Contacts of the helix formed by residues 112 - 127 (chain Z) 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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75Z ILE* 3.9 16.4 - - + -
110Z LEU 3.3 9.0 - - - +
111Z ASN* 1.3 94.2 - - - +
113Z LYS* 1.3 56.4 + - - +
114Z ALA* 3.0 5.8 - - + +
115Z ASN* 2.8 47.9 + - - +
116Z ARG* 3.5 4.0 + - - +
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Residues in contact with LYS 113 (chain Z).
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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111Z ASN 3.4 4.3 + - - -
112Z PRO* 1.3 69.0 - - - +
114Z ALA* 1.3 56.6 + - - +
116Z ARG* 3.4 4.0 + - - +
117Z GLU* 3.1 37.4 + - - +
371Z HIS* 3.2 44.2 + - + +
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Residues in contact with ALA 114 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Z PRO* 4.5 5.2 - - + +
113Z LYS* 1.3 77.7 - - - +
115Z ASN* 1.3 64.0 + - - +
117Z GLU* 3.7 13.7 - - - +
118Z LYS* 3.0 24.8 + - - +
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Residues in contact with ASN 115 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75Z ILE* 3.5 24.2 - - - +
76Z ILE* 3.8 16.3 + - + +
79Z TRP* 3.6 26.9 + - + -
111Z ASN* 3.3 26.4 + - - +
112Z PRO* 2.8 26.7 + - - +
114Z ALA* 1.3 72.4 - - - +
116Z ARG* 1.4 59.1 + - - +
118Z LYS* 2.8 3.8 + - - +
119Z MET* 2.8 36.5 + - - +
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Residues in contact with ARG 116 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Z GLU* 3.1 43.1 + - - +
111Z ASN* 4.1 2.1 - - - +
112Z PRO 3.5 3.0 + - - +
113Z LYS* 3.4 10.6 + - - +
115Z ASN* 1.4 77.5 - - - +
117Z GLU* 1.3 56.8 + - - +
119Z MET* 3.4 11.6 - - - +
120Z THR* 2.6 33.1 + - - +
134Z VAL* 3.2 40.3 + - + +
136Z ILE* 4.0 20.2 - - - +
370Z VAL* 3.5 18.7 + - + +
371Z HIS* 3.7 38.6 + - + +
372Z ARG* 3.6 32.5 - - - +
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Residues in contact with GLU 117 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Z LYS* 3.1 21.7 + - - +
114Z ALA* 3.7 14.2 - - - +
116Z ARG* 1.3 76.5 - - - +
118Z LYS* 1.3 55.6 + - - +
120Z THR* 3.4 5.6 + - - -
121Z GLN* 3.0 27.2 + - - +
367Z PRO* 3.6 25.9 - - + +
368Z SER* 3.9 18.7 + - - -
371Z HIS* 3.7 35.0 - - + +
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Residues in contact with LYS 118 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Z TRP* 3.8 45.4 - - + +
114Z ALA 3.0 15.5 + - - +
115Z ASN 2.8 14.2 + - - +
117Z GLU* 1.3 71.7 - - - +
119Z MET* 1.3 55.8 + - - +
120Z THR 3.0 0.4 - - - -
121Z GLN* 3.1 38.0 + - + +
122Z ILE* 3.0 39.9 + - + +
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Residues in contact with MET 119 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z ASN* 4.8 3.1 - - - +
76Z ILE* 4.5 14.4 - - + -
79Z TRP* 3.8 10.0 - - + -
86Z TRP* 3.9 26.0 - - + -
105Z LEU* 3.7 29.2 - - + -
106Z THR 4.1 19.1 - - - +
107Z GLU* 5.0 0.9 - - + -
111Z ASN* 4.5 11.2 - - - -
115Z ASN* 2.8 20.6 + - - +
116Z ARG* 3.4 20.9 - - - +
118Z LYS* 1.3 70.8 - - - +
120Z THR* 1.3 60.9 + - - +
122Z ILE* 3.8 7.7 - - - +
123Z MET* 2.9 35.0 + - - +
132Z MET* 4.5 0.4 - - - -
134Z VAL* 4.3 16.4 - - + -
