Contacts of the helix formed by residues 112 - 127 (chain V) in PDB entry 1O1F
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 PRO 112 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75V ILE* 3.9 16.4 - - + -
110V LEU 3.3 9.4 - - - +
111V ASN* 1.3 93.8 - - - +
113V LYS* 1.3 56.3 + - - +
114V ALA* 3.0 6.3 - - + +
115V ASN* 2.8 48.1 + - - +
116V ARG* 3.5 4.2 + - - +
195W GLU* 5.3 20.0 - - + +
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Residues in contact with LYS 113 (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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111V ASN 3.4 4.5 + - - -
112V PRO* 1.3 68.6 - - - +
114V ALA* 1.3 56.7 + - - +
116V ARG* 3.4 4.4 + - - +
117V GLU* 3.1 36.8 + - - +
371V HIS* 3.2 44.6 + - + +
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Residues in contact with ALA 114 (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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112V PRO* 4.5 5.4 - - + +
113V LYS* 1.3 77.6 - - - +
115V ASN* 1.3 62.9 + - - +
117V GLU* 3.7 13.3 - - - +
118V LYS* 3.0 24.8 + - - +
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Residues in contact with ASN 115 (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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75V ILE* 3.5 24.2 - - - +
76V ILE* 3.8 16.3 + - + +
79V TRP* 3.6 26.9 + - + -
111V ASN* 3.3 26.4 + - - +
112V PRO* 2.8 26.4 + - - +
114V ALA* 1.3 72.7 - - - +
116V ARG* 1.4 56.9 + - - +
117V GLU 3.2 0.2 - - - -
118V LYS* 2.8 3.4 + - - +
119V MET* 2.8 36.4 + - - +
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Residues in contact with ARG 116 (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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107V GLU* 3.1 43.7 + - - +
111V ASN* 4.1 1.9 - - - +
112V PRO 3.5 2.7 + - - +
113V LYS* 3.4 11.3 + - - +
115V ASN* 1.4 77.1 - - - +
117V GLU* 1.3 56.3 + - - +
119V MET* 3.4 11.7 - - - +
120V THR* 2.6 32.7 + - - +
134V VAL* 3.2 39.9 + - + +
136V ILE* 4.0 20.8 - - - +
370V VAL* 3.5 19.1 + - + +
371V HIS* 3.7 38.3 + - + +
372V ARG* 3.6 32.3 - - - +
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Residues in contact with GLU 117 (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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113V LYS* 3.1 22.1 + - - +
114V ALA* 3.7 13.4 - - - +
116V ARG* 1.3 76.6 - - - +
118V LYS* 1.3 55.5 + - - +
120V THR* 3.4 4.8 + - - -
121V GLN* 3.0 26.7 + - - +
367V PRO* 3.6 26.8 - - + +
368V SER* 3.9 18.9 + - - -
371V HIS* 3.7 34.8 - - + +
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Residues in contact with LYS 118 (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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79V TRP* 3.8 45.5 - - + +
114V ALA 3.0 14.8 + - - +
115V ASN 2.8 14.2 + - - +
117V GLU* 1.3 71.1 - - - +
119V MET* 1.3 56.3 + - - +
120V THR 3.0 0.4 - - - -
121V GLN* 3.1 37.5 + - + +
122V ILE* 3.0 39.4 + - + +
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Residues in contact with MET 119 (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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12V ASN* 4.8 3.1 - - - +
76V ILE* 4.5 14.4 - - + -
79V TRP* 3.8 10.6 - - + -
86V TRP* 3.9 25.8 - - + -
105V LEU* 3.7 29.2 - - + -
106V THR 4.1 19.5 - - - +
107V GLU* 5.0 0.9 - - + -
111V ASN* 4.5 11.7 - - - -
115V ASN 2.8 20.0 + - - +
116V ARG* 3.4 20.6 - - - +
118V LYS* 1.3 71.4 - - - +
120V THR* 1.3 60.9 + - - +
122V ILE* 3.8 7.5 - - - +
123V MET* 2.9 35.0 + - - +
132V MET* 4.5 0.2 - - - -
134V VAL* 4.3 16.8 - - + -
