Contacts of the helix formed by residues 118 - 130 (chain C) in PDB entry 1M54
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 VAL 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C GLU* 3.0 31.0 - - + -
113C ASN* 3.9 0.7 - - - +
117C SER* 1.3 70.5 - - - +
119C LYS* 1.3 62.6 + - + +
120C ASP 3.0 10.4 + - - -
121C ARG* 3.2 21.1 + - - +
232C HIS* 3.8 23.1 - - + -
236C THR* 5.8 1.1 - - + -
260C THR* 3.9 13.0 - - + -
373C ILE* 4.9 5.8 - - + -
375C PRO* 2.5 42.5 + - + +
376C ASP* 4.5 0.2 - - - +
1310C PLP 3.9 23.8 - - + +
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Residues in contact with LYS 119 (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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117C SER* 3.2 2.5 - - - -
118C VAL* 1.3 77.1 - - + +
120C ASP* 1.3 60.8 + - - +
121C ARG 3.0 1.6 - - - -
122C ILE* 3.3 22.5 - - + +
123C SER* 2.8 32.5 + - - -
149C ASN* 4.2 5.8 - - + -
150C THR* 3.2 47.1 - - + +
222C GLN* 3.7 15.7 - - - -
228C ASN* 5.6 0.2 - - - +
232C HIS* 5.7 1.6 - - - +
257C THR* 4.3 5.8 - - - +
260C THR* 6.3 0.2 - - + -
305C GLY 4.4 2.0 + - - -
1310C PLP 1.1 94.8 + - + +
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Residues in contact with ASP 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ILE* 3.5 31.3 - - + +
113C ASN* 3.3 7.4 - - + +
115C GLY* 3.4 21.4 - - - -
117C SER* 2.4 49.5 + - - +
118C VAL 3.0 1.0 + - - -
119C LYS* 1.3 77.3 - - - +
121C ARG* 1.3 60.0 + - - +
123C SER* 3.6 7.1 - - - -
124C LEU* 3.0 32.6 + - - +
152C ILE* 5.3 0.2 - - - +
153C GLY* 3.3 20.3 + - - +
156C LEU* 5.0 2.5 - - + +
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Residues in contact with ARG 121 (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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84C ILE* 4.0 15.7 - - + -
85C GLY* 3.0 17.4 - - - +
86C ASP 3.3 0.4 - - - +
87C THR* 4.2 1.6 + - - +
108C LYS* 4.5 0.2 - - - +
110C GLU* 2.2 35.2 + - - -
113C ASN* 4.5 2.0 - - - +
118C VAL 3.2 15.8 + - - +
120C ASP* 1.3 80.6 - - - +
122C ILE* 1.3 63.0 + - + +
124C LEU* 3.9 2.5 - - - +
125C ARG* 3.0 26.4 + - - +
231C ALA* 4.2 8.5 + - + +
232C HIS* 3.8 16.4 - - + +
235C THR* 2.9 26.1 + - - +
236C THR* 2.3 37.0 + - - +
239C GLU* 2.5 39.2 + - - -
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Residues in contact with ILE 122 (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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119C LYS* 3.3 28.7 - - + +
121C ARG* 1.3 73.1 - - - +
123C SER* 1.3 71.9 + - - +
125C ARG* 3.6 5.3 - - - +
126C MET* 2.7 33.1 + - + +
150C THR* 3.5 27.1 - - + -
222C GLN* 3.9 19.5 - - + -
227C SER* 5.0 0.5 - - - -
228C ASN* 2.8 57.0 - - + +
231C ALA* 4.6 3.1 - - + -
232C HIS* 3.5 20.2 - - + +
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Residues in contact with SER 123 (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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119C LYS 2.8 23.5 + - - -
120C ASP 3.6 4.9 - - - -
122C ILE* 1.3 81.5 - - - +
124C LEU* 1.3 51.6 + - - +
126C MET* 2.9 5.5 + - - +
127C ILE* 2.6 41.0 + - - +
150C THR* 3.3 13.2 + - - +
153C GLY* 3.2 27.3 - - - -
154C LEU* 3.2 27.6 + - - +
157C ALA* 5.7 0.2 - - - -
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Residues in contact with LEU 124 (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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81C LEU* 4.3 32.5 - - + +
