Contacts of the helix formed by residues 111 - 125 (chain D) in PDB entry 1MA1
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 SER 111 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D ILE* 3.8 6.4 - - - +
106D GLU* 4.0 9.8 + - - +
109D PHE* 3.2 10.5 + - - +
110D GLY* 1.3 77.6 - - - +
112D PHE* 1.3 64.6 + - - +
113D GLU* 3.3 16.6 + - - +
114D ARG* 3.0 23.4 + - - +
115D PHE* 3.2 18.0 + - - +
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Residues in contact with PHE 112 (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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95D GLY 4.2 7.6 - - - -
96D GLU* 3.7 44.6 - - + +
97D PRO* 3.3 32.8 - - + -
105D ILE* 3.9 14.4 - - + +
106D GLU* 5.2 3.4 - - - +
111D SER* 1.3 70.8 - - - +
113D GLU* 1.3 66.1 + - - +
115D PHE* 3.2 19.1 + + - +
116D ARG* 2.7 60.7 + - + +
188D TRP* 4.5 8.7 - + - -
193D TRP* 3.7 22.0 - + - -
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Residues in contact with GLU 113 (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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96D GLU* 4.6 10.7 - - - +
111D SER* 3.3 16.2 + - - +
112D PHE* 1.3 87.1 + - - +
114D ARG* 1.3 64.3 + - - +
116D ARG* 3.1 12.7 + - - +
117D LYS* 2.9 26.2 + - - +
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Residues in contact with ARG 114 (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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109D PHE* 3.0 31.2 - - + +
111D SER* 3.0 13.8 + - - +
113D GLU* 1.3 77.8 - - - +
115D PHE* 1.3 64.3 + - - +
117D LYS* 3.1 26.4 + - - +
118D GLU* 2.9 56.5 + - - +
54F ALA* 3.5 26.0 + - - +
55F ARG* 3.6 12.0 - - + +
58F ASP* 3.6 29.9 + - - +
59F THR 2.7 31.3 + - - -
60F ASP* 4.8 0.4 - - - +
61F VAL* 4.8 7.7 - - - +
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Residues in contact with PHE 115 (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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105D ILE* 3.6 30.1 - - + -
109D PHE* 3.7 37.1 - + + +
111D SER 3.2 3.5 + - - +
112D PHE* 3.2 21.9 + + - +
114D ARG* 1.3 80.2 - - - +
116D ARG* 1.3 58.2 + - - +
117D LYS 3.0 0.3 + - - -
118D GLU* 3.1 1.4 + - - +
119D PHE* 2.8 62.2 + + + +
134D LEU* 4.0 32.5 - - + -
145D ILE* 4.2 2.7 - - + -
163D LEU* 4.1 13.2 - - + -
188D TRP* 3.8 13.7 - + - -
193D TRP* 3.8 23.3 - + - -
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Residues in contact with ARG 116 (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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112D PHE* 2.7 43.8 + - + +
113D GLU* 3.4 11.0 - - - +
115D PHE* 1.3 80.3 - - - +
117D LYS* 1.3 54.7 + - - +
120D SER* 2.7 40.2 + - - -
185D GLU* 2.7 41.6 + - - -
188D TRP* 3.5 55.4 - - + +
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Residues in contact with LYS 117 (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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113D GLU 2.9 17.1 + - - +
114D ARG* 3.5 29.5 - - - +
116D ARG* 1.3 76.7 - - - +
118D GLU* 1.3 61.4 + - + +
120D SER* 3.1 6.8 + - - -
121D GLN* 2.9 54.7 + - + +
58F ASP* 5.5 3.2 + - - -
60F ASP* 3.8 25.7 + - - +
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Residues in contact with GLU 118 (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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109D PHE* 3.6 10.3 - - - -
114D ARG* 2.9 52.2 + - - +
115D PHE* 3.8 3.8 - - - +
117D LYS* 1.3 79.0 - - + +
119D PHE* 1.3 62.1 + - - +
121D GLN* 3.2 7.4 + - - +
122D ALA* 2.9 3.3 + - - +
145D ILE* 4.2 11.9 - - + +
