
142F ASP* 4.7 7.0 + - - +
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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