Contacts of the helix formed by residues 148 - 162 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146F THR* 3.4 11.2 + - - -
147F SER* 1.3 86.8 + - - +
149F ASN* 1.3 69.1 + - - +
150F THR 3.2 2.2 - - - -
151F GLY* 3.3 7.3 + - - -
152F ILE* 3.7 13.0 + - - +
177F LYS* 5.4 3.1 - - - +
181F LEU* 5.5 0.5 - - - +
380F ASN* 5.1 2.5 - - - -
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Residues in contact with ASN 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F SER* 3.2 37.2 + - - +
119F LYS* 3.2 14.9 - - + +
148F GLY* 1.3 68.5 - - - -
150F THR* 1.3 54.6 + - - +
151F GLY 3.0 1.8 - - - -
152F ILE* 2.6 34.0 + - + +
153F GLY* 2.6 17.0 + - - -
376F ASP* 3.5 4.6 + - - +
379F ARG* 4.5 0.9 + - - -
380F ASN* 2.4 34.0 + - - -
1610F PLP 2.7 44.2 + - - +
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Residues in contact with THR 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F LYS* 3.1 34.1 - - - +
122F ILE* 4.0 6.0 - - + +
123F SER* 4.1 0.5 + - - -
126F MET* 4.5 10.1 - - + -
144F GLU* 3.3 27.6 - - - +
146F THR* 3.3 6.1 - - + -
149F ASN* 1.3 78.2 - - - +
151F GLY* 1.3 54.8 - - - +
153F GLY* 3.1 1.8 + - - -
154F LEU* 2.9 36.7 + - + +
222F GLN* 2.8 35.1 + - + +
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Residues in contact with GLY 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F GLU* 4.5 3.4 - - - -
146F THR* 3.1 19.0 - - - +
147F SER 5.2 0.2 - - - -
148F GLY 3.3 6.9 + - - -
149F ASN 3.0 1.0 - - - -
150F THR* 1.3 81.0 - - - +
152F ILE* 1.3 52.0 + - - +
154F LEU* 3.9 1.5 - - - +
155F ALA* 2.6 39.2 + - - +
167F ILE* 3.3 21.1 - - - +
181F LEU* 3.5 6.3 - - - -
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Residues in contact with ILE 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345E LEU* 5.7 2.2 - - + -
115F GLY* 3.8 25.6 - - - +
117F SER* 5.6 1.1 - - - +
120F ASP* 4.7 1.2 - - - +
148F GLY 3.7 7.6 + - - +
149F ASN* 2.6 16.9 + - - +
151F GLY* 1.3 69.8 - - - +
153F GLY* 1.3 65.4 + - - +
155F ALA* 4.0 0.3 - - - +
156F LEU* 3.0 24.9 + - + +
177F LYS* 4.1 11.2 - - + -
180F VAL* 4.4 13.2 - - + -
181F LEU* 3.3 23.6 - - + -
184F LEU* 4.4 14.1 - - + -
379F ARG* 3.6 17.5 - - - +
380F ASN* 3.3 32.8 - - - +
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Residues in contact with GLY 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F ASP* 3.9 24.1 + - - +
123F SER* 2.7 23.8 + - - -
149F ASN 2.6 16.5 + - - -
150F THR* 3.1 3.8 + - - -
152F ILE* 1.3 74.5 - - - +
154F LEU* 1.3 56.6 + - - +
156F LEU* 3.8 2.3 - - - +
157F ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F SER* 2.7 23.0 + - - +
126F MET* 4.0 16.8 - - + -
127F ILE* 2.8 44.3 - - + +
142F ILE* 4.0 14.6 - - + -
144F GLU* 3.6 43.5 - - + +
150F THR* 2.9 17.9 + - + +
151F GLY* 4.1 2.2 - - - +
153F GLY* 1.3 69.4 - - - +
155F ALA* 1.3 68.8 + - - +
156F LEU 3.0 2.2 - - - -
157F ALA* 4.1 0.2 - - - +
158F ALA* 2.9 27.4 + - - +
165F CYS* 4.0 8.7 - - - -
167F ILE* 6.2 0.2 - - + -
220F LEU* 4.5 7.9 - - + +
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Residues in contact with ALA 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F GLY 2.6 25.5 + - - +
152F ILE 4.0 1.1 - - - +
154F LEU* 1.3 74.2 - - - +
156F LEU* 1.3 61.1 + - - +
158F ALA* 3.4 11.4 - - - +
159F ALA 3.8 2.9 + - - -
165F CYS* 3.4 16.6 - - - +
167F ILE* 4.2 0.9 - - + -
