Contacts of the helix formed by residues 132 - 136 (chain B) in PDB entry 2HR7
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 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B THR 3.8 1.2 + - - -
131B ILE* 1.3 71.4 - - - +
133B TRP* 1.3 61.5 + - - +
134B SER* 2.6 31.6 + - - -
135B ARG* 3.2 24.0 + - + +
136B ILE* 4.2 1.7 + - - +
172B THR* 2.8 27.7 + - + +
173B VAL 4.7 3.5 - - - +
181B ARG* 3.6 27.6 + - + +
189B GLN* 2.8 35.6 + - - +
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Residues in contact with TRP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 4.1 19.7 - - + -
104B LEU* 4.0 8.7 - - + -
109B LEU* 4.5 2.9 - - + -
112B ILE* 4.4 10.8 - - + -
117B VAL* 4.0 14.4 - - + -
119B ILE* 3.9 18.8 - - + -
128B LEU* 4.4 8.1 + - + +
131B ILE* 3.7 42.9 + - + +
132B ASP* 1.3 68.4 + - - +
134B SER* 1.3 56.7 + - - +
135B ARG 3.0 5.6 - - - -
136B ILE* 2.9 40.6 + - + +
137B LEU* 3.0 34.6 + - + +
140B VAL* 3.7 17.3 - - + -
143B ASN* 3.9 11.9 - - - +
145B ILE* 3.7 23.8 - - + +
183B TRP* 4.1 10.8 - + - -
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Residues in contact with SER 134 (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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132B ASP* 2.6 26.7 + - - -
133B TRP* 1.3 76.8 - - - +
135B ARG* 1.3 62.6 + - - +
136B ILE 3.3 0.2 - - - -
137B LEU 3.5 9.4 - - - +
138B ASP* 5.4 0.2 - - - -
140B VAL* 3.7 16.1 - - - +
1I NAG 3.3 18.9 - - - +
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Residues in contact with ARG 135 (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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110B MET 3.5 9.7 - - - +
132B ASP* 3.5 32.0 + - + +
133B TRP 3.0 0.8 - - - -
134B SER* 1.3 84.8 + - - +
136B ILE* 1.3 59.7 + - + +
172B THR* 3.9 18.9 - - + +
189B GLN* 3.7 16.6 - - - +
190B LYS 5.3 4.0 - - - +
191B VAL* 3.3 37.4 - - + +
192B CYS 3.4 16.0 + - - +
194B THR* 4.6 16.7 - - - +
1I NAG 3.7 14.1 - - - +
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Residues in contact with ILE 136 (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 LEU* 3.5 25.8 - - + +
110B MET* 3.5 11.4 - - - +
111B ASN* 3.4 9.3 - - - +
112B ILE* 2.9 58.9 + - + +
131B ILE* 4.1 5.6 - - + -
132B ASP 4.2 6.1 - - - +
133B TRP* 2.9 28.1 + - + +
135B ARG* 1.3 81.9 - - + +
137B LEU* 1.3 57.3 + - + +
183B TRP* 3.6 24.2 - - + -
189B GLN* 4.1 17.0 - - - +
1I NAG 3.7 8.0 + - - -
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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