Contacts of the helix formed by residues 148 - 156 (chain B) in PDB entry 3E0D
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 ALA 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B PHE* 3.9 1.3 - - - -
95B HIS* 3.1 28.8 - - - +
96B LEU* 5.8 0.2 - - + -
143B SER 3.3 24.5 - - - +
144B GLY* 3.8 7.4 - - - -
145B CYS 2.7 17.4 + - - +
147B GLY* 1.3 78.4 - - - +
149B GLU* 1.3 62.2 + - - +
150B ILE 3.7 0.7 - - - -
151B PRO* 3.7 3.5 - - + +
152B GLN* 2.9 28.9 + - - +
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Residues in contact with GLU 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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75B VAL* 3.5 30.1 - - - +
94B PHE* 3.4 35.5 - - + -
95B HIS 4.1 3.1 + - - +
96B LEU* 4.8 9.0 - - - +
129B ARG* 3.2 15.5 + - - +
143B SER 4.9 0.4 + - - -
148B ALA* 1.3 73.9 - - - +
150B ILE* 1.3 59.5 + - + +
152B GLN* 3.2 4.0 + - - +
153B PHE* 2.8 48.0 + - + -
165B ARG* 2.7 40.9 + - + -
169B ASP* 4.5 9.2 - - - +
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Residues in contact with ILE 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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143B SER* 4.8 9.6 + - - +
148B ALA* 4.8 0.2 - - - +
149B GLU* 1.3 74.7 - - + +
151B PRO* 1.3 72.3 - - + +
153B PHE* 3.1 9.4 + - - +
154B ILE* 3.0 41.3 + - + +
162B ALA* 4.0 21.5 - - + +
165B ARG* 4.3 14.8 - - + -
166B LEU* 3.8 36.3 - - + +
169B ASP* 4.6 5.2 - - - +
177B PHE* 4.0 19.5 - - + -
179B ILE* 5.6 0.9 - - + -
196B LEU* 4.0 13.9 - - + -
199B PHE* 4.3 11.0 - - + -
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Residues in contact with PRO 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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143B SER* 4.0 13.7 - - - +
144B GLY 4.0 7.6 - - - +
145B CYS 3.3 26.2 - - - +
146B LEU* 4.2 11.2 - - - +
148B ALA* 3.7 7.0 - - + +
150B ILE* 1.3 96.1 - - + +
152B GLN* 1.3 63.0 + - - +
154B ILE* 3.2 7.6 + - + +
155B LEU* 3.0 21.5 + - - +
192B VAL* 3.5 40.3 - - + +
196B LEU* 4.9 7.2 - - + -
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Residues in contact with GLN 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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94B PHE* 3.7 26.2 - - + -
146B LEU 2.8 26.5 + - - +
147B GLY* 3.9 6.5 - - - -
148B ALA 2.9 21.5 + - - +
149B GLU 3.2 5.1 + - - +
151B PRO* 1.3 78.6 - - - +
153B PHE* 1.3 62.1 + - + +
155B LEU* 3.3 23.3 + - - +
156B GLN* 3.3 50.4 + - - +
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Residues in contact with PHE 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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94B PHE* 5.0 15.3 - + - -
149B GLU* 2.8 48.1 + - + -
150B ILE* 3.1 2.9 + - - +
152B GLN* 1.3 72.6 - - + +
154B ILE* 1.3 61.9 + - - +
156B GLN* 3.1 25.2 + - - +
158B ARG* 3.1 28.2 + - + +
161B LEU* 3.5 40.6 - - + -
162B ALA* 3.5 29.4 - - + -
165B ARG* 4.0 35.2 - - + -
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Residues in contact with ILE 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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150B ILE* 3.0 39.5 + - + +
151B PRO* 3.5 10.3 - - + +
153B PHE* 1.3 78.0 - - - +
155B LEU* 1.3 61.9 + - - +
157B ASP* 3.1 13.7 + - - -
159B LEU* 4.3 13.6 - - + +
162B ALA* 4.0 12.3 - - + -
191B LYS* 3.7 18.5 + - + +
192B VAL* 4.1 21.8 - - + +
195B VAL* 3.8 46.7 - - + -
196B LEU* 3.9 17.3 - - + -
199B PHE* 4.4 2.2 - - + -
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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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146B LEU* 3.8 23.8 - - + -
151B PRO 3.0 14.3 + - - +
152B GLN* 3.5 31.6 - - - +
154B ILE* 1.3 76.4 - - - +
156B GLN* 1.3 59.6 + - + +
157B ASP* 3.2 4.3 + - - +
188B GLU* 3.8 35.9 - - + +
191B LYS* 3.5 25.5 + - + +
192B VAL* 3.9 11.0 - - + -
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Residues in contact with GLN 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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94B PHE* 5.6 3.0 - - - -
152B GLN* 3.3 41.1 + - - +
153B PHE* 3.1 22.9 + - - +
155B LEU* 1.3 75.1 - - + +
157B ASP* 1.3 67.7 + - - +
158B ARG* 3.1 22.2 + - + +
161B LEU* 5.8 0.5 - - - +
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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