Contacts of the helix formed by residues 121 - 135 (chain V) in PDB entry 1P7G
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 SER 121 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115V ILE* 3.9 3.9 - - - +
116V ASN* 3.7 13.8 - - - +
119V PHE* 3.1 5.0 + - - +
120V GLY* 1.3 80.5 - - - +
122V PHE* 1.3 64.2 + - - +
123V GLU* 3.3 20.2 + - - +
124V LYS* 3.2 23.2 + - - +
125V PHE* 3.1 21.7 + - - +
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Residues in contact with PHE 122 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105V GLY 4.5 7.2 - - - -
106V LYS* 3.4 39.9 - - + +
107V PRO* 3.4 35.0 - - + -
115V ILE* 3.9 11.4 - - + -
116V ASN* 3.8 7.6 + - - +
121V SER* 1.3 74.2 - - - +
123V GLU* 1.3 61.6 + - + +
125V PHE* 3.1 19.4 + + - +
126V LYS* 2.7 67.0 + - + +
198V TRP* 4.6 4.3 - + + -
203V TRP* 3.5 26.7 - + - -
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Residues in contact with GLU 123 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106V LYS* 2.5 33.7 + - - +
121V SER* 3.3 21.5 + - - +
122V PHE* 1.3 84.2 + - + +
124V LYS* 1.3 56.4 + - - +
126V LYS* 3.3 9.7 + - - +
127V GLU* 3.0 25.3 + - - +
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Residues in contact with LYS 124 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119V PHE* 3.3 25.6 - - + +
120V GLY 5.4 0.2 - - - -
121V SER* 3.2 14.5 + - - +
123V GLU* 1.3 72.7 - - - +
125V PHE* 1.3 66.3 + - - +
127V GLU* 3.2 27.3 + - - +
128V GLU* 3.0 21.3 + - - +
64W PHE* 2.7 44.6 + - + +
65W ARG* 3.3 33.2 - - + +
67W GLY* 4.3 9.4 - - - +
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Residues in contact with PHE 125 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115V ILE* 3.6 20.0 - - + -
119V PHE* 3.8 30.5 - + + +
121V SER 3.1 15.3 + - - +
122V PHE* 3.3 24.0 - + - +
124V LYS* 1.3 76.5 - - - +
126V LYS* 1.3 61.1 + - - +
128V GLU 3.4 0.6 + - - +
129V PHE* 3.0 46.5 + + + +
144V LEU* 4.0 26.7 - - + -
155V ILE* 3.8 25.2 - - + +
173V LEU* 4.3 12.8 - - + -
198V TRP* 3.9 16.8 - + - -
203V TRP* 3.8 22.2 - + - -
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Residues in contact with LYS 126 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122V PHE* 2.7 57.9 + - + +
123V GLU* 3.4 9.9 - - - +
125V PHE* 1.3 77.3 - - - +
127V GLU* 1.3 49.8 + - - +
130V SER* 2.7 41.1 + - - -
198V TRP* 3.6 55.0 - - + +
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Residues in contact with GLU 127 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123V GLU 3.0 12.3 + - - +
124V LYS* 3.2 32.0 + - - +
126V LYS* 1.3 74.3 - - - +
128V GLU* 1.3 55.9 + - - +
130V SER* 3.5 5.1 - - - -
131V GLN* 2.7 51.9 + - + +
64W PHE* 3.4 27.9 - - + -
70W GLN* 4.8 4.9 + - - -
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Residues in contact with GLU 128 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119V PHE* 3.5 11.8 - - + -
124V LYS 3.0 15.4 + - - +
125V PHE 3.9 1.3 - - - +
127V GLU* 1.3 75.6 - - - +
129V PHE* 1.3 63.0 + - - +
131V GLN* 3.8 3.5 - - - +
132V ALA* 3.0 25.8 + - - +
155V ILE* 3.6 25.2 + - + +
61W LEU* 3.8 15.7 - - - +
