Contacts of the helix formed by residues 130 - 143 (chain M) in PDB entry 3HOU
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 130 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128M ILE* 3.4 3.9 + - + -
129M LYS* 1.3 77.7 - - - +
131M SER* 1.3 71.7 + - - +
132M LYS* 4.0 13.8 - - - +
133M LYS* 2.8 48.8 + - + +
134M ARG* 2.8 25.1 + - - +
1393M ASN* 4.2 14.0 - - - +
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Residues in contact with SER 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130M ASP* 1.3 73.6 + - - +
132M LYS* 1.3 78.2 + - - +
134M ARG* 4.0 14.8 + - - +
135M PHE* 2.9 28.4 + - - +
223M GLY* 3.8 32.5 + - - -
224M PHE 5.7 0.2 + - - -
1415M SER* 4.8 7.9 + - - -
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Residues in contact with LYS 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130M ASP* 3.1 17.0 + - - +
131M SER* 1.3 83.4 - - - +
133M LYS* 1.3 62.7 + - + +
135M PHE* 4.1 5.9 - - - +
136M ALA* 3.2 19.2 + - - +
1399M ARG* 5.8 3.8 - - - +
1411M GLU* 3.6 36.1 - - + +
1415M SER* 3.1 30.2 - - - +
1417M GLU* 3.7 26.1 - - - +
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Residues in contact with LYS 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M ILE* 4.0 17.3 - - + +
130M ASP* 2.8 28.5 + - + +
132M LYS* 1.3 76.7 - - + +
134M ARG* 1.3 66.4 + - - +
136M ALA* 3.0 10.1 - - - +
137M ALA* 3.0 21.1 + - - +
215Q MET* 6.1 2.8 - - - +
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Residues in contact with ARG 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M ALA 4.1 10.3 - - - +
126M LEU* 4.9 9.0 + - - +
128M ILE* 3.3 32.7 + - - +
129M LYS* 4.5 4.6 - - - +
130M ASP 2.8 33.0 + - - +
131M SER* 3.5 15.7 + - - +
133M LYS* 1.3 67.6 - - - +
135M PHE* 1.3 55.2 + - - +
136M ALA 2.9 4.0 - - - -
137M ALA* 2.7 24.9 + - - +
138M ILE* 2.8 26.5 + - + +
220M THR* 2.8 40.8 + - - +
221M SER* 2.6 32.5 - - - +
223M GLY* 4.2 4.2 - - - +
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Residues in contact with PHE 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98M LYS* 4.2 25.1 - - + -
101M LYS* 4.1 37.2 - - + -
102M VAL* 4.3 22.4 - - + -
105M CYS* 4.5 7.6 - - - -
131M SER 2.9 15.4 + - - +
132M LYS* 4.2 4.3 - - - +
134M ARG* 1.3 79.4 - - - +
136M ALA* 1.3 64.2 + - - +
138M ILE* 4.1 8.1 - - - -
139M TRP* 3.3 22.5 + - + +
221M SER 4.7 0.4 - - - -
222M LEU* 3.5 56.3 - - + +
223M GLY* 4.3 1.8 - - - +
224M PHE* 4.9 0.2 - + - -
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Residues in contact with ALA 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132M LYS 3.2 17.1 + - - +
133M LYS* 3.0 19.0 + - - +
134M ARG 2.9 0.4 - - - -
135M PHE* 1.3 82.5 - - - +
137M ALA* 1.3 57.6 + - - +
139M TRP* 4.0 4.4 - - - +
140M THR* 2.9 26.2 + - - -
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Residues in contact with ALA 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M ALA* 3.6 21.5 - - + -
128M ILE* 4.2 13.9 - - + -
133M LYS 3.0 9.8 + - - +
134M ARG 2.7 8.3 + - - +
136M ALA* 1.3 73.7 - - - +
138M ILE* 1.3 68.8 + - - +
139M TRP 2.6 4.0 + - - -
140M THR* 2.8 8.4 + - - -
141M LEU* 2.8 25.1 + - + +
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Residues in contact with ILE 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105M CYS* 4.3 0.7 - - - -
113M LEU* 4.8 4.3 - - + -
122M MET* 4.2 16.4 - - + -
125M ALA* 4.1 10.9 - - + +
126M LEU* 4.3 10.8 - - + +
134M ARG* 2.8 33.8 + - + +
135M PHE* 4.2 4.9 - - - +
137M ALA* 1.3 71.2 - - - +
139M TRP* 1.3 57.0 + - - +
141M LEU* 3.2 10.7 - - - +
142M CYS* 3.0 47.4 + - - -
221M SER* 2.9 43.3 - - - +
222M LEU* 3.6 24.0 - - + +
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Residues in contact with TRP 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65 T 6.0 1.6 - - - -
101M LYS* 3.0 69.8 + - + +
104M GLU* 3.0 39.7 + - + +
105M CYS* 3.2 17.9 - - - -
135M PHE* 3.3 21.5 + + + +
136M ALA* 4.0 4.0 - - - +
137M ALA 2.6 4.4 + - - -
138M ILE* 1.3 71.6 - - - +
140M THR* 1.3 90.6 + - - +
141M LEU 2.7 3.0 + - - -
142M CYS 3.0 1.4 + - - -
143M LYS* 2.8 58.4 + - + +
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Residues in contact with THR 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136M ALA 2.9 14.0 + - - -
137M ALA* 2.8 10.5 + - - -
139M TRP* 1.3 86.8 - - - +
141M LEU* 1.3 63.2 + - - +
143M LYS* 3.4 41.6 - - - +
144M THR* 4.8 2.6 + - - -
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Residues in contact with LEU 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M LEU* 3.9 13.0 - - + +
119M ASN* 5.3 2.2 - - - +
121M LEU* 3.3 41.5 - - + +
122M MET* 3.1 48.0 - - + +
125M ALA* 3.9 12.8 - - + -
137M ALA* 2.8 12.6 + - + +
138M ILE* 3.2 9.6 - - - +
139M TRP 2.7 4.2 + - - -
140M THR* 1.3 77.8 - - - +
142M CYS* 1.3 58.2 + - - +
143M LYS 3.6 2.3 + - - -
144M THR* 4.2 9.9 + - - -
145M LYS* 4.6 1.6 + - - +
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Residues in contact with CYS 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M GLU 2.9 13.9 - - - +
105M CYS* 3.9 26.7 - - - -
113M LEU* 5.1 1.6 - - - -
114M LEU* 3.6 26.9 - - + +
115M LEU* 3.2 33.7 - - + -
122M MET* 5.1 1.3 - - - -
138M ILE* 3.0 38.1 + - - -
139M TRP 3.0 0.9 + - - -
141M LEU* 1.3 75.8 - - - +
143M LYS* 1.3 60.7 + - - +
144M THR 3.3 1.1 - - - -
145M LYS* 3.8 9.7 - - + +
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Residues in contact with LYS 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M GLU* 3.3 24.1 - - + +
114M LEU* 5.6 0.2 - - - +
139M TRP* 2.8 56.9 + - + +
140M THR* 3.4 47.2 - - - +
141M LEU 3.4 0.2 - - - -
142M CYS* 1.3 74.5 - - - +
144M THR* 1.3 74.6 + - - +
145M LYS 4.1 1.4 - - - +
146M MET* 4.0 13.5 - - - +
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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