Contacts of the helix formed by residues 131 - 138 (chain B) in PDB entry 2H07
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 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLN* 3.6 17.3 - - + +
98B ASP* 3.1 27.1 - - - +
129B LEU* 3.6 6.8 - - - +
130B HIS* 1.3 82.1 - - + +
132B ALA* 1.3 59.9 + - - +
133B GLN* 3.7 9.9 - - - +
134B ILE* 2.8 34.0 + - + +
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Residues in contact with ALA 132 (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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98A ASP 4.7 0.2 - - - +
99A LYS* 3.7 27.1 - - + +
107A ILE* 5.5 0.2 - - - +
129B LEU* 4.4 8.0 + - - -
131B ALA* 1.3 70.8 - - - +
133B GLN* 1.3 60.2 + - - +
134B ILE 2.9 6.1 + - - -
135B GLN* 3.1 22.4 + - - +
136B GLY 4.5 0.2 + - - -
144B ASN* 4.9 2.5 - - - +
1005B SO4 3.2 40.7 + - - +
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Residues in contact with GLN 133 (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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98A ASP* 3.0 49.5 + - + +
99A LYS* 3.6 27.7 + - - +
130A HIS* 5.8 1.4 + - - -
131A ALA* 3.8 13.5 - - + +
133A GLN* 3.5 34.9 + - + -
134A ILE 5.5 0.2 - - - +
137A PHE* 3.2 19.4 - - + -
131B ALA* 3.0 11.6 + - - +
132B ALA* 1.3 81.3 + - - +
134B ILE* 1.3 62.0 + - - +
135B GLN 3.2 0.7 - - - -
136B GLY* 3.0 13.0 + - - -
137B PHE* 3.8 3.1 + - - -
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Residues in contact with ILE 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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92B PHE* 4.4 15.7 - - + -
95B ALA* 3.7 41.5 - - + +
98B ASP* 4.3 7.2 - - + +
109B ALA* 4.5 2.9 - - + -
129B LEU* 3.8 24.5 - - + -
130B HIS 4.4 3.1 - - - +
131B ALA* 2.8 34.6 + - + +
133B GLN* 1.3 76.6 - - + +
135B GLN* 1.3 66.1 + - - +
137B PHE* 2.9 44.8 + - + +
138B PHE* 3.7 12.4 - - + -
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Residues in contact with GLN 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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100A LYS* 2.9 33.1 + - - +
107A ILE* 3.8 14.2 - - + +
129B LEU* 3.8 12.3 - - + +
132B ALA 3.1 11.7 + - - +
134B ILE* 1.3 76.6 - - - +
136B GLY* 1.3 59.3 + - - +
137B PHE 3.1 4.7 + - - -
138B PHE* 3.2 21.9 + - - +
140B ILE 5.1 0.7 - - - +
142B VAL* 2.9 54.1 + - + +
144B ASN* 3.4 17.0 - - - +
1005B SO4 2.6 29.1 + - - +
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Residues in contact with GLY 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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107A ILE* 3.7 20.0 - - - +
110A LYS* 3.1 36.1 - - - +
137A PHE* 3.5 20.4 - - - -
133B GLN 3.0 12.1 + - - -
135B GLN* 1.3 78.8 - - - +
137B PHE* 1.3 53.6 + - - +
138B PHE 3.1 6.1 - - - -
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Residues in contact with PHE 137 (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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110A LYS* 4.9 2.0 - - - -
133A GLN* 3.2 34.5 - - + -
136A GLY* 3.6 18.2 - - - -
137A PHE* 3.7 14.8 - + - -
98B ASP* 3.6 26.5 - - + -
107B ILE* 4.0 10.8 - - + -
109B ALA* 3.8 24.5 - - + -
110B LYS* 3.3 53.6 - - + +
113B ALA* 3.6 17.4 - - + +
114B ASN* 4.4 3.1 - - - +
117B SER* 5.6 0.2 + - - -
133B GLN 3.9 5.8 - - - -
134B ILE* 2.9 27.3 + - + +
136B GLY* 1.3 78.1 - - - +
138B PHE* 1.3 59.9 + - + +
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Residues in contact with PHE 138 (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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110A LYS* 4.1 4.9 - - - +
92B PHE* 3.6 31.9 - + - -
113B ALA* 3.4 40.4 - - + -
116B LEU* 4.1 6.5 - - + -
117B SER* 3.9 9.2 - - - -
124B ILE* 3.7 24.9 - - + -
129B LEU* 6.2 0.4 - - + -
134B ILE* 3.7 21.8 - - + -
135B GLN* 3.2 12.3 + - - +
136B GLY* 3.1 8.2 - - - +
137B PHE* 1.3 81.7 - - - +
139B ASP* 1.3 67.5 + - - +
140B ILE* 3.6 36.3 - - + +
142B VAL* 3.7 22.4 - - + -
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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