Contacts of the helix formed by residues 146 - 161 (chain B) in PDB entry 1OE5
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 GLU 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B GLY* 3.4 27.2 + - - -
99B PRO* 5.0 0.6 - - + +
100B PHE* 3.8 31.1 + - + +
101B GLY* 3.3 27.0 + - - +
102B MET 4.4 0.3 + - - -
109B PHE* 4.2 9.1 - - - -
111B GLU* 3.2 11.1 - - + +
144B GLN 3.8 3.4 + - - -
145B SER* 1.3 68.7 - - - +
147B VAL* 1.3 55.8 + - - +
148B SER* 3.8 12.3 - - - +
149B GLY* 2.8 30.6 + - - +
150B ALA* 2.8 36.6 + - - +
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Residues in contact with VAL 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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145B SER 3.1 9.6 + - - +
146B GLU* 1.3 71.6 - - - +
148B SER* 1.4 62.3 + - - +
150B ALA* 3.9 5.1 - - - +
151B ARG* 2.9 60.5 + - + +
253B PRO* 3.9 26.7 - - + -
292E G 3.9 39.0 - - - +
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 4.6 7.0 - - - -
146B GLU* 3.5 14.8 - - - +
147B VAL* 1.4 79.2 - - - +
149B GLY* 1.3 60.0 + - - +
151B ARG 3.4 0.2 + - - -
152B PHE* 3.0 24.9 + - - +
250B HIS* 3.5 12.9 - - - -
251B PRO* 3.4 28.8 - - - +
252B SER* 3.2 27.4 + - - -
253B PRO* 4.1 4.0 - - - +
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Residues in contact with GLY 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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109B PHE* 3.2 26.5 - - - -
111B GLU* 3.6 8.5 - - - -
146B GLU* 2.8 27.9 + - - -
147B VAL 3.3 0.2 - - - -
148B SER* 1.3 71.3 - - - +
150B ALA* 1.3 63.7 + - - +
152B PHE 3.3 0.2 + - - -
153B TRP* 3.0 29.6 + - - +
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Residues in contact with ALA 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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111B GLU* 3.4 26.6 - - - +
114B HIS* 3.8 11.9 - - + +
145B SER* 3.6 9.6 - - - +
146B GLU 2.8 23.8 + - - +
147B VAL* 4.0 4.7 - - - +
149B GLY* 1.3 72.3 - - - +
151B ARG* 1.3 63.0 + - - +
154B SER* 2.9 29.4 + - - -
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Residues in contact with ARG 151 (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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147B VAL* 2.9 31.7 + - + +
148B SER 3.6 4.5 - - - +
150B ALA* 1.3 78.0 - - - +
152B PHE* 1.4 63.1 + - - +
154B SER* 3.8 3.2 - - - -
155B LEU* 3.0 20.8 + - - +
251B PRO* 2.6 48.5 + - + -
253B PRO* 3.7 7.7 - - - +
258B ALA 3.8 18.4 + - - -
259B ASN* 2.7 38.2 + - - +
262B TRP* 3.4 25.8 - - + -
263B GLU* 4.6 1.7 - - - +
292E G 3.0 29.3 + - - +
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Residues in contact with PHE 152 (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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92B PHE* 4.1 12.6 - + + -
109B PHE* 3.8 29.4 - + + -
148B SER 3.0 17.4 + - - +
149B GLY 3.6 4.3 - - - +
151B ARG* 1.4 77.4 - - - +
153B TRP* 1.3 90.8 + + - +
155B LEU* 3.4 7.4 + - - +
156B PHE* 3.3 51.0 - + - -
172B VAL* 3.9 39.3 - - + -
224B VAL* 4.1 26.2 - - + -
248B ILE* 4.9 3.1 - - + -
251B PRO* 4.7 0.9 - - + -
262B TRP* 3.9 17.2 - + + -
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Residues in contact with TRP 153 (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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79B TYR* 4.9 2.2 - + - -
107B VAL* 4.7 3.4 - - + -
108B PRO 3.3 19.2 + - - -
109B PHE* 2.9 31.5 + - - +
110B GLY* 4.3 2.4 - - - +
111B GLU 4.8 3.1 - - - -
114B HIS* 3.7 31.6 - - + -
115B VAL* 5.0 3.6 - - + -
118B TRP* 3.8 23.4 - + + -
119B LEU* 4.1 25.3 - - + +
149B GLY 3.0 13.8 + - - +
152B PHE* 1.3 98.3 - + - +
