Contacts of the helix formed by residues 126 - 137 (chain M) in PDB entry 5MQF
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 VAL 126 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125M ARG* 1.3 71.8 - - - +
127M THR* 1.3 60.0 + - - +
128M HIS 3.4 0.4 - - - -
129M THR* 3.5 9.2 + - - +
130M ARG* 2.9 30.6 + - + +
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Residues in contact with THR 127 (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 ARG* 3.2 8.7 - - - +
126M VAL* 1.3 76.4 - - - +
128M HIS* 1.3 61.4 + - - +
130M ARG* 3.8 5.1 - - - +
131M ARG* 2.9 32.7 + - - +
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Residues in contact with HIS 128 (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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120M LEU* 4.1 30.8 - - + +
123M GLN* 4.5 8.7 - - + -
125M ARG* 3.9 10.6 + - + +
126M VAL 3.4 0.2 - - - -
127M THR* 1.3 78.6 - - - +
129M THR* 1.3 57.9 + - - +
131M ARG* 4.0 3.2 - - - +
132M THR* 2.9 29.1 + - - -
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Residues in contact with THR 129 (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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120M LEU 5.5 2.6 + - - -
125M ARG 4.5 2.1 + - - -
126M VAL* 3.5 14.3 + - - -
127M THR 3.3 0.2 - - - -
128M HIS* 1.3 76.3 - - - +
130M ARG* 1.3 62.2 + - - +
132M THR* 3.5 6.6 - - - -
133M PHE* 2.9 32.4 + - - +
151M LEU* 5.3 13.9 - - - -
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Residues in contact with ARG 130 (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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126M VAL* 2.9 20.1 + - + +
127M THR* 3.4 6.3 + - - +
129M THR* 1.3 77.4 - - - +
131M ARG* 1.3 56.6 + - - +
133M PHE* 4.4 2.0 - - - +
134M ASP* 2.9 31.4 + - - +
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Residues in contact with ARG 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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127M THR 2.9 17.6 + - - +
128M HIS* 4.4 3.4 - - - +
130M ARG* 1.3 73.6 - - - +
132M THR* 1.3 60.0 + - - +
134M ASP* 3.7 6.8 - - - +
135M ARG* 2.9 30.8 + - - +
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Residues in contact with THR 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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113M TRP* 4.8 6.7 - - - +
116M TYR 5.6 0.2 - - - -
117M CYS* 3.7 35.2 - - - -
120M LEU* 5.9 0.2 - - - -
128M HIS 2.9 22.0 + - - -
129M THR* 3.5 8.7 - - - -
130M ARG 3.3 0.4 - - - -
131M ARG* 1.3 75.5 - - - +
133M PHE* 1.3 58.9 - - - +
135M ARG* 3.0 7.3 + - - +
136M ALA* 2.9 27.8 + - - +
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Residues in contact with PHE 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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129M THR 2.9 19.1 + - - +
130M ARG* 4.4 1.8 - - - +
132M THR* 1.3 73.6 - - - +
134M ASP* 1.3 56.4 + - - +
136M ALA* 3.6 8.9 - - - +
137M LEU* 2.9 31.4 + - - +
147M ARG 6.3 0.2 - - - -
148M ILE* 5.1 18.2 - - + -
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Residues in contact with ASP 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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130M ARG 2.9 21.7 + - - +
131M ARG* 3.7 8.1 - - - +
133M PHE* 1.3 78.9 - - - +
135M ARG* 1.3 59.2 + - - +
137M LEU* 3.4 16.5 + - - +
138M ARG* 4.1 3.8 + - - +
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Residues in contact with ARG 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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110M PRO* 5.6 2.1 - - - +
113M TRP* 4.5 15.8 - - + +
131M ARG 2.9 18.3 + - - +
132M THR* 3.0 4.5 + - - +
134M ASP* 1.3 76.5 - - - +
136M ALA* 1.3 61.1 + - - +
137M LEU 3.2 1.4 + - - -
138M ARG* 3.6 17.4 + - - +
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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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110M PRO* 4.6 18.1 - - + +
113M TRP* 4.4 18.5 - - + +
114M LEU* 5.4 1.6 - - - +
132M THR 2.9 15.7 + - - +
133M PHE* 3.6 9.6 - - - +
135M ARG* 1.3 75.3 - - - +
137M LEU* 1.3 56.9 + - - +
138M ARG* 3.3 3.1 + - - -
139M ALA 3.8 9.9 + - - +
141M PRO* 5.6 1.0 - - - +
144M GLN* 3.8 32.7 - - + +
147M ARG* 5.8 4.3 - - + -
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Residues in contact with LEU 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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133M PHE 2.9 17.2 + - - +
134M ASP* 3.7 11.4 - - - +
135M ARG 3.2 1.0 - - - -
136M ALA* 1.3 76.5 - - - +
138M ARG* 1.3 63.5 + - - +
139M ALA 3.3 9.7 + - - +
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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