Contacts of the helix formed by residues 137 - 149 (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 LYS 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B ASP* 3.3 29.4 + - - +
103B GLU* 3.2 28.4 + - - -
104B THR* 4.5 2.2 + - + -
107B ILE 5.4 1.0 + - - +
108B ASP* 5.6 1.8 + - - -
109B VAL* 4.0 24.3 - - + +
136B ALA* 1.3 68.5 - - - +
138B MET* 1.3 59.3 + - - +
139B ASP 3.5 1.8 - - - -
140B GLU* 3.4 25.8 + - - +
141B ILE* 3.0 31.4 + - + +
164B TYR* 4.3 1.8 - - - -
273B LEU* 3.9 30.3 - - + -
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Residues in contact with MET 138 (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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128B LEU* 3.7 24.0 - - + -
130B HIS* 3.5 20.0 - - - -
136B ALA* 2.9 20.0 + - - +
137B LYS* 1.3 70.5 - - - +
139B ASP* 1.3 68.7 + - - +
141B ILE* 4.4 3.1 - - + +
142B VAL* 2.8 38.7 + - + +
152B LEU* 4.2 5.4 - - + -
154B GLU* 3.8 13.0 - - - +
164B TYR* 3.5 36.8 - - + -
169B LEU* 4.3 8.1 - - + -
172B PHE* 3.5 38.8 - - + -
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Residues in contact with ASP 139 (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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138B MET* 1.3 76.8 - - - +
140B GLU* 1.3 69.4 + - - +
142B VAL* 4.1 3.1 - - - +
143B GLU* 3.3 21.7 + - - +
164B TYR* 3.1 32.4 + - - +
165B LYS* 3.9 19.9 - - - +
172B PHE* 5.3 3.5 - - - -
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Residues in contact with GLU 140 (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* 3.8 28.9 - - + -
137B LYS* 3.4 35.1 - - - +
138B MET 3.2 0.2 - - - -
139B ASP* 1.3 84.7 + - + +
141B ILE* 1.3 58.3 + - - +
143B GLU* 3.4 4.9 + - - +
144B ILE* 2.9 35.8 + - + +
164B TYR* 4.0 3.8 + - - -
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE* 4.1 18.8 - - + +
109B VAL* 4.1 14.4 - - + -
112B LEU* 4.1 13.2 - - + -
126B LEU* 3.9 26.9 - - + -
128B LEU* 4.0 25.6 - - + -
136B ALA* 3.8 28.0 - - + -
137B LYS* 3.0 23.1 + - - +
138B MET* 4.2 3.8 - - + +
140B GLU* 1.3 73.0 - - - +
142B VAL* 1.3 66.5 + - - +
144B ILE* 3.4 6.0 + - - +
145B CYS* 3.0 22.7 + - - -
152B LEU* 4.2 10.3 - - + -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B MET* 2.8 30.0 + - + +
139B ASP* 4.1 3.1 - - - +
141B ILE* 1.3 73.7 - - - +
143B GLU* 1.3 60.1 + - - +
145B CYS* 3.3 2.6 + - - +
146B LYS* 2.8 32.9 + - + +
152B LEU* 3.8 26.5 - - + -
172B PHE* 4.0 33.4 - - + +
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Residues in contact with GLU 143 (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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139B ASP 3.3 16.5 + - - +
140B GLU* 3.7 5.2 - - - +
141B ILE 3.3 0.2 - - - -
142B VAL* 1.3 78.1 - - - +
144B ILE* 1.3 61.1 + - + +
146B LYS* 3.1 25.5 + - - +
147B GLU* 2.8 41.9 + - + +
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Residues in contact with ILE 144 (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* 3.7 30.5 - - + +
112B LEU* 3.9 22.9 - - + -
113B LYS* 3.8 32.1 - - + -
116B ILE* 3.3 31.4 - - + -
140B GLU* 2.9 25.9 + - + +
141B ILE* 3.8 4.3 - - - +
143B GLU* 1.3 76.9 - - + +
145B CYS* 1.3 63.0 + - - +
147B GLU* 4.6 2.5 - - - -
148B ASN* 2.9 38.1 + - - +
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Residues in contact with CYS 145 (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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112B LEU* 5.1 4.7 - - - -
116B ILE* 5.9 0.2 - - - -
126B LEU* 3.8 29.4 - - - -
141B ILE* 3.0 23.1 + - - +
142B VAL* 3.8 4.0 - - - +
144B ILE* 1.3 77.5 - - - +
146B LYS* 1.3 63.0 + - - +
148B ASN 3.3 0.2 + - - -
149B ASP* 3.0 4.7 + - - -
150B ILE* 2.9 65.3 + - - +
152B LEU* 4.3 20.4 - - + -
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Residues in contact with LYS 146 (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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142B VAL* 2.8 23.0 + - + +
143B GLU* 3.1 25.6 + - - +
145B CYS* 1.3 79.0 - - - +
147B GLU* 1.3 62.6 - - - +
148B ASN 3.2 0.9 + - - -
149B ASP* 3.3 10.6 + - - +
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Residues in contact with GLU 147 (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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143B GLU* 2.8 31.6 + - + +
144B ILE* 3.9 5.2 - - - +
145B CYS 3.3 0.2 - - - -
146B LYS* 1.3 72.6 - - - +
148B ASN* 1.3 68.2 + - - +
149B ASP 3.5 0.2 - - - -
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Residues in contact with ASN 148 (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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116B ILE* 3.6 23.4 - - + +
122B LYS* 3.5 17.5 - - + +
144B ILE* 2.9 39.3 + - - +
146B LYS 3.1 0.4 - - - -
147B GLU* 1.3 86.7 - - - +
149B ASP* 1.3 71.5 + - - +
150B ILE* 3.3 21.3 + - + +
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Residues in contact with ASP 149 (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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122B LYS* 2.7 43.9 + - + +
124B LYS 4.5 1.4 - - - +
145B CYS 3.0 5.6 + - - -
146B LYS 3.3 9.7 + - - +
147B GLU 3.5 0.8 + - - -
148B ASN* 1.3 80.3 - - - +
150B ILE* 1.3 60.0 + - - +
151B VAL* 4.1 2.8 + - - +
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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