82C LYS* 6.1 0.4 - - - -
84C ILE* 4.2 28.7 - - + +
120C ASP 3.0 16.7 + - - +
121C ARG* 3.9 2.5 - - - +
123C SER* 1.3 75.5 - - - +
125C ARG* 1.3 64.9 + - - +
126C MET 2.9 1.0 + - - -
127C ILE* 3.0 17.8 + - + +
128C GLU* 3.0 43.2 + - + +
157C ALA* 4.8 8.9 - - + +
161C ARG* 4.8 9.0 - - + +
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Residues in contact with ARG 125 (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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66C HIS 2.3 33.9 + - - -
68C THR* 4.0 16.5 + - - -
121C ARG 3.0 18.8 + - - +
122C ILE 3.8 2.9 - - - +
124C LEU* 1.3 77.3 - - - +
126C MET* 1.3 52.3 + - - +
128C GLU* 3.7 15.0 - - - -
129C ASP* 2.7 71.1 + - - +
132C ARG* 5.5 0.2 - - - +
227C SER* 3.6 16.8 - - - +
230C LEU* 3.5 12.8 + - - +
231C ALA* 3.2 40.9 - - + +
234C ASP* 2.7 27.1 + - - +
235C THR* 5.9 0.2 + - - -
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Residues in contact with MET 126 (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 ILE* 2.7 27.5 + - + +
123C SER* 3.2 4.5 - - - +
125C ARG* 1.3 76.6 - - - +
127C ILE* 1.4 54.0 + - - +
128C GLU 2.7 14.8 + - - -
129C ASP* 3.3 7.5 + - - +
130C ALA* 3.4 17.9 + - + +
150C THR* 6.2 0.4 - - + -
154C LEU* 5.2 3.8 - - + -
220C LEU* 3.1 45.9 - - + +
221C ASP 3.5 33.4 - - - +
222C GLN* 3.9 10.1 - - + +
225C ASN* 4.0 14.1 - - + +
227C SER* 4.0 15.9 - - - +
228C ASN* 4.4 18.2 - - + +
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Residues in contact with ILE 127 (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 SER 2.6 22.3 + - - +
124C LEU* 3.0 8.0 + - + +
126C MET* 1.4 69.9 - - - +
128C GLU* 1.3 50.7 + - - +
131C GLU* 2.7 30.0 - - - +
136C LEU* 3.8 7.6 - - - +
142C ILE* 3.5 20.6 - - + -
154C LEU* 3.4 56.5 - - + +
157C ALA* 3.8 20.4 - - + +
158C ALA 4.5 1.8 - - - +
161C ARG* 4.6 11.7 - - + -
163C TYR* 4.0 21.8 - - + -
220C LEU* 3.7 6.1 - - + -
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Residues in contact with GLU 128 (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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124C LEU* 3.0 41.9 + - + +
125C ARG* 3.7 14.6 - - - +
126C MET 2.7 2.0 - - - -
127C ILE* 1.3 82.9 - - - +
129C ASP* 1.3 65.0 + - - +
130C ALA 2.6 10.6 + - - -
131C GLU* 2.9 32.5 + - + +
132C ARG* 3.2 21.2 + - - +
161C ARG* 5.1 3.3 + - - -
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Residues in contact with ASP 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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66C HIS* 4.7 13.1 - - - +
125C ARG* 2.7 63.5 + - - +
126C MET* 3.3 2.4 + - + +
128C GLU* 1.3 74.2 - - - +
130C ALA* 1.3 56.2 + - - +
132C ARG* 3.3 23.4 + - - +
133C ASP* 2.9 25.3 + - - +
227C SER* 3.5 29.2 + - - +
230C LEU* 5.0 4.0 - - - +
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Residues in contact with ALA 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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126C MET 3.4 16.2 - - - +
128C GLU 2.6 0.6 - - - -
129C ASP* 1.3 80.7 - - - +
131C GLU* 1.3 59.0 + - - +
132C ARG 3.2 1.1 - - - -
133C ASP* 3.6 8.4 + - - -
135C THR* 3.5 12.1 + - - -
136C LEU* 2.6 45.8 + - + +
220C LEU* 4.5 15.9 - - + -
225C ASN* 6.1 2.0 - - - +
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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