Contacts of the helix formed by residues 112 - 127 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75Y ILE* 3.9 16.4 - - + -
110Y LEU 3.3 9.4 - - - +
111Y ASN* 1.3 94.8 - - - +
113Y LYS* 1.3 56.7 + - - +
114Y ALA* 3.0 5.2 - - + +
115Y ASN* 2.8 47.7 + - - +
116Y ARG* 3.5 4.0 + - - +
195Z GLU* 5.3 19.7 - - + +
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Residues in contact with LYS 113 (chain Y).
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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111Y ASN 3.4 4.8 + - - -
112Y PRO* 1.3 69.2 - - - +
114Y ALA* 1.3 56.3 + - - +
116Y ARG* 3.4 3.9 + - - -
117Y GLU* 3.1 36.9 + - - +
371Y HIS* 3.2 46.3 + - + +
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Residues in contact with ALA 114 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Y PRO* 4.5 4.5 - - + +
113Y LYS* 1.3 78.7 - - - +
115Y ASN* 1.3 63.2 + - - +
117Y GLU* 3.7 14.7 - - - +
118Y LYS* 3.0 25.2 + - - +
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Residues in contact with ASN 115 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75Y ILE* 3.5 23.6 - - - +
76Y ILE* 3.8 16.5 + - + +
79Y TRP* 3.6 26.8 + - + -
111Y ASN* 3.3 26.1 + - - +
112Y PRO* 2.8 26.8 + - - +
114Y ALA* 1.3 71.6 - - - +
116Y ARG* 1.4 58.6 + - - +
118Y LYS* 2.8 3.5 + - - +
119Y MET* 2.8 36.7 + - - +
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Residues in contact with ARG 116 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Y GLU* 3.1 42.6 + - - +
111Y ASN* 4.1 2.0 - - - +
112Y PRO 3.5 2.5 + - - +
113Y LYS* 3.4 11.7 + - - +
115Y ASN* 1.4 76.5 - - - +
117Y GLU* 1.3 57.0 + - - +
119Y MET* 3.4 11.4 - - - +
120Y THR* 2.6 32.9 + - - +
134Y VAL* 3.2 39.2 + - + +
136Y ILE* 4.0 20.0 - - - +
370Y VAL* 3.5 20.5 + - + +
371Y HIS* 3.7 37.7 + - - +
372Y ARG* 3.6 32.5 - - - +
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Residues in contact with GLU 117 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Y LYS* 3.1 20.3 + - - +
114Y ALA* 3.7 13.1 - - - +
116Y ARG* 1.3 77.3 - - - +
118Y LYS* 1.3 55.6 + - - +
120Y THR* 3.4 4.9 + - - -
121Y GLN* 3.0 26.9 + - - +
367Y PRO* 3.6 27.1 - - + +
368Y SER* 3.9 18.4 + - - -
371Y HIS* 3.7 35.0 - - + +
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Residues in contact with LYS 118 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Y TRP* 3.8 45.6 - - + +
114Y ALA 3.0 15.7 + - - +
115Y ASN 2.8 14.8 + - - +
117Y GLU* 1.3 71.3 - - - +
119Y MET* 1.3 56.2 + - - +
120Y THR 3.0 0.2 - - - -
121Y GLN* 3.1 35.9 + - + +
122Y ILE* 3.0 39.2 + - + +
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Residues in contact with MET 119 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Y ASN* 4.8 3.1 - - - +
76Y ILE* 4.5 14.4 - - + -
79Y TRP* 3.8 9.1 - - + -
86Y TRP* 3.9 26.7 - - + -
105Y LEU* 3.7 29.4 - - + -
106Y THR 4.1 19.7 - - - +
107Y GLU* 5.0 1.1 - - - -
111Y ASN* 4.5 10.5 - - - -
115Y ASN* 2.8 21.6 + - - +
116Y ARG* 3.4 20.6 - - - +
118Y LYS* 1.3 72.1 - - - +
120Y THR* 1.3 61.2 + - - +
122Y ILE* 3.8 7.9 - - - +
123Y MET* 2.9 35.2 + - - +
132Y MET* 4.5 0.2 - - - -
134Y VAL* 4.3 16.8 - - + -
