Contacts of the helix formed by residues 148 - 161 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146E THR* 3.3 16.2 + - - +
147E SER* 1.3 81.6 - - - +
149E ASN* 1.3 55.4 + - - -
150E THR* 2.9 5.2 - - - -
151E GLY 2.5 30.8 + - - -
152E ILE* 3.4 6.5 - - - +
173E MET* 5.8 1.8 - - - -
177E LYS* 5.5 6.3 - - - -
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Residues in contact with ASN 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E GLY 5.4 1.2 - - - +
117E SER* 3.3 23.0 + - - +
119E LYS* 3.3 21.5 - - + +
148E GLY* 1.3 67.9 - - - -
150E THR* 1.3 63.9 + - - +
152E ILE* 2.8 26.1 + - - +
153E GLY* 2.9 9.9 + - - -
177E LYS* 5.9 0.4 - - - +
376E ASP* 3.0 25.5 + - - +
380E ASN* 2.5 33.1 + - - +
1510E PLP 3.1 30.1 + - - +
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Residues in contact with THR 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E LYS* 3.0 30.7 - - + +
122E ILE* 4.0 10.1 - - + -
123E SER* 3.7 5.3 + - - +
126E MET* 4.8 4.7 - - + -
144E GLU* 3.6 16.8 - - - +
146E THR* 3.9 5.1 - - - +
148E GLY* 2.7 5.5 + - - -
149E ASN* 1.3 72.0 - - - +
151E GLY* 1.3 61.5 + - - -
153E GLY* 3.1 0.9 + - - -
154E LEU* 3.0 31.1 + - + +
222E GLN* 2.0 51.1 + - + +
1510E PLP 5.3 0.2 + - - -
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Residues in contact with GLY 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E GLU* 3.6 22.1 - - - +
146E THR 3.9 4.1 + - - -
147E SER* 4.6 2.7 - - - -
148E GLY 2.5 17.5 + - - -
150E THR* 1.3 74.3 - - - +
152E ILE* 1.3 54.9 - - - -
154E LEU 3.5 0.3 + - - -
155E ALA* 2.8 32.9 + - - +
167E ILE* 3.9 15.7 - - - +
181E LEU* 4.0 7.0 - - - -
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Residues in contact with ILE 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E GLY* 3.8 30.9 - - - +
117E SER* 5.7 0.7 - - - +
120E ASP* 4.9 2.0 - - - +
147E SER 4.0 8.1 - - - +
148E GLY 3.4 20.2 - - - +
149E ASN* 2.8 22.8 + - + +
151E GLY* 1.3 75.3 - - - +
153E GLY* 1.3 55.9 + - - +
155E ALA* 3.5 1.2 - - - +
156E LEU* 2.8 28.8 + - + +
177E LYS* 4.8 9.2 - - + -
180E VAL* 4.4 7.0 - - + -
181E LEU* 3.7 22.9 - - + -
184E LEU* 4.4 9.8 - - + +
379E ARG* 3.8 19.7 - - - +
380E ASN* 4.1 12.6 - - - +
345F LEU* 6.2 2.0 - - + -
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Residues in contact with GLY 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E ASP* 3.8 20.6 + - - -
123E SER* 2.9 20.4 - - - -
149E ASN 2.9 11.2 + - - -
150E THR* 3.1 1.9 + - - -
152E ILE* 1.3 74.1 - - - +
154E LEU* 1.3 66.7 + - - +
155E ALA 2.9 2.2 + - - -
156E LEU* 3.0 13.7 + - - +
157E ALA* 3.1 16.2 + - - +
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Residues in contact with LEU 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E SER* 2.7 28.3 + - - +
126E MET* 4.9 6.1 - - + -
127E ILE* 3.6 26.2 - - + +
142E ILE* 4.2 18.6 - - + -
143E ILE 4.2 2.2 - - - +
144E GLU* 2.9 51.8 - - + +
150E THR* 3.0 17.5 + - + +
151E GLY 4.2 2.2 - - - +
153E GLY* 1.3 70.6 - - - -
155E ALA* 1.3 51.1 + - - +
158E ALA* 2.7 40.4 + - - +
165E CYS* 4.2 5.4 - - - -
220E LEU* 3.6 20.2 - - + -
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Residues in contact with ALA 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E GLY 2.8 21.9 + - - +