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Residues in contact with THR 120 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Z ARG 2.6 22.4 + - - -
117Z GLU* 3.4 7.0 - - - +
118Z LYS 3.0 0.2 - - - -
119Z MET* 1.3 75.6 - - - +
121Z GLN* 1.3 66.1 + - - +
124Z PHE* 2.9 51.6 + - + +
132Z MET* 3.8 17.8 - - - +
134Z VAL* 4.5 1.7 - - - +
362Z TYR* 4.3 14.4 - - + -
367Z PRO* 4.6 2.2 - - + +
370Z VAL* 3.2 34.1 - - + +
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Residues in contact with GLN 121 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Z GLU 3.0 14.5 + - - +
118Z LYS* 3.1 46.4 + - + +
120Z THR* 1.3 75.1 - - - +
122Z ILE* 1.3 64.1 + - - +
125Z GLU* 2.8 65.4 + - - +
126Z THR* 4.9 7.1 - - - +
362Z TYR* 3.6 17.9 + - - +
367Z PRO* 4.7 6.9 - - + +
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Residues in contact with ILE 122 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Z TRP* 3.6 42.4 - - + +
83Z GLU* 4.1 18.2 - - + +
86Z TRP* 4.1 14.6 - - + -
118Z LYS* 3.0 30.0 + - - +
119Z MET* 4.1 5.2 - - - +
121Z GLN* 1.3 90.2 - - - +
123Z MET* 1.3 68.7 + - - +
126Z THR* 2.9 43.2 + - + +
127Z PHE* 3.2 19.3 + - + -
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Residues in contact with MET 123 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Z TRP* 3.3 55.6 - - + +
90Z PHE* 4.1 17.5 - - + -
103Z THR* 4.6 9.4 - - - -
105Z LEU* 3.7 14.8 - - + -
119Z MET 2.9 24.0 + - - +
120Z THR 3.2 0.6 + - - +
122Z ILE* 1.3 80.0 - - - +
124Z PHE* 1.3 58.4 + - - +
127Z PHE* 3.2 24.5 + - + +
128Z ASN 3.0 21.3 + - - -
129Z VAL* 3.6 21.7 + - + +
132Z MET* 3.6 28.5 - - + -
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Residues in contact with PHE 124 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120Z THR* 2.9 28.3 + - + +
123Z MET* 1.3 79.8 - - - +
125Z GLU* 1.3 60.2 + - - +
128Z ASN* 3.3 23.0 - - - +
129Z VAL* 3.5 27.4 - - + +
130Z PRO 3.7 11.0 - - - -
131Z ALA* 3.8 4.7 - - - -
132Z MET* 3.4 26.7 - - + -
357Z ILE* 3.0 48.0 - - + -
358Z THR 4.0 3.1 - - - -
359Z LYS* 3.8 13.5 - - + -
362Z TYR* 3.6 38.4 - + + -
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Residues in contact with GLU 125 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121Z GLN* 2.8 50.1 + - - +
124Z PHE* 1.3 74.8 - - - +
126Z THR* 1.4 59.1 + - + +
128Z ASN* 4.7 1.6 - - - +
362Z TYR* 3.5 33.6 + - + -
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Residues in contact with THR 126 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Z GLU* 4.2 25.5 + - - +
121Z GLN* 4.9 9.2 - - - +
122Z ILE* 2.9 38.4 + - + +
125Z GLU* 1.4 80.0 - - + +
127Z PHE* 1.3 71.5 + - - +
128Z ASN* 3.6 2.4 - - - +
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Residues in contact with PHE 127 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Z GLU* 3.7 22.4 - - + -
86Z TRP* 3.6 31.4 - + + -
87Z HIS* 4.0 20.2 - - + -
90Z PHE* 3.6 30.5 - + + -
91Z TYR* 4.9 7.2 - + - -
98Z PRO* 3.7 19.0 - - + +
99Z GLU* 3.5 12.6 + - - +
122Z ILE* 3.4 36.6 - - + -
123Z MET* 3.2 28.6 + - + +
126Z THR* 1.3 82.4 + - - +
128Z ASN* 1.3 72.3 + - - +
129Z VAL* 3.4 8.2 + - + -
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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