Contacts of the helix formed by residues 119 - 134 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B SER* 2.8 7.4 + - - +
118B VAL* 1.3 89.0 - - + +
120B ASP* 1.3 55.8 + - - +
121B ARG 2.9 1.6 - - - -
122B ILE* 3.3 17.9 - - + +
123B SER* 2.9 34.0 + - - -
149B ASN* 3.6 27.1 - - + -
150B THR* 3.2 31.0 - - - +
153B GLY* 5.0 0.9 - - - -
222B GLN* 4.0 12.3 - - - +
232B HIS* 5.8 0.7 - - - -
257B THR* 4.6 2.2 - - - -
1210B PLP 1.0 97.7 + - + +
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Residues in contact with ASP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ILE* 3.5 22.4 - - + +
113B ASN* 2.9 18.3 - - + +
115B GLY* 3.7 20.4 - - - +
116B GLY 3.4 3.6 + - - -
117B SER* 2.4 45.4 + - - +
118B VAL 2.8 0.8 + - - -
119B LYS* 1.3 76.4 - - - +
121B ARG* 1.3 57.1 + - - +
123B SER* 3.8 8.4 - - - -
124B LEU* 3.1 25.5 + - - +
149B ASN 4.9 0.2 - - - +
152B ILE* 4.1 3.5 - - - +
153B GLY* 3.6 18.8 - - - +
156B LEU* 5.5 2.6 - - + +
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ILE* 3.7 21.7 + - + -
85B GLY* 3.4 18.0 - - - -
87B THR* 3.4 5.1 + - - -
108B LYS* 4.2 1.8 - - - +
110B GLU* 2.6 30.1 + - - -
113B ASN* 4.4 4.2 - - - +
118B VAL* 2.9 12.4 + - - +
119B LYS 2.9 1.8 - - - -
120B ASP* 1.3 78.3 - - - +
122B ILE* 1.3 54.8 + - - +
124B LEU* 3.3 4.3 + - - +
125B ARG* 2.7 33.6 + - - +
231B ALA* 4.0 9.0 - - + +
232B HIS* 3.8 18.6 - - + -
235B THR* 3.5 20.6 + - - +
236B THR* 2.8 34.8 + - - +
239B GLU* 2.9 40.6 + - - -
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LYS* 3.3 28.2 - - + +
121B ARG* 1.3 71.9 - - - +
123B SER* 1.3 80.1 + - - +
124B LEU 2.8 1.8 - - - -
125B ARG* 4.0 1.3 - - - +
126B MET* 2.8 36.3 + - + +
150B THR* 3.7 21.1 - - - +
222B GLN* 4.3 9.4 - - + -
227B SER 4.1 7.6 - - - +
228B ASN* 3.2 65.5 - - + +
231B ALA* 4.4 1.3 - - + -
232B HIS* 3.7 19.5 - - + +
1210B PLP 5.9 0.7 - - - +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LYS 2.9 20.3 + - - -
120B ASP 3.8 4.9 - - - -
122B ILE* 1.3 81.3 - - - +
124B LEU* 1.3 57.1 + - - +
126B MET* 4.1 6.4 - - - +
127B ILE* 3.1 30.4 + - - +
150B THR* 3.5 6.7 + - - -
153B GLY* 2.7 15.4 - - - -
154B LEU* 2.4 54.0 + - - +
157B ALA* 5.5 0.7 - - - -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 4.5 18.8 - - + +
84B ILE* 3.8 39.0 - - + +
120B ASP 3.1 15.1 + - - +
121B ARG 3.5 4.5 - - - +
122B ILE 2.8 1.0 - - - -
123B SER* 1.3 78.8 - - - +
125B ARG* 1.3 56.6 + - - +
126B MET 3.1 1.6 - - - -
127B ILE* 3.6 5.7 - - + +
128B GLU* 2.7 68.9 + - + +
157B ALA* 4.2 19.5 - - + -
161B ARG* 5.2 4.3 - - - +
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B HIS 2.7 26.3 + - - -
67B HIS* 3.8 0.4 - - - +
68B THR* 3.0 33.7 - - - +
121B ARG 2.7 19.6 + - - +
122B ILE 3.1 0.6 + - - +
124B LEU* 1.3 69.0 - - - +
126B MET* 1.3 56.1 + - - +
128B GLU* 4.5 6.5 - - - -
129B ASP* 2.6 66.8 + - - +
132B ARG* 4.4 9.3 - - - +
227B SER* 2.9 34.5 - - - +
230B LEU* 3.7 15.5 + - - +
231B ALA* 3.4 26.6 - - + +
234B ASP* 2.7 24.7 + - - -
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Residues in contact with MET 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 2.8 35.1 + - + +
