Contacts of the helix formed by residues 104 - 114 (chain F) 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 GLY 104 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102F VAL 3.4 1.4 + - - -
103F MET* 1.3 71.7 - - - +
105F ALA* 1.3 59.9 + - - +
106F GLU 3.1 0.9 + - - -
107F LEU* 3.1 13.0 + - - +
108F ARG* 3.2 25.4 + - - +
131F GLU* 3.1 25.6 - - - -
135F GLY* 2.9 13.9 + - - -
137F ILE* 3.6 10.8 - - - +
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Residues in contact with ALA 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F MET* 3.4 1.6 - - + +
104F GLY* 1.3 73.3 - - - +
106F GLU* 1.3 62.3 + - + +
108F ARG* 3.7 25.9 - - - +
109F HIS* 3.0 52.3 + - + -
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Residues in contact with GLU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F PHE* 3.8 32.6 - - + +
95F ASP* 5.1 4.0 - - - +
96F LYS* 5.8 1.6 + - - -
102F VAL* 3.8 5.2 - - - +
103F MET* 2.9 55.8 + - + +
105F ALA* 1.3 76.7 - - + +
107F LEU* 1.3 59.6 + - - +
109F HIS* 4.1 1.8 - - - +
110F VAL* 3.0 34.4 + - - +
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Residues in contact with LEU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LEU* 4.7 13.2 - - + -
94F PHE* 4.4 4.7 - - + -
102F VAL* 3.6 31.2 - - + -
103F MET 3.5 0.8 + - - -
104F GLY 3.1 1.6 + - - -
106F GLU* 1.3 79.2 - - - +
108F ARG* 1.3 57.5 + - - +
110F VAL* 3.4 4.1 + - + +
111F LEU* 2.9 46.3 + - + +
127F MET* 3.9 21.8 - - + -
137F ILE* 3.8 26.9 - - + -
139F TYR* 5.6 0.2 - - + -
142F PHE* 3.9 30.5 - - + -
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Residues in contact with ARG 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F GLY* 3.2 14.6 + - - +
105F ALA* 3.7 32.6 - - - +
106F GLU 3.3 0.2 - - - -
107F LEU* 1.3 79.4 - - + +
109F HIS* 1.3 69.5 + - + +
111F LEU* 3.9 1.9 - - - +
112F ALA* 3.1 24.6 + - - +
120F GLU* 3.7 25.7 + - - +
123F VAL* 3.6 19.6 - - + +
124F GLU* 5.3 8.3 - - - +
127F MET* 4.4 16.4 - - + -
131F GLU* 3.5 25.6 + - - +
137F ILE* 5.6 0.2 - - + -
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Residues in contact with HIS 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F ALA* 3.0 40.5 + - + +
106F GLU* 4.2 2.5 - - - +
108F ARG* 1.3 84.5 + - + +
110F VAL* 1.3 59.3 + - + +
112F ALA* 3.3 3.6 + - + -
113F THR* 2.8 43.6 + - + +
120F GLU* 5.0 7.0 - - - -
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Residues in contact with VAL 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F PHE* 3.7 26.9 - - + -
106F GLU* 3.0 20.2 + - - +
107F LEU* 3.9 4.9 - - + +
109F HIS* 1.3 78.3 - - + +
111F LEU* 1.3 58.6 + - - +
114F LEU* 2.9 67.7 + - + +
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Residues in contact with LEU 111 (chain F).
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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794D CYS* 5.6 12.3 - - + -
107F LEU* 2.9 32.9 + - + +
108F ARG 3.9 3.8 - - - +
110F VAL* 1.3 77.7 - - - +
112F ALA* 1.3 59.3 + - - +
114F LEU 4.8 1.8 + - - +
116F GLU 4.0 5.1 - - - +
118F MET* 3.2 43.5 + - + +
123F VAL* 3.8 28.7 - - + -
126F LEU* 4.2 26.0 - - + -
127F MET* 5.3 1.6 - - - -
142F PHE* 5.9 2.5 - - + -
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Residues in contact with ALA 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ARG 3.1 16.5 + - - +
109F HIS* 4.0 4.3 - - + +
111F LEU* 1.3 80.1 - - - +
113F THR* 1.3 66.1 + - + +
114F LEU 3.8 0.4 - - - -
117F LYS* 3.3 29.9 - - - +
118F MET 3.1 19.8 + - - +
120F GLU* 3.7 19.5 - - + +
123F VAL* 4.4 1.6 - - + -
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Residues in contact with THR 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F HIS* 2.8 27.1 + - + +
112F ALA* 1.3 86.9 - - + +
114F LEU* 1.3 78.6 + - - +
115F GLY 3.7 1.6 + - - -
117F LYS* 3.2 29.4 + - - +
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Residues in contact with LEU 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787D ILE* 5.3 8.0 - - + +
791D GLN* 4.4 6.6 + - - -
110F VAL* 2.9 52.6 + - + +
111F LEU* 4.8 1.8 - - - +
112F ALA 3.8 1.0 - - - -
113F THR* 1.3 91.8 - - - +
115F GLY* 1.3 63.7 + - - +
116F GLU 3.7 5.8 + - - +
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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