Contacts of the helix formed by residues 148 - 162 (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 GLY 148 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C THR* 2.8 21.9 + - - +
147C SER* 1.3 77.0 - - - +
149C ASN* 1.3 66.3 + - - -
150C THR* 3.0 3.4 - - - -
151C GLY 3.1 7.6 + - - -
152C ILE* 3.4 19.1 + - - +
177C LYS* 6.4 1.1 - - - -
181C LEU* 5.3 0.3 - - - +
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Residues in contact with ASN 149 (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* 3.3 31.6 + - - -
119C LYS* 4.2 7.2 - - + +
148C GLY* 1.3 71.5 - - - -
150C THR* 1.3 57.5 + - - +
152C ILE* 3.4 11.1 + - - +
153C GLY* 2.8 26.5 + - - -
305C GLY* 5.7 0.4 - - - -
376C ASP* 2.4 28.2 + - - +
379C ARG* 4.8 0.2 + - - -
380C ASN* 2.9 29.5 + - - -
381C TYR* 4.4 0.6 + - - -
1310C PLP 2.6 34.0 + - - +
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Residues in contact with THR 150 (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* 3.2 30.8 - - + +
122C ILE* 3.5 22.7 - - + -
123C SER* 3.3 7.5 + - - +
126C MET* 6.2 0.7 - - + -
144C GLU* 4.8 5.4 - - - +
146C THR* 3.7 9.6 - - - +
148C GLY* 4.6 0.2 - - - -
149C ASN* 1.3 76.3 + - - +
151C GLY* 1.3 58.5 + - - +
154C LEU* 2.9 40.2 + - + +
222C GLN* 3.1 37.2 + - + +
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Residues in contact with GLY 151 (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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144C GLU* 4.4 11.7 - - - -
146C THR 3.5 19.9 + - - -
147C SER* 5.1 1.3 - - - -
148C GLY 3.1 7.6 + - - -
150C THR* 1.3 75.7 - - - +
152C ILE* 1.3 55.1 + - - +
154C LEU* 3.3 4.0 + - - +
155C ALA* 2.8 35.9 + - - +
165C CYS* 4.9 1.6 - - - -
167C ILE* 4.9 6.7 - - - +
181C LEU* 3.9 10.7 - - - +
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Residues in contact with ILE 152 (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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115C GLY* 4.5 16.4 - - - +
117C SER* 5.3 2.2 - - - +
120C ASP* 5.3 0.4 - - - +
147C SER 6.0 0.2 - - - -
148C GLY 3.4 16.2 - - - +
149C ASN* 3.5 17.7 - - - +
151C GLY* 1.3 72.7 - - - +
153C GLY* 1.3 56.1 + - - +
155C ALA* 3.5 2.3 - - - +
156C LEU* 2.6 38.2 + - + +
177C LYS* 4.9 11.2 - - + +
180C VAL* 4.7 11.4 - - + -
181C LEU* 3.8 23.6 - - + -
184C LEU* 3.9 17.8 - - + +
379C ARG* 3.5 30.5 - - - +
380C ASN* 3.8 11.4 - - - +
345D LEU* 5.5 2.0 - - + -
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Residues in contact with GLY 153 (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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120C ASP* 3.3 24.2 + - - +
123C SER* 3.2 25.6 - - - -
149C ASN 2.8 13.8 + - - -
152C ILE* 1.3 76.7 - - - +
154C LEU* 1.3 62.6 + - - +
156C LEU* 3.3 4.4 + - - +
157C ALA* 3.2 21.0 + - - +
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Residues in contact with LEU 154 (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* 3.2 13.4 + - - +
126C MET* 5.2 2.9 - - - -
127C ILE* 3.4 37.0 - - + +
142C ILE* 4.3 14.8 - - + -
144C GLU* 3.1 52.5 - - + +
150C THR* 2.9 21.0 + - + +
151C GLY 3.6 2.9 - - - +
153C GLY* 1.3 77.1 - - - +
155C ALA* 1.3 52.0 + - - +
156C LEU 3.2 0.2 + - - -
157C ALA 3.2 0.3 + - - -
158C ALA* 2.7 37.1 + - - +
165C CYS* 4.8 5.8 - - - -
220C LEU* 3.8 20.0 - - + -
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Residues in contact with ALA 155 (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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151C GLY 2.8 22.4 + - - +
152C ILE* 3.7 5.2 - - - +
154C LEU* 1.3 69.9 - - - +
156C LEU* 1.3 68.1 + - - +
158C ALA* 3.4 8.5 - - - +