181F LEU* 3.3 22.7 - - + -
184F LEU* 3.9 24.0 - - + +
186F ALA* 3.7 19.1 + - + -
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Residues in contact with LEU 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E ILE 4.3 0.9 - - - +
343E GLY* 3.3 39.7 - - - +
345E LEU* 5.4 4.3 - - + -
80F ILE* 4.4 7.2 - - + -
81F LEU* 4.5 8.5 - - + -
84F ILE* 6.0 0.7 - - + -
114F ALA* 5.0 11.2 - - + +
115F GLY* 5.2 9.6 - - - +
120F ASP* 5.4 3.8 - - - +
152F ILE* 3.0 21.0 + - + +
153F GLY* 3.8 2.2 - - - +
154F LEU 3.0 1.2 + - - -
155F ALA* 1.3 75.3 - - - +
157F ALA* 1.3 69.1 + - - +
158F ALA 2.8 5.7 + - - -
159F ALA* 2.8 16.1 + - + -
160F VAL* 3.4 13.4 + - + +
184F LEU* 3.1 34.7 - - + +
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Residues in contact with ALA 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F LEU* 4.0 31.4 - - + -
123F SER 4.3 8.3 - - - +
124F LEU* 5.5 4.3 - - + -
127F ILE* 4.1 22.9 - - + -
153F GLY 3.0 17.4 + - - +
154F LEU 4.1 2.0 - - - +
156F LEU* 1.3 76.1 - - - +
158F ALA* 1.3 62.5 + - - +
160F VAL* 3.3 3.0 + - - +
161F ARG* 3.0 28.8 + - + +
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Residues in contact with ALA 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F ILE* 4.9 4.6 - - + +
142F ILE* 5.8 1.6 - - + -
154F LEU 2.9 19.8 + - - +
155F ALA 3.4 8.7 - - - +
156F LEU 2.8 0.4 + - - -
157F ALA* 1.3 76.9 - - - +
159F ALA* 1.3 58.6 + - - +
160F VAL 3.1 0.3 + - - -
161F ARG* 3.1 1.5 + - - -
162F GLY* 2.7 32.3 + - - +
163F TYR* 3.2 34.7 + - + +
165F CYS* 3.6 14.8 - - + -
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Residues in contact with ALA 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E LYS* 3.3 17.0 - - - -
340E ALA* 2.9 32.9 - - - +
341E GLN* 4.2 2.9 - - - +
343E GLY 5.2 1.8 - - - +
155F ALA 3.8 1.5 + - - +
156F LEU* 2.8 21.4 + - + +
158F ALA* 1.3 76.0 - - - +
160F VAL* 1.3 63.4 + - + +
162F GLY* 4.5 3.1 + - - -
184F LEU 3.7 18.8 - - - +
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Residues in contact with VAL 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ASN* 5.4 2.2 - - - +
94E LYS* 3.1 27.1 + - - +
341E GLN 5.1 3.4 - - - -
342E GLU* 3.8 25.1 - - - +
343E GLY* 4.4 0.9 - - - -
79F ASP* 3.0 38.8 - - + +
80F ILE* 4.1 8.5 - - + -
81F LEU* 3.3 31.2 - - + -
156F LEU* 3.8 17.3 - - + +
157F ALA 3.5 0.9 - - - +
158F ALA 3.1 0.8 - - - -
159F ALA* 1.3 76.4 - - - +
161F ARG* 1.3 62.2 + - - +
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Residues in contact with ARG 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E LYS* 3.9 9.2 + - - -
79F ASP* 3.5 25.1 + - - -
81F LEU* 3.8 22.2 - - + +
82F LYS* 4.5 15.8 - - - +
124F LEU* 5.3 2.8 - - - +
127F ILE* 5.0 5.8 - - + -
128F GLU* 4.2 20.4 + - - +
131F GLU* 4.5 14.6 + - - +
157F ALA* 3.0 16.3 + - + +
158F ALA 4.0 0.4 - - - +
160F VAL* 1.3 81.9 + - - +
162F GLY* 1.3 58.6 + - - +
163F TYR* 4.3 23.3 - - + -
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Residues in contact with GLY 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E LYS* 5.3 3.1 - - - -
139F GLY* 3.4 19.7 - - - -
158F ALA 2.7 15.7 + - - -
159F ALA* 5.0 2.7 - - - -
161F ARG* 1.3 76.9 - - - +
163F TYR* 1.3 65.1 + - - +
164F ARG* 3.4 5.6 + - - +
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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