Contacts of the helix formed by residues 103 - 116 (chain A) in PDB entry 2O0K
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 THR 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A PHE* 5.3 0.7 - - - -
102A TRP* 1.3 76.7 - - - +
104A ARG* 1.3 63.8 + - - +
105A GLU* 3.4 11.5 + - - +
106A MET* 3.1 35.9 + - - +
107A VAL* 3.1 26.7 + - - +
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A THR* 1.3 72.2 - - - +
105A GLU* 1.3 65.6 + - - +
107A VAL* 3.4 6.8 + - + +
108A GLU* 3.0 45.4 + - + +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 3.7 25.2 - - + -
75A GLN* 4.8 5.2 + - - -
103A THR* 3.6 10.4 + - - +
104A ARG* 1.3 79.8 - - - +
106A MET* 1.3 63.3 + - - +
108A GLU* 3.4 5.0 + - - +
109A GLU* 3.0 24.2 + - - +
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Residues in contact with MET 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 3.7 45.5 - - + -
100A THR* 6.0 0.9 - - + -
101A GLN 4.7 2.9 - - - +
102A TRP* 3.8 33.0 - - + +
103A THR* 3.1 40.2 + - - +
105A GLU* 1.3 79.2 - - - +
107A VAL* 1.3 58.2 + - - +
109A GLU* 3.2 3.6 + - - +
110A TRP* 2.8 29.5 + - - +
213A PHE* 3.5 35.1 - - + -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TRP* 3.8 29.6 - - + -
103A THR 3.1 17.2 + - - +
104A ARG* 3.8 9.0 - - + +
106A MET* 1.3 74.7 - - - +
108A GLU* 1.3 70.7 + - - +
110A TRP* 3.1 7.5 + - + +
111A LYS* 2.8 47.0 + - + +
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG* 3.0 30.6 + - + +
105A GLU* 3.8 4.7 - - - +
107A VAL* 1.3 87.1 - - - +
109A GLU* 1.3 61.3 + - - +
111A LYS* 3.3 24.2 + - - +
112A LYS* 2.8 28.1 + - - +
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Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 4.2 14.8 - - + -
75A GLN* 4.9 4.9 + - - +
105A GLU* 3.0 17.0 + - + +
106A MET 3.6 3.6 - - - +
108A GLU* 1.3 73.8 - - - +
110A TRP* 1.3 66.1 + - - +
112A LYS* 3.0 24.1 + - - +
113A CYS* 3.1 15.6 + - - -
119A TYR* 2.7 35.8 + - - -
123A THR* 4.7 0.2 - - - +
124A TYR* 2.5 32.0 + - + +
213A PHE* 3.9 15.7 - - + -
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Residues in contact with TRP 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TRP* 3.6 33.0 - + + -
106A MET 2.8 13.8 + - - +
107A VAL* 3.3 11.7 - - + +
109A GLU* 1.3 76.5 - - - +
111A LYS* 1.3 86.1 + - + +
113A CYS* 3.2 2.9 + - - +
114A ARG* 3.1 52.8 + - + +
179A CYS 4.8 8.4 + - - -
180A PHE* 3.6 36.5 - + - -
213A PHE* 3.9 12.9 + - + -
214A LEU* 3.7 26.9 + - + +
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Residues in contact with LYS 111 (chain A).
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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107A VAL* 2.8 33.3 + - - +
108A GLU* 3.6 29.1 + - - +
110A TRP* 1.3 91.1 - - + +
112A LYS* 1.3 66.0 + - - +
114A ARG* 3.4 33.1 + - - +
115A ASP* 3.0 30.6 + - - +
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLU 2.8 15.2 + - - +
109A GLU* 3.0 21.5 + - - +
111A LYS* 1.3 77.9 - - - +
113A CYS* 1.3 56.5 + - - +
115A ASP* 3.8 1.9 - - - +
116A ASP* 2.9 41.4 + - + +
119A TYR* 3.5 51.8 + - + -
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Residues in contact with CYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU* 3.1 16.9 + - - -
110A TRP 3.2 4.0 + - - +
112A LYS* 1.3 73.2 - - - +
114A ARG* 1.3 64.0 + - - +
115A ASP 3.1 2.3 + - - -
116A ASP 3.4 12.0 + - - +
119A TYR* 4.0 11.0 - - - -
120A PHE* 3.8 21.3 - - + -
124A TYR* 3.6 36.3 - - - -
176A HIS* 2.8 23.7 - - - -
180A PHE* 3.4 21.3 - - + -
214A LEU* 4.3 8.7 - - + -
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TRP* 3.1 29.3 + - + +
111A LYS* 3.6 47.4 - - - +
113A CYS* 1.3 77.3 - - - +
115A ASP* 1.3 91.6 + - - +
176A HIS* 3.6 13.4 + - - -
180A PHE* 3.4 45.5 - - + +
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS* 3.0 15.4 + - - +
112A LYS* 4.4 2.0 - - - +
113A CYS 3.1 0.4 - - - -
114A ARG* 1.3 121.9 + - - +
116A ASP* 1.3 57.7 + - + +
117A ILE 3.8 3.0 + - - -
176A HIS* 5.7 0.2 - - - -
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LYS* 2.9 25.2 + - + +
113A CYS 3.7 5.5 - - - +
115A ASP* 1.3 77.1 - - + +
117A ILE* 1.3 63.3 + - - +
118A VAL* 3.3 10.7 + - - +
119A TYR* 2.7 46.8 + - + +
120A PHE 3.0 9.9 + - - -
148A LYS* 5.2 4.3 + - - -
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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