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Residues in contact with THR 120 (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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116V ARG 2.6 22.3 + - - -
117V GLU* 3.4 6.5 - - - -
118V LYS 3.0 0.4 - - - -
119V MET* 1.3 75.7 - - - +
121V GLN* 1.3 67.6 + - - +
124V PHE* 2.9 51.4 + - + +
132V MET* 3.8 18.2 - - - +
134V VAL* 4.5 2.1 - - - +
362V TYR* 4.3 14.4 - - + -
367V PRO* 4.6 2.2 - - + +
370V VAL* 3.2 33.1 - - + +
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Residues in contact with GLN 121 (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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117V GLU 3.0 14.1 + - - +
118V LYS* 3.1 45.5 + - + +
120V THR* 1.3 75.7 - - - +
122V ILE* 1.3 63.7 + - - +
125V GLU* 2.8 64.8 + - - +
126V THR* 4.9 7.3 - - - +
362V TYR* 3.6 19.2 + - - +
367V PRO* 4.7 6.9 - - + +
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Residues in contact with ILE 122 (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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79V TRP* 3.6 41.7 - - + +
83V GLU* 4.1 17.9 - - + +
86V TRP* 4.1 15.3 - - + -
118V LYS* 3.0 30.2 + - - +
119V MET* 4.1 5.2 - - - +
121V GLN* 1.3 89.7 - - - +
123V MET* 1.3 68.3 + - - +
126V THR* 2.9 43.6 + - + +
127V PHE* 3.2 19.2 + - + -
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Residues in contact with MET 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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86V TRP* 3.3 55.2 - - + +
90V PHE* 4.1 17.7 - - + -
103V THR* 4.6 8.7 - - - -
105V LEU* 3.7 15.0 - - + -
119V MET 2.9 23.8 + - - +
120V THR 3.2 0.9 + - - +
122V ILE* 1.3 80.1 - - - +
124V PHE* 1.3 59.5 + - - +
127V PHE* 3.2 25.0 + - + +
128V ASN 3.0 20.8 + - - -
129V VAL* 3.6 21.1 + - + +
132V MET* 3.6 28.5 - - + -
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Residues in contact with PHE 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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120V THR* 2.9 28.0 + - + +
123V MET* 1.3 79.1 - - - +
125V GLU* 1.3 60.2 + - - +
128V ASN* 3.3 23.2 - - - +
129V VAL* 3.5 27.1 - - + +
130V PRO 3.7 11.0 - - - -
131V ALA* 3.8 4.9 - - - -
132V MET* 3.4 26.5 - - + -
357V ILE* 3.0 48.9 - - + -
358V THR 4.0 3.1 - - - -
359V LYS* 3.8 13.0 - - + -
362V TYR* 3.6 38.8 - + + -
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Residues in contact with GLU 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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121V GLN* 2.8 50.1 + - - +
124V PHE* 1.3 74.6 - - - +
126V THR* 1.4 58.7 + - + +
128V ASN* 4.7 1.4 - - - +
362V TYR* 3.5 33.3 + - + -
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Residues in contact with THR 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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83V GLU* 4.2 25.0 + - - +
121V GLN* 4.9 9.4 - - - +
122V ILE* 2.9 38.3 + - + +
125V GLU* 1.4 79.6 - - + +
127V PHE* 1.3 71.7 + - - +
128V ASN* 3.6 2.2 - - - +
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Residues in contact with PHE 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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83V GLU* 3.7 22.0 - - + -
86V TRP* 3.6 30.3 - + + -
87V HIS* 4.0 20.6 - - + -
90V PHE* 3.6 28.5 - + + -
91V TYR* 4.9 7.4 + + - -
98V PRO* 3.7 19.1 - - + +
99V GLU* 3.5 12.8 + - - +
122V ILE* 3.4 37.0 - - + -
123V MET* 3.2 27.3 + - + +
126V THR* 1.3 82.2 + - - +
128V ASN* 1.3 73.5 + - - +
129V VAL* 3.4 9.1 + - + -
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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