Contacts of the helix formed by residues 143 - 157 (chain B) in PDB entry 2ODE
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 PHE 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B PHE* 4.2 11.2 - + + -
89B CYS* 3.6 23.1 - - + -
92B PHE* 3.8 26.8 - + + -
105B ALA* 3.3 46.9 - - + -
108B ILE* 3.6 33.7 - - + -
109B PHE* 4.4 6.1 - + + -
113B VAL* 4.2 8.1 - - + -
131B THR* 3.6 28.5 - - + -
135B LEU* 4.9 1.1 - - + -
140B LEU 5.0 0.4 + - - -
141B THR 3.2 0.4 - - - -
142B CYS* 1.3 85.7 - - + +
144B ASP* 1.3 56.1 + - - +
145B GLN 3.2 3.3 + - - -
146B ALA* 3.3 5.8 + - - -
147B GLN* 2.7 36.4 + - - +
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Residues in contact with ASP 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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93B LYS* 4.1 22.0 + - - +
140B LEU 4.3 0.7 - - - +
141B THR* 3.0 44.6 + - - +
142B CYS 3.5 0.6 - - - -
143B PHE* 1.3 78.9 + - - +
145B GLN* 1.3 57.9 + - - +
147B GLN* 4.0 9.9 - - - +
148B GLY* 3.0 26.0 + - - -
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Residues in contact with GLN 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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126B GLN* 4.5 4.4 + - - +
127B THR* 3.8 24.7 + - + +
130B ALA* 3.5 30.9 - - + +
131B THR* 5.1 4.0 - - - +
134B ASN* 5.3 8.4 + - - +
141B THR 4.8 0.2 + - - -
142B CYS 5.1 1.5 + - - +
143B PHE 3.2 0.6 - - - -
144B ASP* 1.3 77.6 - - - +
146B ALA* 1.3 58.2 + - - +
148B GLY* 3.3 2.5 + - - -
149B LYS* 3.0 33.8 + - + +
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Residues in contact with ALA 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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85B PHE* 3.7 23.6 - - + -
113B VAL* 5.3 0.7 - - + -
123B ILE* 4.1 13.7 - - + -
127B THR* 3.5 16.5 - - + +
131B THR* 3.6 26.1 + - + +
143B PHE 3.3 5.9 + - - +
145B GLN* 1.3 76.4 - - - +
147B GLN* 1.3 64.4 + - - +
149B LYS* 3.3 2.3 + - - +
150B VAL* 3.0 29.5 + - - +
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Residues in contact with GLN 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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85B PHE* 3.8 10.1 - - - -
86B TRP* 3.3 47.6 + - + +
89B CYS* 3.5 24.4 - - + +
90B GLU* 2.7 25.0 + - - +
93B LYS* 3.1 25.1 + - - -
143B PHE 2.7 22.6 + - - +
144B ASP* 4.0 9.0 - - - +
146B ALA* 1.3 72.9 - - - +
148B GLY* 1.3 56.8 + - - +
150B VAL* 3.3 2.4 + - - +
151B HIS* 2.8 28.5 + - + +
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Residues in contact with GLY 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 ASP 3.0 18.1 + - - -
145B GLN* 3.7 1.8 - - - -
146B ALA 3.3 0.2 - - - -
147B GLN* 1.3 74.3 - - - +
149B LYS* 1.3 57.8 + - - +
151B HIS* 3.3 8.4 + - - +
152B SER* 2.9 30.2 + - - -
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Residues in contact with LYS 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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79A GLN* 5.4 6.1 + - - -
122B ASN 5.6 1.3 - - - +
123B ILE* 4.0 17.5 - - + -
124B ASP* 4.7 11.7 + - - -
127B THR* 3.7 27.8 - - + +
145B GLN* 3.0 20.3 + - + +
146B ALA 3.7 7.0 - - - +
147B GLN 3.3 0.2 - - - -
148B GLY* 1.3 77.5 - - - +
150B VAL* 1.3 58.1 + - - +
152B SER* 3.4 8.6 + - - -
153B LEU* 3.0 27.8 + - - +
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Residues in contact with VAL 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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82B ASN* 3.3 47.6 - - + +
85B PHE* 3.8 23.6 - - + -
86B TRP* 4.9 2.9 - - + -
