Contacts of the helix formed by residues 129 - 138 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C TYR* 3.7 18.8 - - + +
89C VAL* 5.4 0.3 - - - +
127C ARG* 4.0 9.1 - - + +
128C ALA* 1.3 74.7 - - - +
130C GLN* 1.3 66.1 + - - +
131C ARG* 3.4 19.5 - - - +
132C MET* 2.8 31.6 + - - +
133C TYR 3.1 9.5 + - - -
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Residues in contact with GLN 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TYR* 2.8 47.0 + - + +
53C ARG* 3.5 28.1 + - - +
129C ASP* 1.3 73.5 - - - +
131C ARG* 1.3 64.8 + - - +
133C TYR* 3.2 12.4 + - - +
134C GLU* 2.7 55.4 + - - +
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ASP* 3.4 19.0 - - - +
130C GLN* 1.3 81.5 - - - +
132C MET* 1.3 63.9 + - + +
134C GLU* 3.3 25.2 + - - +
135C GLU* 3.2 46.3 + - - +
139C HIS* 6.3 1.0 - - - -
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Residues in contact with MET 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C VAL* 3.8 14.8 - - + -
91C ALA* 5.1 1.8 - - - -
99C THR* 4.8 1.6 - - + -
101C ALA* 3.7 24.7 - - + -
122C TYR* 3.9 28.0 - - + +
126C LYS* 3.7 31.4 - - + +
127C ARG 3.6 19.5 - - - +
128C ALA* 4.0 8.1 - - - -
129C ASP* 2.8 25.7 + - - +
131C ARG* 1.3 71.6 - - + +
133C TYR* 1.3 68.0 + - - +
135C GLU* 3.3 11.5 + - - +
136C LEU* 2.9 35.0 + - + +
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Residues in contact with TYR 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TYR* 4.1 10.3 - - + -
53C ARG* 3.8 31.6 + - + +
87C VAL* 3.4 33.0 - - + +
88C GLY 5.4 1.1 - - - -
89C VAL* 3.8 21.1 - - + +
103C LEU* 4.2 13.2 - - + -
105C SER* 5.3 0.2 + - - -
129C ASP 3.1 9.3 + - - +
130C GLN* 3.4 29.4 - - - +
132C MET* 1.3 78.8 - - - +
134C GLU* 1.3 65.5 + - - +
136C LEU* 3.3 1.2 + - - +
137C TYR* 2.9 60.7 + + + +
138C TYR* 4.2 20.2 + + - -
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Residues in contact with GLU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLN* 2.7 54.3 + - - +
131C ARG* 3.5 25.9 + - - +
133C TYR* 1.3 79.2 - - + +
135C GLU* 1.3 63.8 + - + +
138C TYR* 2.9 47.0 + - + -
139C HIS* 3.5 12.1 + - + -
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Residues in contact with GLU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C TYR* 2.7 42.1 + - - +
126C LYS* 5.9 0.9 - - - -
131C ARG* 3.2 46.5 + - - +
132C MET* 3.3 10.8 + - - +
134C GLU* 1.3 78.6 - - - +
136C LEU* 1.3 63.8 + - - +
139C HIS* 3.2 17.4 + - + +
140C ARG* 3.0 38.4 + - + +
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Residues in contact with LEU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C VAL* 3.8 29.4 - - + -
101C ALA* 4.0 13.0 - - + -
103C LEU* 3.6 32.3 - - + +
118C ASN* 2.8 36.3 + - + +
120C ARG* 3.5 31.9 - - + +
122C TYR* 3.8 13.2 - - + +
132C MET* 2.9 30.2 + - + +
133C TYR* 3.9 3.4 - - - +
135C GLU* 1.3 75.2 - - - +
137C TYR* 1.3 59.8 + - - +
140C ARG* 4.1 6.1 - - + +
142C PRO* 3.5 7.6 - - - +
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LEU* 3.9 14.6 - - + -
105C SER* 3.6 31.4 + - - -
107C PRO* 6.0 0.3 - - - +
113C TYR* 4.9 15.6 - - - +
114C SER 5.1 1.0 + - - -
116C TRP* 4.0 30.2 + + + -
133C TYR* 2.9 52.0 + + + +
134C GLU 4.3 0.4 - - - +
136C LEU* 1.3 75.7 - - - +
138C TYR* 1.3 92.6 + + + +
142C PRO* 3.4 20.6 - - + +
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Residues in contact with TYR 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C ARG* 5.5 3.6 + - - -
133C TYR* 4.2 18.5 + + - -
134C GLU* 2.9 46.5 + - + -
137C TYR* 1.3 106.1 - + + +
139C HIS* 1.3 81.7 + + + +
140C ARG 3.4 1.6 + - - -
141C SER* 3.8 8.1 + - - -
142C PRO* 4.8 0.2 - - - +
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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