Contacts of the helix formed by residues 134 - 141 (chain A) in PDB entry 2BZG
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 SER 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.3 19.1 - - - +
89A VAL* 4.0 2.0 - - - +
91A ILE* 3.7 5.4 - - - +
133A CYS* 1.3 80.0 - - - +
135A ILE* 1.3 66.4 + - - +
136A PHE* 3.2 21.2 + - - +
137A ASP* 2.9 39.6 + - - +
138A LEU* 3.9 1.4 + - - +
1246A SAH 3.1 23.7 + - - -
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 3.6 21.3 - - + -
68A PRO* 3.7 18.6 - - + -
69A LEU* 3.8 22.4 - - + -
89A VAL* 3.2 33.0 - - + -
134A SER* 1.3 74.9 + - - +
136A PHE* 1.3 90.9 + - + +
138A LEU* 3.2 26.7 + - + +
139A PRO* 3.9 4.2 - - - +
158A ILE* 4.1 4.7 - - + -
166A TYR* 4.4 10.5 - - + -
169A THR* 3.9 14.8 - - + +
170A MSE 4.2 6.1 - - + -
1246A SAH 3.0 14.1 + - - +
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Residues in contact with PHE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A SER* 3.0 17.0 + - - +
135A ILE* 1.3 89.0 - - + +
137A ASP* 1.3 61.1 + - - +
138A LEU 3.3 0.4 - - - -
139A PRO* 3.5 13.0 - - - +
140A ARG* 3.9 12.2 + - - -
158A ILE* 3.9 20.6 - - + -
162A ASP* 3.7 39.5 - - + -
165A CYS* 3.6 32.8 - - + -
166A TYR* 3.9 20.2 - - + -
169A THR* 4.4 6.7 - - - -
1246A SAH 4.2 5.8 - - - -
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Residues in contact with ASP 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 3.9 33.4 - - + +
118A THR* 5.1 0.5 - - - +
133A CYS* 3.3 16.7 - - - +
134A SER* 2.9 39.8 + - - +
136A PHE* 1.3 79.6 - - - +
138A LEU* 1.3 62.9 + - - +
139A PRO* 3.4 0.7 - - - -
140A ARG* 3.1 41.2 + - - +
141A THR* 3.7 8.1 - - + +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 3.6 32.3 - - + -
89A VAL* 4.1 9.2 - - + -
131A TYR* 3.8 31.2 - - + -
133A CYS* 3.9 16.8 - - - -
134A SER 4.1 4.0 - - - +
135A ILE* 3.2 25.1 + - + +
137A ASP* 1.3 77.7 - - - +
139A PRO* 1.3 62.2 - - + +
141A THR* 2.8 35.7 + - + +
143A ILE* 3.8 28.1 - - + +
169A THR* 4.8 4.3 - - + -
173A LEU* 4.5 9.4 - - + -
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Residues in contact with PRO 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE 3.9 3.4 - - - +
136A PHE 3.5 15.0 - - - +
137A ASP 3.4 4.5 - - - -
138A LEU* 1.3 93.0 - - + +
140A ARG* 1.3 61.7 + - + +
141A THR 3.3 5.5 + - - +
169A THR* 3.9 25.6 - - + +
172A SER* 4.7 13.0 - - - +
173A LEU* 6.1 1.1 - - + -
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLU* 3.3 24.3 + - + +
115A ILE* 4.0 25.9 - - + +
136A PHE* 3.9 15.2 + - - +
137A ASP* 3.1 31.1 + - - +
138A LEU 3.1 1.4 - - - -
139A PRO* 1.3 79.8 - - + +
141A THR* 1.3 60.4 + - - +
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Residues in contact with THR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ILE* 4.0 25.8 - - + -
114A GLU* 4.0 5.8 - - - +
115A ILE* 4.5 6.1 - - + -
131A TYR* 4.3 8.9 - - + -
133A CYS* 5.7 0.2 - - - -
137A ASP* 3.7 15.7 - - + +
138A LEU* 2.8 26.1 + - + +
139A PRO 4.0 5.5 - - - +
140A ARG* 1.3 83.2 - - - +
142A ASN* 1.3 67.3 + - - +
143A ILE* 3.2 24.1 + - - +
144A GLY 5.1 0.2 + - - -
1247A B3P 3.6 15.5 - - - -
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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