123B SER* 4.1 7.4 - - - +
125B ARG* 1.3 73.5 - - - +
127B ILE* 1.3 59.7 + - - +
129B ASP* 2.4 25.8 + - - -
130B ALA* 2.7 13.6 + - - -
150B THR* 5.0 7.6 - - + -
154B LEU* 5.2 2.2 - - + -
220B LEU* 3.2 58.6 - - + +
221B ASP 3.8 0.2 - - - -
222B GLN* 4.3 21.5 - - + +
225B ASN* 3.6 25.8 - - + +
227B SER* 3.4 25.1 - - - -
228B ASN* 5.4 1.3 - - + -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B SER 3.1 14.0 + - - +
124B LEU* 3.4 7.4 + - + +
126B MET* 1.3 78.1 - - - +
128B GLU* 1.3 69.9 + - + +
130B ALA 3.4 0.3 + - - -
131B GLU* 3.1 47.6 + - - +
136B LEU* 3.7 9.6 - - + +
142B ILE* 3.8 20.6 - - + -
154B LEU* 3.3 26.7 - - + -
157B ALA* 3.4 36.6 - - + -
158B ALA 4.5 1.3 - - - +
161B ARG* 4.5 11.0 - - - +
163B TYR* 3.8 11.7 - - + -
220B LEU* 4.0 3.8 - - + +
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 5.7 0.7 + - - -
82B LYS* 4.5 15.2 + - - -
124B LEU* 2.7 55.7 + - + +
125B ARG* 4.0 6.2 - - - +
127B ILE* 1.3 76.8 - - + +
129B ASP* 1.3 64.7 + - - +
131B GLU* 3.1 16.5 + - - +
132B ARG* 3.0 52.1 + - - +
161B ARG* 4.5 13.9 + - - +
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Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B HIS* 4.3 14.8 + - - +
125B ARG* 2.6 50.6 + - - +
126B MET* 2.4 12.5 + - - +
128B GLU* 1.3 68.8 - - - +
130B ALA* 1.3 54.8 + - - +
132B ARG* 2.6 39.2 + - - +
133B ASP* 2.8 18.9 + - - +
225B ASN* 6.0 0.7 - - - +
227B SER* 2.3 35.0 + - - +
230B LEU* 5.1 3.8 - - - +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B MET 2.7 12.6 + - - +
127B ILE 3.9 5.2 - - - +
129B ASP* 1.3 71.0 - - - +
131B GLU* 1.3 61.7 + - - +
133B ASP* 3.0 25.2 + - - +
134B GLY 3.0 10.4 + - - -
135B THR* 4.0 9.2 - - - +
136B LEU* 3.3 33.6 + - + +
218B HIS* 5.5 4.0 - - + +
220B LEU* 4.2 19.7 - - + -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ILE* 3.1 30.8 + - - +
128B GLU* 3.4 14.8 - - - +
129B ASP 3.1 0.8 - - - -
130B ALA* 1.3 75.8 - - - +
132B ARG* 1.3 61.0 + - + +
134B GLY* 3.7 8.8 + - - -
136B LEU* 3.7 21.7 - - + +
138B PRO* 6.0 0.9 - - + -
161B ARG* 3.8 14.5 + - - -
163B TYR* 2.2 38.8 + - - +
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B HIS* 2.8 43.4 + - + +
68B THR* 3.8 22.0 + - - +
125B ARG* 4.4 9.1 - - - +
128B GLU* 3.0 48.8 + - - +
129B ASP* 2.6 30.0 + - - +
131B GLU* 1.3 73.2 - - + +
133B ASP* 1.3 62.4 + - - +
134B GLY* 4.6 0.2 - - - -
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ASP* 2.8 13.8 + - - +
130B ALA* 3.0 23.0 + - - +
132B ARG* 1.3 79.9 - - - +
134B GLY* 1.3 57.7 + - - +
135B THR* 3.4 17.6 + - + +
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ALA 3.0 3.6 + - - -
131B GLU 3.7 7.6 + - - -
132B ARG 3.3 2.6 - - - -
133B ASP* 1.3 78.3 - - - +
135B THR* 1.3 63.7 + - - +
136B LEU 3.5 4.3 - - - -
137B LYS* 4.6 9.4 - - - +
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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
------------------------------------------------------------
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