Contacts of the helix formed by residues 128 - 139 (chain C) in PDB entry 1ZVM
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 ILE 128 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C TRP* 3.6 6.6 - - + -
126C SER 3.3 13.2 - - - +
127C ARG* 1.3 78.4 - - - +
129C LYS* 1.3 66.9 + - - +
130C ASP* 3.4 2.8 + - + -
131C LEU* 3.5 17.9 + - + +
132C ALA* 3.3 12.5 + - - +
207C MET* 3.7 32.1 - - + +
208C LEU 4.3 2.5 - - - +
209C ASP* 4.2 20.9 - - + +
243C ILE* 3.7 39.9 - - + -
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Residues in contact with LYS 129 (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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125C TRP* 3.3 41.0 - - + -
127C ARG 3.8 0.4 - - - -
128C ILE* 1.3 75.7 - - - +
130C ASP* 1.3 72.1 + - - +
132C ALA* 3.1 2.3 + - - +
133C HIS* 3.0 57.4 + - + +
146C GLU* 4.8 0.7 - - + -
155C ASP* 2.8 22.2 + - - +
156C ASP* 2.7 33.8 + - - +
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Residues in contact with ASP 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ILE* 3.4 1.5 + - + -
129C LYS* 1.3 85.0 - - - +
131C LEU* 1.3 62.0 + - - +
133C HIS* 3.4 4.8 + - - +
134C GLN* 3.1 40.5 + - - +
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Residues in contact with LEU 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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128C ILE* 3.5 18.1 + - + +
129C LYS 3.3 0.6 - - - -
130C ASP* 1.3 76.5 - - - +
132C ALA* 1.3 65.9 + - - +
134C GLN* 3.2 9.3 + - + +
135C PHE* 2.9 22.9 + - - +
207C MET* 3.6 14.8 - - + -
243C ILE* 3.5 48.9 - - + -
281C PRO* 4.2 17.5 - - + +
284C PHE* 5.0 5.2 - - + -
285C LEU* 3.9 35.0 - - + -
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Residues in contact with ALA 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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123C LEU* 3.9 9.5 - - + +
125C TRP* 3.6 43.7 - - + -
128C ILE 3.3 6.3 + - - +
129C LYS 3.1 8.8 + - - +
131C LEU* 1.3 76.3 - - - +
133C HIS* 1.3 63.4 + - - +
135C PHE* 3.3 4.0 - - - +
136C THR* 3.2 26.2 + - - +
144C THR* 4.2 2.5 - - + -
207C MET* 3.5 18.0 - - - -
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Residues in contact with HIS 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C TRP* 4.0 5.2 - - - -
129C LYS* 3.0 49.5 + - + +
130C ASP* 3.8 4.7 - - - +
132C ALA* 1.3 74.4 - - - +
134C GLN* 1.3 65.1 + - + +
135C PHE 3.1 2.0 - - - -
136C THR* 3.1 9.1 + - - +
137C GLN* 3.1 29.9 + - + +
144C THR* 3.5 16.3 + - - +
146C GLU* 2.8 45.8 + - + +
147C ASP* 5.0 3.0 + - - +
155C ASP* 3.7 9.9 + - - -
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Residues in contact with GLN 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 ASP* 3.1 39.0 + - - +
131C LEU* 3.2 9.4 + - - +
133C HIS* 1.3 75.9 - - + +
135C PHE* 1.3 63.9 + - - +
137C GLN* 3.4 10.7 + - - +
138C VAL* 3.4 24.1 + - - +
285C LEU* 3.7 30.0 - - + +
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Residues in contact with PHE 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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123C LEU* 3.8 20.4 - - + -
131C LEU 2.9 12.4 + - - +
132C ALA 3.3 9.4 - - - +
134C GLN* 1.3 78.8 - - - +
136C THR* 1.3 56.8 + - + +
138C VAL* 3.0 6.2 + - - +
139C GLN* 2.7 58.3 + - + +
142C MET* 3.7 27.1 - - + -
207C MET* 4.3 9.9 - - + -
241C TRP* 3.6 23.1 - + - -
284C PHE* 3.7 36.1 - + + -
285C LEU* 3.9 11.4 - - + +
288C VAL* 3.9 19.5 - - + -
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Residues in contact with THR 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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123C LEU* 4.3 2.7 - - + -
132C ALA 3.2 7.3 + - - +
133C HIS* 3.1 15.2 + - - -
135C PHE* 1.3 90.0 - - + +
137C GLN* 1.3 63.4 + - - +
138C VAL 3.2 0.2 - - - -
139C GLN 3.8 7.0 - - - -
140C ARG* 3.3 24.6 - - - +
142C MET* 3.5 27.5 - - + +
143C PHE 4.1 0.9 - - - +
144C THR* 3.6 19.9 - - + +
147C ASP* 3.0 35.0 + - - +
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Residues in contact with GLN 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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133C HIS* 3.1 26.3 + - + +
134C GLN* 3.6 11.0 - - - +
135C PHE 3.1 1.2 - - - -
136C THR* 1.3 79.3 + - - +
138C VAL* 1.3 61.9 + - + +
140C ARG* 3.3 37.8 + - - +
147C ASP* 4.4 15.0 + - - -
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Residues in contact with VAL 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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134C GLN 3.4 12.8 + - - +
135C PHE* 3.0 6.7 + - - +
137C GLN* 1.3 81.9 - - + +
139C GLN* 1.3 56.3 + - - +
140C ARG* 3.2 10.7 + - - +
285C LEU* 4.4 12.1 - - + +
288C VAL* 3.7 15.9 - - + +
289C LYS* 3.4 63.5 - - + +
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Residues in contact with GLN 139 (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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135C PHE* 2.7 46.6 + - + +
136C THR* 3.4 9.0 - - - +
138C VAL* 1.3 69.8 - - - +
140C ARG* 1.3 55.6 + - - +
141C ASP* 2.6 41.0 + - - +
142C MET* 2.9 30.4 + - + +
288C VAL* 3.4 23.7 - - + +
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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