Contacts of the helix formed by residues 139 - 150 (chain B) in PDB entry 4OL0
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 SER 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B GLN* 5.3 2.8 - - - +
98B LYS* 3.9 7.1 + - - +
133B TYR* 4.0 23.7 - - - -
136B ASP* 2.6 29.2 + - - -
137B VAL 3.0 0.2 - - - -
138B THR* 1.3 77.6 - - - +
140B LEU* 1.3 61.2 + - - +
141B PRO* 3.3 3.8 - - - -
142B PHE* 3.3 34.9 - - - -
143B LEU* 3.2 20.8 + - - +
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Residues in contact with LEU 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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133B TYR 4.0 1.1 - - - +
134B SER* 3.6 21.8 - - - +
136B ASP 3.7 7.8 + - - +
137B VAL* 2.8 33.1 + - + +
139B SER* 1.3 78.8 - - - +
141B PRO* 1.3 60.8 - - + +
143B LEU* 3.4 23.9 - - + +
144B LEU* 2.8 35.6 + - + +
183B LEU* 4.7 2.2 - - + -
187B CYS* 3.9 24.5 - - + +
190B LYS* 5.1 14.4 - - + +
191B ALA* 5.9 3.6 - - + -
197B MET* 3.9 25.1 - - + -
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Residues in contact with PRO 141 (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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137B VAL 3.5 11.2 - - - +
138B THR* 3.6 11.7 - - - +
139B SER 3.3 5.2 - - - -
140B LEU* 1.3 91.3 - - + +
142B PHE* 1.3 57.0 + - + +
144B LEU* 3.6 1.3 + - + -
145B GLU 3.2 13.3 + - - -
197B MET* 5.3 7.4 - - - -
200B LYS* 3.2 45.8 + - + +
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Residues in contact with PHE 142 (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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94B ILE* 3.8 39.7 - - + +
95B GLN* 4.5 9.4 - - + -
98B LYS* 4.1 25.1 - - + -
105B VAL* 3.5 28.5 - - + -
133B TYR* 4.0 33.0 - + - -
138B THR 4.8 0.4 - - - -
139B SER* 3.3 49.8 + - - -
141B PRO* 1.3 77.6 - - + +
143B LEU* 1.3 68.8 + - - +
144B LEU 3.3 0.2 - - - -
145B GLU* 3.3 8.3 - - - +
146B ILE* 3.1 35.6 + - + +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 4.0 40.8 - - + +
130B VAL* 4.4 4.7 - - - +
133B TYR* 3.7 36.1 - - + +
134B SER* 4.1 5.2 - - - +
139B SER 3.2 14.5 + - - +
140B LEU* 3.1 24.3 + - + +
142B PHE* 1.3 85.2 - - + +
144B LEU* 1.3 61.6 + - + +
146B ILE* 3.5 5.7 + - + +
147B LEU* 3.2 40.4 + - + +
183B LEU* 4.5 13.9 - - + -
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Residues in contact with LEU 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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140B LEU* 2.8 16.8 + - + +
141B PRO 3.9 4.7 - - - +
143B LEU* 1.3 74.5 - - + +
145B GLU* 1.3 56.4 + - - +
147B LEU* 3.4 4.4 + - + +
148B THR* 2.5 40.9 + - - +
183B LEU* 4.6 12.8 - - + -
184B LEU* 3.5 28.9 - - + -
187B CYS* 4.2 13.9 - - - -
197B MET* 3.6 32.8 - - + -
200B LYS* 3.9 30.5 - - + +
201B VAL* 4.1 13.2 - - + +
204B CYS* 4.1 9.5 - - + -
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Residues in contact with GLU 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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110A ARG* 5.9 1.0 - - - +
105B VAL* 4.6 6.5 - - + +
106B THR* 3.8 33.8 + - - +
109B ALA* 3.6 21.5 - - + -
141B PRO 3.2 13.4 + - - +
142B PHE* 3.3 15.0 - - + +
144B LEU* 1.3 74.9 - - - +
146B ILE* 1.3 55.0 - - - +
148B THR* 2.7 32.3 + - - +
149B VAL* 3.0 19.3 + - + +
200B LYS* 3.2 21.3 + - - +
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Residues in contact with ILE 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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94B ILE* 4.5 1.3 - - + -
109B ALA* 3.8 26.0 - - + +
112B ILE* 3.8 33.4 - - + -
113B ALA* 4.8 8.7 - - + -
129B LEU* 4.0 38.6 - - + -
142B PHE* 3.1 28.2 + - + +
143B LEU* 3.7 8.7 - - + +
145B GLU* 1.3 77.8 - - - +
147B LEU* 1.3 64.2 + - + +
149B VAL* 2.8 29.5 + - - +
150B LEU* 3.0 17.5 + - + +
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Residues in contact with LEU 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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126B VAL* 4.2 31.2 - - + +
129B LEU* 5.7 3.8 - - + -
130B VAL* 4.4 7.6 - - + -
143B LEU* 3.2 28.5 + - + +
144B LEU* 3.8 9.2 - - + +
146B ILE* 1.3 85.2 - - + +
148B THR* 1.3 58.3 + - - +
150B LEU* 4.1 10.1 - - + -
151B PRO* 3.3 7.6 - - - +
180B VAL* 4.8 15.7 - - + -
183B LEU* 3.1 36.1 - - + -
204B CYS* 3.9 11.2 - - - -
208B TRP* 2.6 32.4 + - + +
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Residues in contact with THR 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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144B LEU* 2.5 21.8 + - - +
145B GLU* 2.7 18.6 + - - +
147B LEU* 1.3 79.8 - - - +
149B VAL* 1.3 58.9 + - - +
150B LEU 3.5 0.2 - - - -
151B PRO* 3.7 2.1 - - - +
152B GLU* 3.3 22.1 - - - +
200B LYS 4.4 2.4 + - - -
203B ARG* 4.0 20.8 - - + +
204B CYS* 3.2 22.1 + - - +
207B SER* 3.1 27.9 + - - +
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 3.1 33.7 - - + +
106B THR* 5.8 2.0 - - + +
109B ALA* 3.9 16.8 - - + +
110B LEU* 3.3 24.5 - - + -
113B ALA* 3.6 21.3 - - + -
145B GLU* 3.0 17.3 + - - +
146B ILE* 2.8 16.0 + - - +
148B THR* 1.3 77.4 - - - +
150B LEU* 1.3 60.3 + - - +
151B PRO* 3.5 1.3 - - - -
152B GLU* 3.7 6.7 - - - +
153B GLU* 3.0 27.5 + - - +
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Residues in contact with LEU 150 (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 ALA* 4.0 23.8 - - + +
116B ALA* 4.5 9.2 - - + -
117B LEU* 3.8 31.1 - - + +
123B LYS* 6.3 1.1 - - - +
126B VAL* 3.7 29.2 - - + -
146B ILE* 3.0 17.8 + - + +
147B LEU* 4.2 10.8 - - + +
149B VAL* 1.3 80.6 - - - +
151B PRO* 1.3 68.9 - - + +
152B GLU 3.4 0.2 + - - -
153B GLU* 3.5 6.6 + - - +
154B VAL* 3.4 16.6 + - - +
173B LEU* 3.8 23.6 - - + -
208B TRP* 4.5 9.2 - - + -
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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