64W PHE* 3.7 20.7 - - + -
65W ARG* 2.8 55.1 + - - +
73W ILE* 4.1 16.9 - - + +
77W LEU* 5.0 1.0 - - - +
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Residues in contact with PHE 129 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125V PHE* 3.0 36.0 + + + +
128V GLU* 1.3 77.2 - - - +
130V SER* 1.3 64.2 + - - +
132V ALA* 3.3 3.6 + - - +
133V ALA* 3.0 19.8 + - - +
142V ALA* 3.5 25.0 - - + +
143V ILE* 3.9 4.0 - - - -
144V LEU* 3.8 26.9 - - + -
155V ILE* 3.3 24.2 - - + +
173V LEU* 4.1 12.1 - - + -
175V LEU* 3.6 20.2 - - + -
197V TRP* 3.5 32.5 - + - -
198V TRP* 3.5 25.1 - + + -
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Residues in contact with SER 130 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126V LYS* 2.7 27.2 + - - -
127V GLU* 3.5 6.5 - - - -
129V PHE* 1.3 74.4 - - - +
131V GLN* 1.3 58.8 + - - +
133V ALA* 3.2 3.3 + - - +
134V LYS* 2.9 52.9 + - - +
194V VAL* 3.4 26.4 - - - +
195V ASP* 4.0 4.0 + - - -
198V TRP* 4.4 10.4 + - - -
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Residues in contact with GLN 131 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127V GLU* 2.7 41.5 + - + +
128V GLU* 3.8 5.4 - - - +
130V SER* 1.3 70.8 + - - +
132V ALA* 1.3 61.0 + - - +
134V LYS* 4.2 19.7 - - - +
135V ASN* 2.9 55.9 + - - +
64W PHE* 5.2 5.2 - - + -
71W ILE* 5.7 2.3 - - + +
73W ILE* 3.9 16.6 - - + +
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Residues in contact with ALA 132 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128V GLU 3.0 19.5 + - - +
129V PHE 3.5 5.2 - - - +
130V SER 3.3 0.2 - - - -
131V GLN* 1.3 76.3 - - - +
133V ALA* 1.3 63.1 + - - +
136V VAL* 3.2 11.2 + - - +
142V ALA* 4.2 6.5 - - + -
155V ILE* 3.9 11.2 - - + -
156V LEU 4.9 0.7 - - - +
157V GLN* 2.8 29.5 - - + +
73W ILE* 3.9 10.0 - - + +
77W LEU* 3.8 27.4 - - + -
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Residues in contact with ALA 133 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129V PHE* 3.0 10.1 + - + +
130V SER 3.5 7.6 - - - +
131V GLN 3.2 0.2 - - - -
132V ALA* 1.3 76.3 - - - +
134V LYS* 1.3 61.9 + - - +
135V ASN 3.3 0.5 + - - -
136V VAL* 3.3 12.3 + - - +
142V ALA* 3.6 23.7 - - + +
175V LEU* 3.8 25.8 - - + -
177V VAL* 3.9 10.6 - - + +
190V ARG* 3.3 19.1 + - - -
194V VAL* 3.9 9.2 - - + -
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Residues in contact with LYS 134 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130V SER* 2.9 36.4 + - - +
131V GLN* 3.8 19.7 - - - +
133V ALA* 1.3 77.7 - - - +
135V ASN* 1.3 66.2 + - - +
136V VAL 3.4 0.4 - - - +
190V ARG* 3.3 24.5 + - - +
191V GLY* 3.6 33.2 + - - +
194V VAL* 3.9 9.9 - - + -
195V ASP* 3.1 29.0 + - - -
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Residues in contact with ASN 135 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131V GLN* 2.9 51.4 + - - +
134V LYS* 1.3 83.8 - - - +
136V VAL* 1.3 60.2 + - - +
157V GLN* 2.8 12.3 - - - +
73W ILE* 3.7 19.8 - - + +
74W ARG* 3.0 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
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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