Contacts of the helix formed by residues 171 - 178 (chain B) in PDB entry 2PX7
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 ASP 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A THR* 4.4 7.9 - - - +
132A TYR* 2.8 21.6 + - - -
70B ARG* 4.0 14.1 - - - +
71B GLN* 6.1 0.2 - - - +
144B VAL* 3.5 9.1 - - + +
146B THR* 6.1 0.2 - - - +
148B GLN* 3.0 30.8 + - - +
169B ALA* 3.3 8.6 - - - +
170B SER* 1.3 79.5 - - - +
172B ASP* 1.3 64.6 + - - +
173B ALA* 3.7 3.2 - - - +
174B GLN* 2.7 38.0 + - - +
175B LEU* 3.8 15.5 - - - +
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Residues in contact with ASP 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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70B ARG* 2.6 29.2 + - - -
74B VAL* 3.5 8.8 - - - +
88B VAL* 3.4 19.9 - - - +
148B GLN* 3.4 10.3 + - - +
150B PHE* 3.7 19.1 - - + -
155B LEU* 3.8 10.7 - - + +
159B HIS* 2.7 34.8 + - - -
171B ASP* 1.3 75.6 - - - +
173B ALA* 1.3 65.2 + - - +
174B GLN 3.2 0.2 - - - -
175B LEU* 3.0 18.9 + - - +
176B VAL* 3.2 14.4 + - - +
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Residues in contact with ALA 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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132A TYR* 3.4 36.1 - - + -
115B VAL* 3.7 13.7 - - + -
148B GLN* 3.0 17.1 + - - +
150B PHE* 3.8 10.9 - - - -
171B ASP* 3.5 2.2 - - - +
172B ASP* 1.3 74.9 - - - +
174B GLN* 1.3 56.9 + - - +
176B VAL* 3.3 3.3 + - - +
177B GLN* 2.9 30.0 + - - +
183B VAL* 3.9 11.4 - - + +
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Residues in contact with GLN 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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123A THR* 3.8 7.9 - - - +
132A TYR* 3.6 12.6 - - + +
135A VAL* 3.5 32.3 - - + +
167B LEU* 4.5 3.0 - - + +
169B ALA* 3.7 22.5 - - + +
170B SER* 3.0 27.1 + - - +
171B ASP* 2.7 31.7 + - - +
173B ALA* 1.3 75.8 - - - +
175B LEU* 1.3 59.7 + - - +
177B GLN* 3.6 14.8 - - - +
178B ALA* 3.1 26.9 + - - +
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Residues in contact with LEU 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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71B GLN* 3.8 22.7 - - + +
155B LEU* 5.4 0.2 - - + -
158B ALA* 3.6 25.8 - - + +
159B HIS* 3.4 44.2 - - + +
161B TYR* 5.4 1.0 - - - -
162B ALA* 3.9 14.8 - - + -
167B LEU* 3.8 23.8 - - + -
169B ALA* 3.9 17.9 - - + -
171B ASP 3.8 12.8 - - - +
172B ASP* 3.0 9.6 + - - +
174B GLN* 1.3 73.4 - - - +
176B VAL* 1.3 66.8 + - - +
178B ALA* 3.3 17.1 + - - +
179B LEU* 3.6 6.4 + - - +
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Residues in contact with VAL 176 (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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113B ALA* 4.1 2.7 - - + -
150B PHE* 3.7 29.8 - - + -
154B LEU* 3.9 23.8 - - + -
155B LEU* 4.1 9.2 - - + -
158B ALA* 3.8 19.1 - - + -
172B ASP 3.2 6.3 + - - +
173B ALA 3.7 6.7 - - - +
175B LEU* 1.3 73.3 - - - +
177B GLN* 1.3 60.6 + - - +
179B LEU* 2.9 27.7 + - - +
181B TYR* 3.5 28.4 + - + +
183B VAL* 3.8 17.9 - - + -
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Residues in contact with GLN 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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132A TYR* 3.7 16.3 - - + +
133A GLY* 2.6 44.5 + - - +
135A VAL* 5.0 1.4 - - - +
173B ALA 2.9 17.5 + - - +
174B GLN* 3.6 16.1 - - - +
176B VAL* 1.3 76.6 - - - +
178B ALA* 1.3 54.3 + - - +
180B GLY* 2.8 27.2 + - - -
181B TYR 3.9 12.6 - - - +
183B VAL* 4.4 5.8 - - + +
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Residues in contact with ALA 178 (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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161B TYR* 3.7 25.1 + - + -
167B LEU* 3.7 24.2 - - + -
174B GLN 3.1 15.1 + - - +
175B LEU 3.5 11.0 - - - +
176B VAL 3.2 0.4 - - - -
177B GLN* 1.3 75.3 - - - +
179B LEU* 1.3 58.7 + - - +
180B GLY 3.3 0.4 + - - -
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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