Contacts of the helix formed by residues 119 - 131 (chain D) 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 LYS 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D SER* 2.7 7.2 - - - +
118D VAL* 1.3 78.3 - - + +
120D ASP* 1.3 56.4 + - - +
121D ARG 3.0 1.8 - - - +
122D ILE* 3.5 23.2 - - + +
123D SER* 2.6 35.5 + - - -
149D ASN* 4.1 5.5 - - + +
150D THR* 2.7 45.1 - - - +
153D GLY* 4.4 0.3 - - - -
222D GLN* 3.4 13.2 - - - -
228D ASN* 5.2 0.9 - - - +
232D HIS* 5.8 2.0 - - - +
257D THR* 4.4 4.0 - - - -
305D GLY* 3.9 7.3 + - - -
1410D PLP 1.5 73.1 + - + +
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Residues in contact with ASP 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ILE* 3.5 28.9 - - + +
113D ASN* 3.4 8.4 - - + +
115D GLY* 2.5 41.3 + - - -
116D GLY 2.9 5.4 + - - -
117D SER* 2.3 48.9 + - - +
119D LYS* 1.3 73.1 - - - +
121D ARG* 1.3 64.2 + - - +
123D SER* 3.7 8.1 - - - -
124D LEU* 3.3 24.4 + - - +
152D ILE* 5.7 0.2 - - - +
153D GLY* 3.7 14.2 + - - -
156D LEU* 6.1 1.1 - - - -
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Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ILE* 3.9 15.7 - - + -
85D GLY* 3.4 21.6 - - - +
87D THR* 3.5 5.7 + - - -
108D LYS* 4.1 1.4 - - - +
110D GLU* 2.8 27.5 + - - +
113D ASN* 5.1 1.8 - - - +
118D VAL* 3.1 12.7 + - - +
120D ASP* 1.3 81.7 - - - +
122D ILE* 1.3 57.7 + - - +
124D LEU* 4.1 2.2 - - - +
125D ARG* 3.1 26.3 + - - +
231D ALA* 3.6 9.7 - - + +
232D HIS* 3.6 19.1 - - + +
235D THR* 3.2 27.4 + - - +
236D THR* 2.6 31.0 + - - +
239D GLU* 2.7 43.6 + - - -
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Residues in contact with ILE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LYS* 3.5 25.1 - - + +
121D ARG* 1.3 74.9 - - - +
123D SER* 1.3 69.3 + - - +
124D LEU 3.0 2.5 + - - -
125D ARG* 4.0 6.1 - - - +
126D MET* 3.1 46.0 + - + +
150D THR* 3.8 24.0 - - + +
222D GLN* 4.2 5.8 - - + -
228D ASN* 3.1 61.9 - - + +
231D ALA* 4.6 1.6 - - + -
232D HIS* 3.6 22.4 - - + +
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Residues in contact with SER 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LYS 2.6 23.2 + - - -
120D ASP* 3.7 7.0 - - - -
121D ARG 3.4 0.4 - - - -
122D ILE* 1.3 79.8 - - - +
124D LEU* 1.3 58.1 + - - +
126D MET* 4.5 1.3 - - - +
127D ILE* 3.1 34.0 + - - +
150D THR* 3.3 11.1 + - - +
153D GLY* 3.0 42.2 - - - -
154D LEU* 3.1 14.7 + - - +
157D ALA* 5.5 1.8 - - - -
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D LEU* 4.0 20.6 - - + +
84D ILE* 3.9 33.7 - - + +
120D ASP 3.3 13.1 + - - +
121D ARG* 4.1 2.5 - - - +
122D ILE 3.0 0.2 - - - -
123D SER* 1.3 79.4 - - - +
125D ARG* 1.3 58.4 + - - +
126D MET 2.9 1.8 - - - -
127D ILE* 3.2 3.9 + - + -
128D GLU* 2.7 58.1 + - + +
157D ALA* 5.7 6.1 - - + -
161D ARG* 3.1 35.9 - - - +
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Residues in contact with ARG 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D HIS 2.9 28.3 + - - -
68D THR* 3.7 16.2 + - - -
