Contacts of the helix formed by residues 137 - 150 (chain H) in PDB entry 1MWA
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 ASP 137 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85H TYR* 2.6 37.5 + - - -
122H ASP 5.0 2.1 - - - +
123H TYR* 4.6 1.8 - - - -
135H ALA* 4.0 3.5 - - - +
136H ALA* 1.3 82.2 - - + +
138H MET* 1.3 59.5 + - - +
139H ALA* 2.8 24.4 + - - +
140H ALA* 2.8 34.2 + - - +
141H LEU* 3.3 7.0 + - - +
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Residues in contact with MET 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137H ASP* 1.3 74.7 - - - +
139H ALA* 1.3 59.0 - - - +
141H LEU* 3.6 32.5 - - + +
142H ILE* 3.9 10.4 - - - +
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Residues in contact with ALA 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H TYR* 3.8 31.1 - - + +
85H TYR* 3.5 28.9 - - + -
123H TYR* 3.2 13.4 + - + -
137H ASP* 2.8 13.8 + - - +
138H MET* 1.3 73.8 - - - +
140H ALA* 1.3 61.4 + - - +
141H LEU 3.0 4.7 - - - -
142H ILE* 3.1 25.5 + - - +
143H THR 3.7 0.7 + - - -
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Residues in contact with ALA 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H TYR* 3.0 47.7 - - + +
124H ILE* 4.1 4.2 - - + +
135H ALA* 3.2 21.8 - - + +
136H ALA 3.3 3.1 - - - +
137H ASP* 2.8 16.2 + - - +
139H ALA* 1.3 78.8 - - - +
141H LEU* 1.3 55.5 + - - +
142H ILE 3.3 0.2 - - - -
143H THR* 3.5 3.3 + - - -
144H LYS* 3.0 26.7 + - - +
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Residues in contact with LEU 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H ALA* 3.9 15.5 - - + -
137H ASP 3.3 10.5 + - - +
138H MET* 3.6 28.7 - - + +
139H ALA 3.0 0.6 - - - -
140H ALA* 1.3 76.9 - - - +
142H ILE* 1.3 63.4 + - + +
144H LYS* 4.1 11.9 - - + -
145H HIS* 2.7 55.6 + - + +
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Residues in contact with ILE 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ASN* 6.4 0.4 - - - +
84H TYR* 3.1 54.7 - - + +
138H MET 3.9 10.8 - - - +
139H ALA* 3.1 14.1 + - - +
141H LEU* 1.3 78.3 - - + +
143H THR* 1.3 57.8 + - - +
145H HIS* 4.3 5.6 - - - +
146H LYS* 3.2 27.3 + - + +
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Residues in contact with THR 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H TYR* 3.5 1.2 - - - -
123H TYR* 3.0 28.2 + - + -
124H ILE* 4.2 6.1 - - + -
139H ALA 3.7 1.0 + - - -
140H ALA 3.5 5.7 + - - -
141H LEU 3.1 0.4 - - - -
142H ILE* 1.3 75.8 - - - +
144H LYS* 1.3 58.7 + - - +
146H LYS* 4.2 2.9 - - - -
147H TRP* 2.7 77.0 + - + +
8P VAL* 2.7 34.2 + - + +
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Residues in contact with LYS 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H ILE* 4.0 13.2 - - + +
132H THR* 4.5 6.1 - - - +
133H TRP* 2.5 52.4 + - + +
135H ALA* 4.5 9.0 - - + +
140H ALA 3.0 18.8 + - - +
141H LEU* 3.1 23.1 + - + +
143H THR* 1.3 77.3 - - - +
145H HIS* 1.3 68.0 + - + +
147H TRP* 3.2 2.4 + - - +
148H GLU* 2.9 56.6 + - - +
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Residues in contact with HIS 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H LEU* 2.7 46.5 + - + +
142H ILE* 4.3 4.5 - - - +
144H LYS* 1.3 90.8 - - + +
146H LYS* 1.3 57.6 + - - +
148H GLU* 3.1 21.4 + - - +
149H GLN* 2.8 40.2 + - + +
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Residues in contact with LYS 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ASN* 3.6 34.0 - - - +
30B ASN* 2.8 31.8 - - - +
72B GLN* 3.7 8.6 + - - +
80H THR* 4.7 3.2 + - - +
84H TYR* 3.5 12.9 + - - -
142H ILE* 3.2 17.9 + - + +
143H THR* 3.2 3.1 + - - +
145H HIS* 1.3 78.8 - - - +
147H TRP* 1.3 67.3 + - + +
149H GLN* 3.0 21.4 + - - +
150H ALA* 3.3 13.3 + - - +
6P TYR* 4.5 5.1 - - - +
7P SER 4.6 1.3 - - - -
8P VAL* 2.7 44.0 + - - -
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Residues in contact with TRP 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H GLN* 5.1 3.8 - - - -
116H TYR* 3.5 35.9 - + - -
124H ILE* 4.0 20.9 - - + -
133H TRP* 3.5 55.6 - + - +
143H THR* 2.7 42.5 + - + +
144H LYS 3.7 2.9 - - - +
146H LYS* 1.3 77.3 - - + +
148H GLU* 1.3 60.8 + - - +
150H ALA 3.3 1.4 + - - +
151H GLY 3.3 2.8 + - - -
152H GLU* 3.0 42.9 + - + +
153H ALA 4.4 0.9 + - - -
6P TYR* 3.1 39.4 + + - -
7P SER 2.7 21.6 + - - -
8P VAL* 4.0 12.1 - - + -
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Residues in contact with GLU 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H THR* 5.1 7.3 - - - +
133H TRP* 4.0 17.1 + - + +
144H LYS* 2.9 54.8 + - - +
145H HIS* 3.3 30.0 + - - +
147H TRP* 1.3 77.8 - - - +
149H GLN* 1.3 61.2 + - - +
150H ALA 3.5 0.2 + - - -
151H GLY* 3.5 10.8 + - - +
153H ALA* 5.9 2.7 - - + +
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Residues in contact with GLN 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B THR 5.2 3.2 + - - -
27B ASN 4.3 12.9 + - - +
28B ASN* 2.5 44.1 + - + +
29B HIS* 3.7 12.5 + - - -
145H HIS* 2.8 23.1 + - + +
146H LYS* 3.0 17.0 + - - +
148H GLU* 1.3 79.3 - - - +
150H ALA* 1.3 54.8 + - + +
151H GLY 3.4 1.3 + - - -
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Residues in contact with ALA 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B HIS* 3.5 27.1 - - + -
96B GLY* 3.6 26.2 - - - +
107B TYR* 6.1 1.6 - - - -
146H LYS 3.3 5.3 + - - +
147H TRP 3.3 1.9 + - - +
149H GLN* 1.3 78.2 - - - +
151H GLY* 1.3 66.4 + - - +
152H GLU* 3.0 3.4 + - - +
155H ARG* 5.2 2.1 - - - -
6P TYR* 3.7 21.8 - - + +
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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