Contacts of the helix formed by residues 108 - 119 (chain B) in PDB entry 1O69
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 ASP 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B ASP 3.0 17.1 + - - +
101B CYS 3.9 6.1 - - - -
102B ASP* 3.7 18.3 - - - +
106B ASN 3.2 2.9 + - - -
107B ILE* 1.3 78.7 - - - +
109B VAL* 1.3 65.5 + - - +
110B ASP* 3.1 17.4 + - - +
111B LEU* 3.1 32.7 + - + +
112B LEU 3.0 18.7 + - - -
137B LYS* 5.6 1.9 + - - -
295B ASN* 4.7 5.8 + - - +
298B GLN* 5.8 1.0 + - - -
349B ASN* 3.8 23.5 + - - +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ASP* 4.8 1.2 + - - -
107B ILE* 4.6 2.5 - - - +
108B ASP* 1.3 75.2 + - - +
110B ASP* 1.3 63.9 + - - +
112B LEU* 3.3 9.0 + - - +
113B LYS* 3.0 42.2 + - + +
137B LYS* 4.0 31.2 - - + +
140B GLU* 3.8 30.5 - - + -
141B ILE* 4.1 14.1 - - + -
144B ILE* 3.7 20.1 - - + +
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ASP* 3.1 13.0 + - - +
109B VAL* 1.3 79.3 - - - +
111B LEU* 1.3 66.1 + - + +
113B LYS* 3.4 22.6 + - - +
114B LEU* 3.0 23.8 + - - +
298B GLN* 6.3 1.6 - - - +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 3.6 15.9 - - + +
100B ASP* 3.6 26.2 - - + +
108B ASP* 3.1 22.6 + - + +
110B ASP* 1.3 78.1 - - + +
112B LEU* 1.3 56.7 + - - +
114B LEU* 3.3 17.0 + - + +
115B ALA* 2.8 31.5 + - - +
298B GLN* 4.7 15.3 - - + +
299B LYS 5.5 0.7 - - - +
347B TYR* 3.7 22.3 - - + +
348B LEU 3.9 16.8 - - - +
349B ASN* 3.3 28.5 - - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LEU* 4.0 12.8 - - + -
99B ILE* 3.6 29.0 - - + +
107B ILE* 3.9 9.0 - - + -
108B ASP 3.0 14.0 + - - +
109B VAL* 3.4 7.9 - - - +
110B ASP 3.3 0.2 - - - -
111B LEU* 1.3 75.8 - - - +
113B LYS* 1.3 63.0 + - - +
115B ALA* 3.4 1.0 + - - +
116B ILE* 3.1 43.1 + - + +
126B LEU* 4.2 25.6 - - + -
141B ILE* 4.1 28.9 - - + +
144B ILE* 3.9 24.7 - - + -
145B CYS* 5.1 1.3 - - - -
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL* 3.0 31.4 + - + +
110B ASP* 3.7 19.7 + - - +
112B LEU* 1.3 75.4 - - - +
114B LEU* 1.3 58.8 + - - +
116B ILE* 3.4 9.7 + - - +
117B LYS* 2.9 30.6 + - - +
144B ILE* 3.8 33.0 - - + -
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ASP 3.0 17.5 + - - +
111B LEU* 3.6 17.0 - - + +
113B LYS* 1.3 72.9 - - - +
115B ALA* 1.3 61.5 + - - +
117B LYS* 3.2 26.8 + - + +
118B GLU* 2.9 59.3 + - - +
300B ASP* 5.7 2.0 - - - +
347B TYR* 3.9 24.0 - - + -
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LEU* 4.3 7.9 - - + -
97B VAL* 4.3 8.1 - - + -
99B ILE* 4.3 15.5 - - + -
111B LEU 2.8 17.6 + - - +
112B LEU 3.8 4.3 - - - +
114B LEU* 1.3 78.0 - - - +
116B ILE* 1.3 61.1 + - - +
118B GLU* 3.4 2.6 + - - +
119B CYS* 3.2 28.0 + - - -
347B TYR* 3.5 38.2 + - + -
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LEU* 3.7 13.2 - - + -
112B LEU* 3.1 26.8 + - + +
113B LYS* 3.6 5.8 - - - +
115B ALA* 1.3 72.1 - - - +
117B LYS* 1.3 67.9 + - - +
119B CYS* 3.3 21.8 + - - +
122B LYS* 6.5 0.7 - - + -
123B PRO* 4.5 8.0 - - + +
144B ILE* 3.3 33.7 - - + -
145B CYS* 5.9 1.1 - - - -
148B ASN* 3.6 31.2 - - + +
150B ILE* 3.5 28.0 - - + -
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LYS 2.9 18.2 + - - +
114B LEU* 3.2 30.7 + - + +
116B ILE* 1.3 80.9 - - - +
118B GLU* 1.3 73.2 + - - +
119B CYS 3.5 4.0 + - - +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 2.9 38.0 + - + +
115B ALA 3.4 1.8 + - - +
116B ILE 3.2 0.2 - - - -
117B LYS* 1.3 91.5 + - - +
119B CYS* 1.3 62.2 + - - +
120B GLU* 3.4 2.6 + - - +
300B ASP* 4.6 5.3 - - - +
345B LYS* 4.1 12.8 + - - +
347B TYR* 2.8 35.7 + - - +
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Residues in contact with CYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ILE* 4.0 24.7 - - - -
76B LEU* 4.3 8.5 - - - -
97B VAL* 4.8 7.4 - - - -
115B ALA 3.2 18.6 + - - -
116B ILE 3.3 13.3 + - - +
117B LYS 3.4 4.0 - - - +
118B GLU* 1.3 78.2 - - - +
120B GLU* 1.3 63.9 + - - +
121B LYS* 3.2 18.2 + - - +
123B PRO* 3.9 26.9 - - + -
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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