152E ILE 3.5 6.3 - - - +
154E LEU* 1.3 76.1 - - - +
156E LEU* 1.3 68.7 + - - +
158E ALA* 3.8 0.7 - - - +
159E ALA* 3.4 18.4 + - - +
165E CYS* 3.9 17.8 - - - +
167E ILE* 4.8 0.4 - - + -
181E LEU* 4.0 15.9 - - + -
184E LEU* 3.9 22.2 - - + +
186E ALA* 4.4 7.2 - - + -
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Residues in contact with LEU 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E ILE* 4.2 4.7 - - + -
81E LEU* 4.2 6.7 - - + -
84E ILE* 5.5 1.8 - - + -
114E ALA* 3.6 34.5 - - + +
115E GLY* 3.6 19.3 - - - +
120E ASP* 5.1 3.1 - - - +
152E ILE* 2.8 22.0 + - + +
153E GLY* 3.8 4.0 - - - +
155E ALA* 1.3 79.7 - - - +
157E ALA* 1.3 65.5 + - - +
159E ALA* 3.1 12.1 + - - +
160E VAL* 3.2 20.0 + - + -
184E LEU* 3.8 17.4 - - + +
343F GLY* 3.5 39.5 - - - +
345F LEU* 5.5 3.1 - - + -
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Residues in contact with ALA 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E LEU* 3.4 33.0 - - + -
123E SER* 4.9 4.9 - - - +
124E LEU* 5.2 8.5 - - + -
127E ILE* 4.6 20.2 - - + -
153E GLY 3.1 11.6 + - - +
154E LEU 4.5 0.9 - - - +
156E LEU* 1.3 76.9 - - - +
158E ALA* 1.3 69.0 + - - +
160E VAL* 3.3 4.0 + - - +
161E ARG* 3.1 23.1 + - - +
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Residues in contact with ALA 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E ILE* 4.6 0.8 - - - +
142E ILE* 4.5 8.3 - - + -
154E LEU 2.7 27.6 + - - +
155E ALA 3.8 4.7 - - - +
157E ALA* 1.3 71.4 - - - +
159E ALA* 1.3 67.4 + - - +
161E ARG* 2.9 12.3 + - - +
162E GLY 3.0 10.9 + - - -
163E TYR* 3.2 40.3 + - + +
164E ARG 5.1 0.2 - - - +
165E CYS* 4.0 15.9 - - + -
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Residues in contact with ALA 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E ALA 3.4 3.0 + - - +
156E LEU* 3.1 11.6 + - - +
158E ALA* 1.3 79.9 - - - +
160E VAL* 1.3 56.7 + - + +
161E ARG 2.7 12.8 + - - -
162E GLY* 3.0 10.2 + - - -
163E TYR 4.3 4.2 + - - +
184E LEU* 3.5 24.9 + - + +
94F LYS* 3.3 15.8 + - - -
340F ALA* 3.2 25.6 - - - +
341F GLN 5.0 0.4 - - - +
343F GLY* 5.5 1.8 - - - -
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Residues in contact with VAL 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E ASP* 4.1 21.5 - - + -
80E ILE* 3.5 29.2 - - + -
81E LEU* 3.8 24.9 - - + -
156E LEU* 3.2 24.4 + - + +
157E ALA 3.3 6.3 + - - +
159E ALA* 1.3 75.0 - - - +
161E ARG* 1.3 61.2 + - + +
93F ASN* 4.9 9.4 + - - +
94F LYS* 4.3 9.6 + - - -
341F GLN 4.0 9.6 + - - +
342F GLU* 3.6 12.3 - - - +
343F GLY* 4.1 0.2 - - - -
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Residues in contact with ARG 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E ASP* 3.5 33.1 + - - +
81E LEU* 3.3 36.5 - - + +
82E LYS* 6.0 0.4 - - - +
124E LEU* 4.8 11.5 - - - +
127E ILE* 5.5 5.6 - - + +
128E GLU* 5.0 9.9 + - - +
131E GLU* 4.4 18.3 + - - -
138E PRO* 5.9 0.7 - - - +
139E GLY 5.3 0.9 + - - -
157E ALA 3.1 7.3 + - - +
158E ALA 2.9 6.2 + - - +
159E ALA 2.7 4.9 + - - -
160E VAL* 1.3 79.6 + - - +
162E GLY* 1.3 56.0 + - - -
163E TYR* 3.6 21.4 - - + -
94F LYS* 5.7 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