Contacts of the helix formed by residues 167 - 177 (chain B) in PDB entry 2A8I
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 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A VAL* 5.5 1.3 - - - -
167A GLY* 6.3 2.2 - - - -
131B GLY 3.1 10.9 + - - -
132B ALA* 3.4 21.4 + - - +
133B LEU* 4.2 4.4 - - - +
134B SER 5.3 1.1 + - - -
166B VAL* 1.3 76.6 - - - +
168B GLU* 1.3 64.8 + - - -
170B ALA* 3.1 12.7 + - - +
171B TYR* 3.1 12.6 + - - +
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Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLU* 5.0 12.0 - - - +
166B VAL 3.6 0.4 + - - -
167B GLY* 1.3 71.0 - - - -
169B GLY* 1.3 56.6 + - - +
171B TYR* 3.2 13.9 + - + +
172B ARG* 2.8 30.8 + - - +
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Residues in contact with GLY 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A HIS* 3.1 15.5 - - - -
260A PRO* 3.3 36.5 - - - +
261A GLY* 4.6 1.8 - - - +
165B LEU* 4.8 0.9 - - - -
166B VAL 3.4 5.5 + - - -
167B GLY 3.1 1.0 - - - -
168B GLU* 1.3 77.3 - - - +
170B ALA* 1.3 63.8 + - - +
172B ARG* 3.4 2.6 + - - -
173B TRP* 3.0 19.8 + - - +
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Residues in contact with ALA 170 (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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130B VAL* 4.4 13.0 - - + -
133B LEU* 3.8 15.8 - - + +
142B VAL* 4.5 4.7 - - - +
165B LEU* 3.6 42.7 - - + +
166B VAL* 3.2 8.4 + - - -
167B GLY 3.1 9.4 + - - +
169B GLY* 1.3 75.5 - - - +
171B TYR* 1.3 62.7 + - - +
173B TRP* 3.4 2.6 + - - +
174B ALA* 3.0 23.6 + - - +
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Residues in contact with TYR 171 (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 LEU* 3.5 12.5 - - + +
134B SER 3.2 22.4 - - - +
135B GLY* 3.8 22.0 - - - -
136B ILE* 4.1 7.2 - - + -
167B GLY 3.1 11.5 + - - +
168B GLU* 3.3 14.6 - - + +
170B ALA* 1.3 74.5 - - - +
172B ARG* 1.3 71.7 + - + +
174B ALA* 3.2 5.4 + - - +
175B VAL* 3.1 40.1 + - + +
181B SER* 3.3 23.3 + - - -
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Residues in contact with ARG 172 (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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109A LEU* 4.0 11.9 - - - +
110A LEU* 3.5 32.6 - - - +
259A HIS* 3.7 29.2 + - - -
260A PRO* 3.7 11.8 - - - +
168B GLU 2.8 19.7 + - - +
169B GLY* 3.7 4.9 - - - +
171B TYR* 1.3 80.1 - - + +
173B TRP* 1.3 56.9 + - - +
175B VAL* 3.3 5.6 + - - +
176B ASP* 2.9 57.1 + - - +
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Residues in contact with TRP 173 (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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259A HIS* 3.6 30.9 - + + +
142B VAL* 4.1 12.8 - - + -
145B ARG* 3.6 29.6 - - + -
146B LEU* 3.7 41.6 - - + +
149B GLU* 3.8 17.0 - - + -
162B PRO* 4.6 9.5 - - + +
165B LEU* 3.4 23.0 - - + +
169B GLY 3.0 18.4 + - - +
170B ALA 3.6 3.4 - - - +
172B ARG* 1.3 77.5 - - - +
174B ALA* 1.3 68.0 + - - +
176B ASP* 3.4 3.4 + - - -
177B HIS* 2.8 70.0 + + + -
179B ILE* 5.6 0.7 - - + -
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Residues in contact with ALA 174 (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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136B ILE* 3.7 24.7 - - + -
142B VAL* 3.8 24.0 - - + -
170B ALA 3.0 13.4 + - - +
171B TYR 3.5 7.6 - - - +
173B TRP* 1.3 84.4 - - - +
175B VAL* 1.3 62.1 + - - +
177B HIS* 3.2 7.4 + - - -
179B ILE* 3.0 34.9 + - + +
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Residues in contact with VAL 175 (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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136B ILE* 4.7 1.8 - - + -
171B TYR* 3.1 45.7 + - + +
172B ARG* 3.7 8.3 - - - +
174B ALA* 1.3 75.2 - - - +
176B ASP* 1.3 69.0 + - - +
178B GLY* 3.2 14.6 + - - -
179B ILE 3.4 16.1 + - - +
180B PRO* 5.9 1.3 - - + -
181B SER* 4.5 10.1 - - - +
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Residues in contact with ASP 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A HIS* 4.8 1.6 + - - -
172B ARG* 2.9 56.7 + - - +
173B TRP* 3.7 7.1 + - - +
174B ALA 3.3 0.2 - - - -
175B VAL* 1.3 81.5 - - - +
177B HIS* 1.3 68.0 + - + +
178B GLY 3.3 1.3 + - - -
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Residues in contact with HIS 177 (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 ARG* 5.2 14.0 + - - +
149B GLU* 4.3 20.7 + - - -
173B TRP* 2.8 82.0 + + + +
174B ALA* 3.2 3.1 + - - +
175B VAL 3.2 0.8 - - - -
176B ASP* 1.3 86.6 - - + +
178B GLY* 1.3 59.7 + - - +
179B ILE* 3.5 9.9 - - + +
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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