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Residues in contact with THR 120 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Y ARG 2.6 23.0 + - - -
117Y GLU* 3.4 6.0 + - - +
118Y LYS 3.0 0.2 - - - -
119Y MET* 1.3 76.4 - - - +
121Y GLN* 1.3 67.3 + - - +
124Y PHE* 2.9 51.5 + - + +
132Y MET* 3.8 17.9 - - - +
134Y VAL* 4.5 1.9 - - - +
362Y TYR* 4.3 14.1 - - + -
367Y PRO 4.6 2.0 - - - +
370Y VAL* 3.2 33.6 - - + +
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Residues in contact with GLN 121 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Y GLU 3.0 14.5 + - - +
118Y LYS* 3.1 47.0 + - + +
120Y THR* 1.3 74.7 - - - +
122Y ILE* 1.3 63.0 + - - +
125Y GLU* 2.8 65.6 + - - +
126Y THR* 4.9 7.5 - - - +
362Y TYR* 3.6 18.3 + - - +
367Y PRO* 4.7 6.3 - - + -
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Residues in contact with ILE 122 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Y TRP* 3.6 42.0 - - + +
83Y GLU* 4.1 17.7 - - + +
86Y TRP* 4.1 15.5 - - + -
118Y LYS* 3.0 29.7 + - - +
119Y MET* 4.1 5.8 - - - +
121Y GLN* 1.3 90.0 - - - +
123Y MET* 1.3 68.0 + - - +
126Y THR* 2.9 42.7 + - + +
127Y PHE* 3.2 20.2 + - + -
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Residues in contact with MET 123 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Y TRP* 3.3 55.4 - - + +
90Y PHE* 4.1 17.3 - - + -
103Y THR* 4.6 8.5 - - - -
105Y LEU* 3.7 15.0 - - + -
119Y MET 2.9 22.9 + - - +
120Y THR 3.2 1.5 + - - +
122Y ILE* 1.3 79.9 - - - +
124Y PHE* 1.3 59.5 + - - +
127Y PHE* 3.2 24.5 + - + +
128Y ASN 3.0 21.1 + - - -
129Y VAL* 3.6 21.3 + - + +
132Y MET* 3.6 28.5 - - + -
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Residues in contact with PHE 124 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120Y THR* 2.9 28.5 + - + +
123Y MET* 1.3 77.0 - - - +
125Y GLU* 1.3 59.9 + - - +
128Y ASN* 3.3 23.8 - - - +
129Y VAL* 3.5 26.5 - - + +
130Y PRO 3.7 10.3 - - - -
131Y ALA* 3.8 5.2 - - - -
132Y MET* 3.4 27.1 - - + -
357Y ILE* 3.0 48.5 - - + -
358Y THR 4.0 2.7 - - - -
359Y LYS* 3.8 14.6 - - + -
362Y TYR* 3.6 38.4 - + + -
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Residues in contact with GLU 125 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121Y GLN* 2.8 49.1 + - - +
124Y PHE* 1.3 74.8 - - - +
126Y THR* 1.3 58.6 + - + +
128Y ASN* 4.7 1.9 - - - +
362Y TYR* 3.5 32.7 + - + -
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Residues in contact with THR 126 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Y GLU* 4.2 25.7 + - - +
121Y GLN* 4.9 9.9 - - - +
122Y ILE* 2.9 38.0 + - + +
125Y GLU* 1.3 79.2 - - + +
127Y PHE* 1.3 72.5 + - - +
128Y ASN* 3.6 2.6 - - - +
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Residues in contact with PHE 127 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Y GLU* 3.7 21.8 - - + -
86Y TRP* 3.6 32.1 - + + -
87Y HIS* 4.0 19.7 - - + -
90Y PHE* 3.6 29.8 - + + -
91Y TYR* 4.9 6.5 + + - -
98Y PRO* 3.6 19.2 - - + +
99Y GLU* 3.5 12.2 + - - +
122Y ILE* 3.4 37.0 - - + -
123Y MET* 3.2 29.2 + - + +
126Y THR* 1.3 80.9 + - - +
128Y ASN* 1.3 72.8 + - - +
129Y VAL* 3.3 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