51F LEU* 5.2 5.2 - - - +
55F ARG* 2.9 40.2 + - - +
61F VAL* 5.4 3.3 - - + +
63F ILE* 2.9 50.0 - - + +
67F LEU* 6.1 0.9 - - - +
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Residues in contact with PHE 119 (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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115D PHE* 2.8 33.0 + + + +
116D ARG 4.0 3.1 - - - +
118D GLU* 1.3 73.3 - - - +
120D SER* 1.3 57.8 + - - +
122D ALA* 3.3 5.1 + - - +
123D ALA* 3.1 23.0 + - - +
132D ALA* 3.3 29.4 - - + +
133D VAL 3.8 5.8 - - - -
134D LEU* 3.7 29.4 - - + -
145D ILE* 3.8 26.8 - - + +
163D LEU* 3.9 22.9 - - + -
165D LEU* 3.8 29.4 - - + -
187D PHE* 4.5 3.6 - + - -
188D TRP* 3.6 27.8 - + + -
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Residues in contact with SER 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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116D ARG* 2.7 27.0 + - - +
117D LYS* 3.1 7.4 + - - -
119D PHE* 1.3 75.4 - - - +
121D GLN* 1.3 59.5 + - - +
123D ALA* 3.3 2.4 + - - +
124D ILE* 2.8 43.2 + - - +
184D VAL* 3.7 17.2 - - - +
185D GLU* 5.6 0.3 + - - -
188D TRP* 3.1 24.0 + - - -
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Residues in contact with GLN 121 (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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117D LYS* 2.9 48.6 + - + +
118D GLU* 3.6 4.8 - - - +
120D SER* 1.3 73.2 - - - +
122D ALA* 1.3 57.3 + - - +
124D ILE* 4.4 6.1 - - + +
125D SER* 2.7 42.1 + - - +
60F ASP* 5.5 4.6 - - - +
61F VAL* 3.5 25.9 + - - +
63F ILE* 3.3 30.0 - - + +
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Residues in contact with ALA 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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118D GLU 2.9 3.5 + - - +
119D PHE 3.4 10.1 - - - +
121D GLN* 1.3 75.2 - - - +
123D ALA* 1.3 62.6 + - - +
126D ALA* 3.8 1.7 + - - +
131D TRP 4.8 0.7 - - - +
132D ALA* 3.9 15.3 - - + +
145D ILE* 4.0 9.2 - - + -
147D GLN* 2.9 38.0 + - + +
63F ILE* 2.8 23.4 - - + +
67F LEU* 3.9 19.3 - - + -
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Residues in contact with ALA 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 PHE 3.1 11.4 + - - +
120D SER 3.6 7.0 - - - +
121D GLN 3.2 0.2 - - - -
122D ALA* 1.3 79.5 - - - +
124D ILE* 1.3 66.6 + - - +
125D SER 3.3 0.5 + - - -
126D ALA 3.4 2.3 + - - -
132D ALA* 3.8 11.4 - - + +
165D LEU* 3.8 21.1 - - + -
167D VAL* 3.5 24.4 - - + +
180D ARG* 3.3 14.7 + - - -
184D VAL* 3.8 21.8 - - + -
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Residues in contact with ILE 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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120D SER* 2.8 32.7 + - - +
121D GLN* 4.2 5.4 - - - +
123D ALA* 1.3 73.1 - - - +
125D SER* 1.3 59.7 + - - +
126D ALA 4.2 0.2 - - - +
180D ARG* 3.0 27.4 + - + +
181D PRO* 3.8 43.3 - - + +
184D VAL* 3.9 22.9 - - + -
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Residues in contact with SER 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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121D GLN* 2.7 26.0 + - - -
122D ALA* 4.2 0.2 - - - -
124D ILE* 1.3 77.7 - - - +
126D ALA* 1.3 65.8 + - - +
127D GLU* 3.3 4.7 + - - +
147D GLN* 3.0 14.5 + - - -
63F ILE* 4.6 1.0 - - - +
64F LYS* 3.4 38.4 + - - +
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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
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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