121D ARG 3.1 17.6 + - - +
122D ILE* 4.4 2.5 - - - -
124D LEU* 1.3 79.4 - - - +
126D MET* 1.3 58.1 + - - +
128D GLU* 3.7 4.4 - - - -
129D ASP* 2.8 68.1 + - - +
132D ARG* 4.1 1.5 - - - +
227D SER* 3.6 18.6 - - - +
230D LEU* 3.1 33.8 - - - +
231D ALA* 3.3 22.8 - - + +
234D ASP* 2.6 29.4 + - - +
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Residues in contact with MET 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ILE* 3.1 48.7 + - + +
123D SER* 4.5 4.5 - - - +
124D LEU 2.9 1.2 - - - -
125D ARG* 1.3 73.5 - - - +
127D ILE* 1.3 57.5 + - - +
128D GLU 2.9 3.8 - - - -
129D ASP* 2.6 23.7 + - - +
130D ALA* 2.7 13.3 + - - +
150D THR* 4.6 8.5 - - + -
154D LEU* 5.0 2.9 - - + -
220D LEU* 2.9 53.8 - - + +
221D ASP 4.3 1.3 - - - +
222D GLN* 4.2 9.0 - - + -
225D ASN* 3.0 32.1 - - - +
227D SER* 3.6 16.4 - - - -
228D ASN* 5.0 1.8 - - + -
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Residues in contact with ILE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D SER 3.1 22.3 + - - +
124D LEU* 3.2 5.9 + - + +
126D MET* 1.3 76.3 - - - +
128D GLU* 1.3 55.6 + - - +
130D ALA 3.9 0.2 - - - -
131D GLU* 2.9 37.8 + - - +
136D LEU* 3.0 23.5 - - + +
142D ILE* 3.4 28.7 - - + -
154D LEU* 4.1 13.9 - - + +
157D ALA* 4.0 23.8 - - + -
158D ALA 4.8 2.7 - - - +
161D ARG* 4.5 11.4 - - + +
163D TYR* 3.7 10.8 - - + -
220D LEU* 3.8 10.7 - - + +
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Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D LEU* 2.7 36.8 + - + +
125D ARG* 4.2 5.1 - - - +
126D MET 2.8 0.2 + - - -
127D ILE* 1.3 71.3 - - - +
129D ASP* 1.3 64.5 + - - +
130D ALA 3.4 0.7 - - - -
131D GLU* 4.4 4.3 - - - +
132D ARG* 3.1 35.9 + - - +
161D ARG* 2.5 47.6 + - - +
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Residues in contact with ASP 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D HIS* 5.7 1.1 - - - -
125D ARG* 2.8 49.9 + - - +
126D MET 2.6 6.5 + - - +
128D GLU* 1.3 75.1 - - - +
130D ALA* 1.3 60.7 + - - +
131D GLU 3.4 0.7 - - - -
132D ARG* 3.1 36.5 + - - +
133D ASP* 3.2 32.7 + - - +
227D SER* 3.0 24.5 + - - +
230D LEU* 5.3 1.4 - - - +
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Residues in contact with ALA 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D MET 2.7 11.2 + - - +
129D ASP* 1.3 77.3 - - - +
131D GLU* 1.3 58.1 + - - +
132D ARG 3.2 1.1 - - - -
133D ASP* 3.6 2.3 + - - -
135D THR* 3.3 19.4 + - - +
136D LEU* 2.8 52.7 + - + +
218D HIS* 6.3 1.6 - - + -
220D LEU* 4.1 15.0 - - + -
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Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ILE* 2.9 23.0 + - - +
128D GLU* 4.4 4.3 - - - +
130D ALA* 1.3 75.2 - - - +
132D ARG* 1.3 66.9 + - - +
133D ASP 3.2 0.4 - - - -
134D GLY* 3.1 6.3 + - - -
136D LEU* 3.4 17.7 - - + +
161D ARG* 2.9 38.9 + - - +
163D TYR* 2.7 41.4 + - - +
91E ARG* 4.7 1.1 + - - +
78F PRO* 3.0 25.9 - - + +
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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