Contacts of the helix formed by residues 124 - 134 (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 GLY 124 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B SER* 2.8 16.1 + - - -
122B TRP 3.7 1.6 - - - -
123B LYS* 1.3 87.4 + - - -
125B CYS* 1.3 66.7 + - - +
126B VAL 3.1 3.9 + - - -
127B GLN* 3.4 13.0 + - - +
128B THR* 2.9 22.6 + - - +
176B TYR* 4.6 2.0 + - - -
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Residues in contact with CYS 125 (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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87B ARG* 4.7 12.6 - - - +
112B ILE* 6.5 0.4 - - - -
116B ALA* 3.7 39.3 - - + -
119B MET* 4.5 10.8 - - - -
121B SER* 4.2 17.5 - - - -
123B LYS* 3.6 8.4 - - + +
124B GLY* 1.3 77.1 - - - +
126B VAL* 1.3 59.6 + - + +
128B THR* 3.3 8.6 + - - -
129B LEU* 2.8 46.1 + - + +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LYS* 5.2 6.3 - - + +
124B GLY 3.1 1.2 + - - -
125B CYS* 1.3 78.5 - - + +
127B GLN* 1.3 59.6 + - - +
129B LEU* 3.5 8.0 - - + +
130B VAL* 2.9 40.0 + - + +
147B LEU* 4.2 18.8 - - + -
150B LEU* 3.7 29.6 - - + -
173B LEU* 5.2 2.2 - - + -
176B TYR* 3.7 48.0 - - + -
179B THR* 4.8 5.2 - - - +
180B VAL* 4.9 6.7 - - + -
208B TRP* 5.8 0.9 - - + -
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLY 3.4 8.7 + - - +
126B VAL* 1.3 78.9 - - - +
128B THR* 1.3 58.1 + - + +
130B VAL* 4.4 11.8 - - - +
131B GLU* 2.8 44.8 + - - +
176B TYR* 3.9 20.1 - - + +
179B THR* 3.2 34.8 - - - +
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Residues in contact with THR 128 (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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87B ARG* 5.9 2.9 - - - -
124B GLY* 2.9 30.7 - - - +
125B CYS* 3.4 8.2 + - - +
126B VAL 3.1 0.2 - - - -
127B GLN* 1.3 72.9 - - + +
129B LEU* 1.3 64.4 + - - +
131B GLU* 3.6 3.7 - - - +
132B LYS* 2.7 41.5 + - - +
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Residues in contact with LEU 129 (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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91B LEU* 4.6 15.7 - - + -
112B ILE* 4.5 11.0 - - + -
116B ALA* 5.9 1.3 - - + -
125B CYS* 2.8 31.7 + - + +
126B VAL* 3.5 7.0 - - + +
128B THR* 1.3 84.3 + - - +
130B VAL* 1.3 57.8 + - + +
132B LYS* 4.6 1.6 - - - -
133B TYR* 2.8 63.2 + - + +
143B LEU* 4.0 13.6 - - + +
146B ILE* 4.0 41.1 - - + -
147B LEU* 5.7 4.3 - - + -
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Residues in contact with VAL 130 (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* 2.9 34.6 + - + +
127B GLN* 3.8 13.9 - - - +
129B LEU* 1.3 74.5 - - - +
131B GLU* 1.3 59.7 + - - +
134B SER* 2.7 39.9 + - - -
143B LEU* 4.5 7.0 - - + -
147B LEU* 4.4 10.1 - - + -
179B THR* 5.8 8.1 - - - +
180B VAL* 6.2 1.3 - - + -
183B LEU* 4.1 42.6 - - + -
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Residues in contact with GLU 131 (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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127B GLN* 2.8 34.2 + - - +
128B THR* 4.0 4.9 - - - +
130B VAL* 1.3 75.8 - - - +
132B LYS* 1.3 59.6 + - - +
134B SER* 4.1 9.3 + - - -
135B ASN* 4.7 4.2 - - - +
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Residues in contact with LYS 132 (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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91B LEU* 4.9 11.2 - - + -
95B GLN* 3.8 6.3 + - - -
128B THR* 2.7 25.4 + - - +
129B LEU* 3.9 2.7 - - - +
131B GLU* 1.3 74.9 - - - +
133B TYR* 1.3 100.8 + - + +
134B SER 3.6 0.4 - - - -
135B ASN* 3.4 14.4 - - - +
136B ASP* 5.2 1.7 - - - +
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Residues in contact with TYR 133 (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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91B LEU* 3.4 30.1 + - + +
95B GLN* 2.6 35.0 + - + -
129B LEU* 2.8 50.8 + - + +
130B VAL 3.7 0.2 - - - -
132B LYS* 1.3 105.6 + - + +
134B SER* 1.3 63.9 + - - +
135B ASN* 3.6 2.7 - - - -
136B ASP* 3.1 21.3 - - + +
139B SER* 4.0 25.5 - - - -
140B LEU* 4.0 2.4 + - - +
142B PHE* 4.0 20.9 - + - -
143B LEU* 3.7 22.2 - - + +
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 2.7 42.6 + - - +
131B GLU* 4.1 9.2 + - - -
132B LYS 3.6 0.6 - - - -
133B TYR* 1.3 73.9 - - - +
135B ASN* 1.3 73.1 + - - +
136B ASP 3.7 1.7 - - - +
140B LEU* 3.6 18.8 - - - +
143B LEU* 4.2 7.4 - - - -
183B LEU* 4.2 11.2 - - - -
190B LYS* 4.1 12.3 + - - -
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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