159C ALA* 3.1 16.5 + - - +
165C CYS* 4.2 15.8 - - + -
181C LEU* 4.4 4.9 - - + -
184C LEU* 3.3 32.5 - - + +
186C ALA* 4.3 13.7 - - + +
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Residues in contact with LEU 156 (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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80C ILE* 4.1 12.8 - - + -
81C LEU* 3.9 20.4 - - + -
84C ILE* 5.5 3.6 - - + -
114C ALA* 5.0 5.4 - - + -
115C GLY* 4.6 22.4 - - - +
120C ASP* 5.0 2.9 - - + +
152C ILE* 2.6 22.6 + - + +
153C GLY* 3.4 8.3 - - - +
155C ALA* 1.3 77.4 - - - +
157C ALA* 1.3 63.6 + - - +
158C ALA 3.2 0.2 + - - -
159C ALA* 3.2 14.7 + - - +
160C VAL* 3.5 15.0 + - + +
184C LEU* 3.4 23.3 - - + +
343D GLY* 3.7 21.0 - - - +
345D LEU* 4.6 11.9 - - + -
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Residues in contact with ALA 157 (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* 3.6 30.3 - - + -
124C LEU* 4.8 11.9 - - + -
127C ILE* 3.8 31.6 - - + -
153C GLY 3.2 8.0 + - - +
156C LEU* 1.3 79.7 - - - +
158C ALA* 1.3 57.9 + - - +
160C VAL 3.9 0.9 - - - -
161C ARG* 2.8 38.2 + - + +
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Residues in contact with ALA 158 (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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127C ILE* 4.5 4.2 - - + +
142C ILE* 5.2 3.1 - - + -
154C LEU 2.7 18.9 + - - +
155C ALA* 3.4 12.6 - - - +
157C ALA* 1.3 76.8 - - - +
159C ALA* 1.3 59.2 + - - +
161C ARG* 4.9 1.3 - - - -
162C GLY 2.8 27.0 + - - +
163C TYR* 3.3 34.5 - - + +
165C CYS* 3.9 16.6 - - + -
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Residues in contact with ALA 159 (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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155C ALA 3.1 12.6 + - - +
156C LEU 3.2 10.1 + - - +
158C ALA* 1.3 78.3 - - - +
160C VAL* 1.3 60.3 + - + +
162C GLY* 3.9 2.9 + - - -
184C LEU* 3.7 26.4 + - + +
94D LYS* 2.9 21.1 + - - -
339D ILE 4.7 2.2 - - - +
340D ALA 4.1 19.7 - - - +
341D GLN* 4.2 5.5 - - - +
343D GLY 4.9 3.4 - - - +
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Residues in contact with VAL 160 (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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79C ASP* 3.7 37.5 - - + +
80C ILE* 4.4 4.5 - - + -
81C LEU* 4.0 20.0 - - + -
156C LEU* 3.5 21.9 + - + +
157C ALA 4.0 1.3 - - - +
158C ALA 3.3 0.4 - - - -
159C ALA* 1.3 73.5 - - - +
161C ARG* 1.3 73.5 + - - +
162C GLY 3.1 2.1 + - - -
94D LYS* 3.2 25.6 + - - +
341D GLN 4.9 2.5 - - - -
342D GLU* 3.8 26.5 - - - +
343D GLY 4.6 0.7 - - - +
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Residues in contact with ARG 161 (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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79C ASP* 4.0 7.3 + - - -
81C LEU* 3.0 37.9 - - + +
82C LYS* 2.9 32.3 - - - +
124C LEU* 4.8 10.2 - - + +
127C ILE* 4.6 9.0 - - + -
128C GLU* 5.1 2.8 + - - -
131C GLU* 3.5 32.5 + - - -
157C ALA* 2.8 25.3 + - + +
158C ALA 4.6 0.2 - - - +
160C VAL* 1.3 83.7 + - - +
162C GLY* 1.3 57.6 + - - +
163C TYR* 3.8 25.8 + - + -
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Residues in contact with GLY 162 (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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139C GLY* 5.2 5.6 - - - -
158C ALA 2.8 12.7 + - - +
159C ALA 4.3 4.5 - - - -
160C VAL 3.1 4.2 - - - -
161C ARG* 1.3 79.4 - - - +
163C TYR* 1.3 68.1 + - - +
164C ARG* 3.6 0.7 + - - -
94D LYS* 4.9 4.0 - - - -
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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