154B SER* 1.3 60.7 + - - +
156B PHE* 3.8 6.5 - - + +
157B LYS* 2.8 30.7 + - - +
166B PHE* 3.8 22.9 - + - -
167B PHE* 3.6 27.1 - + - -
172B VAL* 3.8 22.4 - - + -
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Residues in contact with SER 154 (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 HIS* 3.5 21.2 + - - -
150B ALA 2.9 21.5 + - - -
151B ARG* 3.8 4.3 - - - -
153B TRP* 1.3 76.2 - - - +
155B LEU* 1.3 63.2 + - - +
157B LYS* 3.8 4.9 - - - +
158B SER* 3.0 28.8 + - - -
263B GLU* 3.9 7.1 + - - -
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Residues in contact with LEU 155 (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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151B ARG 3.0 13.7 + - - +
152B PHE 3.5 7.6 - - - +
154B SER* 1.3 77.2 - - - +
156B PHE* 1.3 97.6 + - + +
158B SER* 3.1 4.2 + - - -
159B LEU* 2.8 39.9 + - + +
262B TRP* 3.9 15.9 - - + -
263B GLU* 3.2 36.7 + - + +
266B VAL* 4.3 11.2 - - + -
267B ARG* 4.1 24.2 - - + +
270B LEU* 3.9 13.2 - - + -
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Residues in contact with PHE 156 (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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92B PHE* 3.7 25.4 - + - -
118B TRP* 3.8 5.1 - - + -
152B PHE* 3.3 59.2 + + - -
153B TRP* 3.4 15.5 + + + +
155B LEU* 1.3 104.9 - - + +
157B LYS* 1.3 54.6 + - - +
159B LEU* 4.2 8.7 - - + -
160B CYS* 2.8 41.4 + - - +
166B PHE* 3.5 39.3 - + + -
248B ILE* 5.3 2.5 - - + -
262B TRP* 5.5 0.4 - + - -
270B LEU* 4.0 14.1 - - + -
279B LEU* 4.1 12.6 - - + -
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Residues in contact with LYS 157 (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 HIS* 4.3 8.5 - - + +
118B TRP* 3.6 53.5 - - + +
153B TRP 2.8 18.6 + - - +
154B SER* 3.8 5.6 - - - +
156B PHE* 1.3 75.1 - - - +
158B SER* 1.3 65.8 + - - +
161B GLY* 3.1 22.4 + - - +
1281B IPA 3.9 25.4 - - + +
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Residues in contact with SER 158 (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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154B SER* 3.0 22.0 + - - -
155B LEU 3.6 3.6 - - - -
157B LYS* 1.3 79.9 - - - +
159B LEU* 1.3 63.5 + - - +
161B GLY* 4.4 2.1 + - - -
263B GLU* 4.2 9.8 + - - -
267B ARG* 3.7 19.1 + - - -
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Residues in contact with LEU 159 (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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155B LEU* 2.8 32.8 + - + +
156B PHE* 3.8 9.9 - - + +
158B SER* 1.3 76.8 - - - +
160B CYS* 1.3 62.7 + - - +
267B ARG* 3.7 28.9 - - + +
270B LEU* 4.0 15.7 - - + -
276B LEU* 3.9 33.4 - - + -
279B LEU* 4.0 35.1 - - + +
280B THR* 4.9 5.9 - - - +
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Residues in contact with CYS 160 (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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118B TRP* 4.6 0.7 - - + -
156B PHE* 2.8 25.5 + - - +
159B LEU* 1.3 79.9 - - - +
161B GLY* 1.3 56.9 + - - +
162B GLN 2.9 21.1 + - - +
165B THR* 3.5 28.5 + - - +
166B PHE* 3.5 33.7 - - + +
279B LEU* 3.8 31.9 - - - -
280B THR* 5.7 1.4 - - - -
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Residues in contact with GLY 161 (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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118B TRP* 2.8 23.6 + - - -
157B LYS* 3.1 17.7 + - - +
158B SER 4.4 1.9 + - - -
159B LEU 3.7 0.8 - - - -
160B CYS* 1.3 74.9 - - - +
162B GLN* 1.3 67.3 + - - -
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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