Contacts of the helix formed by residues 118 - 132 (chain C) in PDB entry 6R7H
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 LEU 118 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU* 4.5 0.2 - - - +
116C GLN* 2.7 26.1 + - - +
117C PRO* 1.3 72.3 - - - +
119C ARG* 1.3 65.4 + - - +
120C GLY 3.3 2.4 + - - -
121C ILE* 3.5 9.0 + - + +
152C ALA* 4.5 9.0 - - + -
24H GLU* 3.7 29.6 - - + +
25H LEU* 3.5 35.1 - - + +
28H PRO* 5.0 4.9 - - + +
30H GLY* 3.8 22.7 - - - +
32H ALA* 4.5 8.7 - - + +
37H TYR* 4.3 13.9 - - - +
59H ARG* 3.5 34.5 - - - +
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Residues in contact with ARG 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PHE* 3.9 34.0 + - + -
79C SER* 3.7 20.8 + - - -
82C GLN* 3.2 38.2 + - - +
111C LEU* 4.2 7.7 - - + +
118C LEU* 1.3 76.5 - - - +
120C GLY* 1.3 62.9 + - - +
121C ILE 3.2 1.0 + - - -
122C GLY 3.4 2.4 + - - -
123C ILE* 3.3 24.5 + - + +
25H LEU 4.0 9.5 - - - +
26H GLU 3.1 19.3 + - - -
27H ALA 3.2 11.7 + - - -
28H PRO 3.0 33.8 + - - +
29H GLY* 3.4 28.0 + - - +
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Residues in contact with GLY 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU* 5.0 4.9 - - - -
108C THR* 5.4 2.9 - - - -
111C LEU* 3.4 20.7 - - - +
117C PRO 4.8 0.4 - - - -
118C LEU 3.3 1.6 - - - +
119C ARG* 1.3 78.6 - - - +
121C ILE* 1.3 60.4 + - - +
123C ILE* 3.9 9.4 - - - -
124C LEU* 3.2 26.2 + - - +
148C LEU* 3.4 23.9 - - - +
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Residues in contact with ILE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C PRO 4.5 5.6 - - - +
118C LEU* 4.1 6.5 - - + +
119C ARG 3.2 1.2 - - - -
120C GLY* 1.3 78.8 - - - +
122C GLY* 1.3 61.2 + - - +
124C LEU* 4.0 0.7 - - - -
125C LYS* 3.2 24.8 + - + +
145C LEU* 4.2 10.6 - - + +
148C LEU* 3.8 36.1 - - + +
149C CYS* 5.1 7.9 - - - +
152C ALA* 3.8 31.0 - - + +
154C CYS* 5.6 4.9 - - + +
157C PRO* 4.0 21.1 - - + -
25H LEU* 3.7 36.6 - - + -
59H ARG* 5.3 2.0 - - - +
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Residues in contact with GLY 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ARG 3.4 4.0 + - - -
121C ILE* 1.3 78.7 - - - +
123C ILE* 1.3 59.3 + - - +
125C LYS* 3.3 24.5 - - - +
126C GLN* 2.9 20.8 + - - +
25H LEU* 3.3 31.7 - - - +
26H GLU* 3.2 9.7 - - - +
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C PHE* 3.9 11.0 - - + +
81C VAL* 3.8 40.4 - - + +
82C GLN* 3.4 31.6 - - + +
85C ILE* 4.3 13.3 - - + +
104C CYS* 5.7 4.3 - - - -
107C LEU* 4.2 19.1 - - + -
111C LEU* 6.3 0.7 - - + -
119C ARG* 3.3 26.0 + - + +
120C GLY* 4.1 4.9 - - - +
121C ILE 3.2 0.8 - - - -
122C GLY* 1.3 76.5 - - - +
124C LEU* 1.3 67.3 + - + +
125C LYS 3.2 1.1 + - - -
126C GLN* 3.4 17.6 + - - +
127C ALA* 3.6 11.9 + - + +
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C CYS* 3.8 41.1 - - + +
107C LEU* 4.8 5.8 - - + -
108C THR* 4.4 4.3 - - + -
120C GLY* 3.2 26.9 + - - +
123C ILE* 1.3 83.4 - - + +
125C LYS* 1.3 60.7 + - - +
126C GLN 3.2 1.0 + - - -
127C ALA* 3.7 5.0 + - - +
128C ILE* 3.4 23.9 + - - +
141C ILE* 4.1 18.2 - - + +
144C ASP* 3.6 33.2 - - + +
145C LEU* 3.8 20.4 - - + +
148C LEU* 4.1 15.3 - - + -
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Residues in contact with LYS 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE* 3.2 14.3 + - + +
122C GLY* 3.3 29.6 + - - +
123C ILE 3.2 0.6 - - - -
124C LEU* 1.3 77.1 - - - +