121B VAL* 3.9 12.8 - - + -
122B ASN 4.9 3.6 - - - +
123B ILE* 3.6 21.1 - - + -
146B ALA 3.0 20.0 + - - +
147B GLN 3.9 3.1 - - - +
149B LYS* 1.3 73.4 - - - +
151B HIS* 1.3 64.3 + - - +
153B LEU* 3.3 7.4 + - + +
154B MET* 3.1 27.5 + - + +
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Residues in contact with HIS 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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57B PHE* 3.7 10.7 - + - -
58B ASP* 2.6 34.7 + - - -
61B LEU* 3.9 13.0 - - + -
86B TRP* 3.8 25.1 - + - +
147B GLN 2.8 18.6 + - - +
148B GLY* 3.3 9.0 + - - +
150B VAL* 1.3 77.6 - - - +
152B SER* 1.3 58.4 + - - +
154B MET* 3.4 12.0 + - - +
155B GLU* 2.9 59.4 + - - +
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Residues in contact with SER 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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148B GLY 2.9 17.0 + - - -
149B LYS* 3.6 9.6 - - - -
151B HIS* 1.3 78.9 + - - +
153B LEU* 1.3 63.7 + - - +
155B GLU* 4.3 7.4 - - - -
156B LYS* 3.0 57.5 + - - +
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Residues in contact with LEU 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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180A LYS* 3.4 50.5 - - + +
182A THR* 3.9 24.2 - - + -
82B ASN* 3.9 28.0 - - - +
122B ASN* 3.8 30.1 - - + +
149B LYS 3.0 17.0 + - - +
150B VAL* 3.6 9.0 - - + +
151B HIS 3.3 0.4 - - - -
152B SER* 1.3 74.8 - - - +
154B MET* 1.3 56.2 + - - +
156B LYS* 4.5 1.1 - - - +
157B ASP* 3.0 36.4 + - - +
158B SER* 3.9 0.6 + - - -
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Residues in contact with MET 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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57B PHE* 3.5 24.5 - - + -
70B PHE* 3.9 22.9 - - + -
74B LEU* 4.3 4.0 - - + -
82B ASN* 3.6 20.4 - - + +
83B LEU* 3.5 32.1 - - + -
86B TRP* 3.7 40.2 - - + -
150B VAL* 3.1 22.8 + - + +
151B HIS* 4.1 3.4 - - - -
153B LEU* 1.3 75.5 - - - +
155B GLU* 1.3 60.3 + - - +
158B SER* 3.3 14.0 + - - +
159B TYR* 2.9 31.3 + - - +
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Residues in contact with GLU 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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56B SER* 5.4 3.5 - - - -
57B PHE* 3.6 39.1 + - + +
58B ASP* 5.3 3.2 + - - +
151B HIS* 2.9 42.5 + - - +
152B SER* 3.3 7.1 + - - +
154B MET* 1.3 75.6 - - - +
156B LYS* 1.3 66.4 + - + +
159B TYR* 3.6 9.4 - - + +
160B PRO* 3.3 20.4 - - - +
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Residues in contact with LYS 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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72A VAL* 5.4 15.6 - - + +
75A SER* 2.6 38.0 + - - -
76A ASN* 5.6 2.6 - - - +
79A GLN* 5.7 0.6 - - - +
115A GLU* 5.5 5.1 + - - -
178A ARG 5.9 1.6 - - - +
179A VAL* 3.5 32.6 - - + +
152B SER* 3.0 39.2 + - - +
153B LEU* 4.5 1.1 - - - +
155B GLU* 1.3 86.7 - - + +
157B ASP* 1.3 60.4 + - - +
160B PRO* 3.6 15.1 - - - +
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Residues in contact with ASP 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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179A VAL* 3.8 11.1 - - + +
180A LYS 3.3 23.4 - - - +
181A THR* 3.5 10.2 + - - +
182A THR* 3.1 25.7 + - + +
153B LEU* 3.0 18.8 + - + +
156B LYS* 1.3 77.1 - - - +
158B SER* 1.3 63.3 + - - +
159B TYR 3.5 0.4 - - - -
160B PRO* 3.4 9.9 - - - +
161B ARG* 2.8 56.2 + - - +
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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