Contacts of the helix formed by residues 129 - 138 (chain E) in PDB entry 3ZWG
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 129 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51E TYR* 3.7 18.4 - - + -
89E VAL* 5.4 0.2 - - - +
127E ARG 4.1 8.2 - - - +
128E ALA* 1.3 75.6 - - - +
130E GLN* 1.3 68.6 + - - +
131E ARG* 3.4 18.4 - - - +
132E MET* 2.9 33.3 + - - +
133E TYR 3.1 9.7 + - - -
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Residues in contact with GLN 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E TYR* 2.7 47.1 + - + +
53E ARG* 3.5 27.4 + - - +
129E ASP* 1.3 73.4 - - - +
131E ARG* 1.3 64.2 + - - +
133E TYR* 3.2 13.0 + - - +
134E GLU* 2.8 57.7 + - - +
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Residues in contact with ARG 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E ASP* 3.4 20.1 - - - +
130E GLN* 1.3 81.7 - - - +
132E MET* 1.3 64.8 + - + +
134E GLU* 3.2 25.6 + - - +
135E GLU* 3.2 44.8 + - - +
139E HIS* 6.2 2.0 - - - -
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Residues in contact with MET 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E VAL* 3.7 22.4 - - + -
91E ALA* 5.0 1.8 - - - -
99E THR* 4.9 0.9 - - + -
101E ALA* 3.9 15.3 - - + -
122E TYR* 4.0 27.4 - - + +
126E LYS* 3.8 31.0 - - + +
127E ARG 3.6 19.3 - - - +
128E ALA* 3.9 10.1 - - - -
129E ASP* 2.9 25.5 + - - +
131E ARG* 1.3 70.7 - - + +
133E TYR* 1.3 66.6 + - - +
135E GLU* 3.2 11.8 + - - +
136E LEU* 2.9 36.3 + - + +
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Residues in contact with TYR 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E TYR* 4.1 11.0 - - + -
53E ARG* 3.8 32.5 + - + +
87E VAL* 3.4 34.0 - - + +
88E GLY 5.4 1.1 - - - -
89E VAL* 3.8 20.7 - - + +
103E LEU* 4.2 10.5 - - + -
105E SER* 5.3 0.2 + - - -
129E ASP 3.1 9.9 + - - +
130E GLN* 3.4 28.9 - - - +
132E MET* 1.3 77.2 - - - +
134E GLU* 1.3 65.4 - - - +
136E LEU* 3.8 1.4 - - - +
137E TYR* 2.9 62.8 + + + +
138E TYR* 4.2 20.8 + + - -
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Residues in contact with GLU 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLN* 2.8 51.3 + - - +
131E ARG* 3.4 26.2 + - - +
132E MET 3.2 0.2 - - - -
133E TYR* 1.3 81.1 - - + +
135E GLU* 1.3 63.4 + - + +
138E TYR* 2.9 47.3 + - + -
139E HIS* 3.6 11.9 + - + -
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Residues in contact with GLU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E TYR* 2.6 43.3 + - - +
126E LYS* 5.9 1.2 - - - -
131E ARG* 3.2 44.8 + - - +
132E MET* 3.2 11.6 + - - +
134E GLU* 1.3 76.7 - - - +
136E LEU* 1.3 64.6 + - - +
139E HIS* 3.1 20.1 + - + +
140E ARG* 3.0 38.4 + - + +
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Residues in contact with LEU 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E VAL* 3.8 30.3 - - + -
101E ALA* 4.0 14.1 - - + +
103E LEU* 3.5 33.0 - - + +
118E ASN* 2.7 36.9 + - + +
120E ARG* 3.5 33.0 - - + +
122E TYR* 3.8 14.1 - - + +
132E MET* 2.9 28.5 + - + +
133E TYR* 4.0 3.4 - - - +
135E GLU* 1.3 74.6 - - - +
137E TYR* 1.3 59.5 + - - +
140E ARG* 4.1 5.9 - - + +
142E PRO* 3.5 6.8 - - - +
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Residues in contact with TYR 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E LEU* 3.8 13.2 - - + -
105E SER* 3.5 32.9 + - - -
107E PRO* 5.9 0.7 - - - +
113E TYR* 4.9 15.6 - - - +
114E SER 5.0 1.0 + - - -
116E TRP* 4.0 30.0 + + + -
133E TYR* 2.9 49.9 + + + +
134E GLU 4.2 0.7 - - - +
136E LEU* 1.3 78.8 - - - +
138E TYR* 1.3 92.2 + + + +
142E PRO* 3.5 19.5 - - + +
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Residues in contact with TYR 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E ARG* 5.5 3.8 + - - -
133E TYR* 4.2 16.9 + + - -
134E GLU* 2.9 50.3 + - + -
137E TYR* 1.3 104.8 - + - +
139E HIS* 1.3 80.9 + + + +
140E ARG 3.4 1.8 + - - -
141E SER* 3.7 9.4 + - - -
142E PRO* 4.7 0.3 - - - +
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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