126C GLN* 1.3 72.1 + - + +
128C ILE* 3.4 11.4 - - - +
129C ASP* 3.1 9.5 - - - +
145C LEU* 4.3 7.2 - - + +
157C PRO* 5.5 9.2 - - + -
161C TYR* 2.9 36.5 + - + +
22H ASN* 5.0 18.6 + - - +
25H LEU* 4.9 14.4 - - + -
26H GLU* 4.6 13.4 + - - +
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Residues in contact with GLN 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C GLN* 4.4 7.1 + - - +
85C ILE* 3.8 18.4 - - + +
86C SER* 2.4 33.8 + - - -
122C GLY 2.9 24.3 + - - +
123C ILE* 3.4 8.1 + - - +
124C LEU 3.2 0.6 - - - -
125C LYS* 1.3 93.8 - - - +
127C ALA* 1.3 63.2 + - - +
128C ILE 3.2 2.0 - - - -
129C ASP* 3.4 14.7 + - - +
130C LYS* 3.8 15.9 + - - +
26H GLU* 3.1 21.4 + - - -
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Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ILE* 3.8 12.2 - - + +
100C PHE* 3.7 27.7 - - + -
104C CYS* 4.9 7.6 - - - -
123C ILE* 3.6 9.6 + - + +
124C LEU* 3.7 5.8 + - - +
125C LYS 3.7 0.2 - - - -
126C GLN* 1.3 77.5 - - - +
128C ILE* 1.3 61.6 + - - +
129C ASP 3.3 0.6 + - - -
130C LYS* 3.5 24.3 + - - +
131C MET* 3.7 17.8 + - - +
141C ILE* 4.7 11.7 - - + +
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Residues in contact with ILE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C LEU 3.4 15.2 + - - +
125C LYS* 3.4 20.0 - - - +
127C ALA* 1.3 77.9 - - - +
129C ASP* 1.3 62.7 + - - +
131C MET* 3.8 5.1 + - + -
132C GLN* 3.3 33.2 + - + +
137C GLN 5.2 0.7 - - - +
139C THR* 3.8 19.7 - - + -
141C ILE* 4.1 9.4 - - + +
142C HIS* 3.7 51.8 - - + +
145C LEU* 4.8 6.3 - - + -
161C TYR* 3.6 25.4 - - + +
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Residues in contact with ASP 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C LYS 3.1 8.6 - - - +
126C GLN* 3.4 10.8 + - - +
127C ALA 3.3 0.4 - - - -
128C ILE* 1.3 79.4 - - - +
130C LYS* 1.3 60.3 + - + +
131C MET 3.4 0.2 - - - -
132C GLN* 3.1 27.6 - - - +
161C TYR* 3.0 37.6 + - - -
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Residues in contact with LYS 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ILE* 3.4 32.7 + - - +
89C ASN* 3.7 48.1 + - + +
90C GLY 4.8 2.5 - - - +
93C ILE* 3.7 32.0 - - + +
94C ARG* 4.5 4.3 + - - -
100C PHE* 4.1 8.8 - - - -
126C GLN 3.8 7.3 + - - +
127C ALA* 3.5 20.8 + - - +
128C ILE 3.4 0.4 - - - -
129C ASP* 1.3 79.8 - - + +
131C MET* 1.3 58.8 + - - +
132C GLN 3.6 2.9 + - - +
133C MET* 5.6 1.7 - - - +
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Residues in contact with MET 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ILE* 3.4 47.3 - - + +
94C ARG* 3.0 21.2 + - - +
97C THR* 4.6 8.3 - - + -
100C PHE* 3.7 32.8 - - + -
127C ALA 3.7 13.7 - - - +
128C ILE* 3.8 7.2 + - + +
129C ASP 3.4 0.4 - - - -
130C LYS* 1.3 77.2 - - - +
132C GLN* 1.3 54.8 + - + +
137C GLN* 2.6 31.5 + - + -
139C THR* 5.3 12.8 - - + -
141C ILE* 4.7 10.5 - - + -
170C CYS* 4.5 22.2 - - + -
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Residues in contact with GLN 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ILE* 3.3 26.8 + - + +
129C ASP* 3.1 22.1 + - - +
130C LYS 3.3 3.0 - - - +
131C MET* 1.3 79.2 - - + +
133C MET* 1.3 59.5 + - - +
134C ASN* 3.2 11.8 + - - +
136C ASN* 3.8 17.8 + - - +
137C GLN* 2.5 55.4 + - + +
142C HIS* 3.4 23.4 + - - -
161C TYR* 4.5 13.5 - - - -
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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