Contacts of the helix formed by residues 98 - 110 (chain A) 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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLU 5.2 0.7 - - - -
97A PRO* 1.3 75.0 - - - +
99A GLY* 1.3 69.9 + - - +
100A LYS 3.7 0.2 + - - -
101A LEU 3.9 0.9 + - - -
102A ALA* 3.4 14.5 + - - -
194A LYS* 5.3 3.5 + - - -
197A GLU* 3.0 34.0 + - - +
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A SER* 1.3 78.0 - - - +
100A LYS* 1.3 66.1 + - - -
102A ALA* 3.0 13.2 + - - +
103A GLU* 3.1 19.3 + - - +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A SER 3.7 0.2 + - - -
99A GLY* 1.3 70.8 - - - -
101A LEU* 1.3 58.7 + - - +
103A GLU* 2.9 22.8 + - - +
104A TYR* 2.8 40.6 + - + -
200A PHE* 3.9 15.5 - - + -
201A GLU* 5.0 23.6 + - + +
204A LEU* 5.0 18.6 + - - +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PRO* 3.8 19.5 - - + -
98A SER 3.9 8.5 + - - +
99A GLY 3.2 0.4 - - - -
100A LYS* 1.3 77.1 - - - +
102A ALA* 1.3 58.1 + - - +
104A TYR* 3.2 0.7 + - - -
105A ILE* 2.9 51.9 + - + +
134A LEU* 4.6 10.8 - - + -
143A LEU* 4.4 12.6 - - + -
162A LEU* 5.0 0.9 - - + -
193A TRP* 3.9 10.3 - - + -
196A VAL* 3.6 28.5 - - + -
197A GLU* 4.0 19.9 - - + +
200A PHE* 3.7 33.8 - - + -
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PRO* 3.5 18.7 - - - +
98A SER* 3.4 26.9 + - - -
99A GLY 3.0 11.8 + - - +
101A LEU* 1.3 80.4 - - - +
103A GLU* 1.3 62.2 - - + +
105A ILE* 3.4 4.8 + - - +
106A GLU* 3.1 26.5 + - - +
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLY* 3.1 12.4 + - - +
100A LYS* 2.9 30.1 + - - +
102A ALA* 1.3 77.3 - - + +
104A TYR* 1.3 64.4 + - + +
106A GLU* 3.4 13.6 + - - +
107A LYS* 3.1 23.8 + - - +
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Residues in contact with TYR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS* 2.8 37.8 + - + +
101A LEU 3.8 2.0 - - - +
103A GLU* 1.3 72.7 - - + +
105A ILE* 1.3 61.6 + - - +
107A LYS* 3.6 17.0 - - - -
108A ASP* 2.9 51.0 + - - +
136A TYR* 4.0 12.7 + + - -
141A ASP* 2.7 45.4 + - - -
143A LEU* 3.6 18.2 - - + -
200A PHE* 3.4 29.8 - + + -
204A LEU 4.7 9.1 + - - -
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PRO* 3.8 28.5 - - + -
101A LEU* 2.9 29.8 + - + +
102A ALA* 3.8 5.2 - - - +
104A TYR* 1.3 75.0 - - - +
106A GLU* 1.3 57.9 + - + +
109A PHE* 2.9 33.8 + - + +
110A GLY 3.6 0.7 + - - -
111A SER 3.8 8.6 - - - +
112A PHE* 3.9 14.6 - - + -
115A PHE* 3.6 51.8 - - + -
134A LEU* 5.1 2.0 - - + -
143A LEU* 3.7 18.8 - - + -
193A TRP* 4.8 2.7 - - + -
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ALA 3.1 16.3 + - - +
103A GLU* 3.4 15.7 - - - +
104A TYR 3.2 0.2 - - - -
105A ILE* 1.3 78.1 - - + +
107A LYS* 1.3 57.3 + - - +
110A GLY* 2.6 48.5 + - - +
111A SER* 4.3 8.5 - - - +
112A PHE 5.2 2.0 - - - +
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU 3.1 12.3 + - - +
104A TYR* 3.6 29.4 - - + +
106A GLU* 1.3 81.3 - - + +
108A ASP* 1.3 92.9 + - - +
110A GLY* 4.5 1.4 + - - -
141A ASP* 2.9 34.0 + - - -
142A ARG* 4.4 3.0 - - - +
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Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR* 2.9 21.9 + - - +
107A LYS* 1.3 111.5 + - - +
109A PHE* 1.3 79.1 + - + +
142A ARG* 3.6 15.7 + - - +
143A LEU* 2.8 37.5 + - - +
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 2.9 25.7 + - - +
108A ASP* 1.3 87.2 - - + +
110A GLY* 1.3 57.8 + - - +
111A SER 3.2 13.2 - - - +
114A ARG* 2.9 28.8 - - + +
115A PHE* 3.7 40.4 - + + +
118A GLU* 3.5 32.1 - - - -
134A LEU* 4.5 1.1 - - + -
143A LEU* 3.9 40.6 - - + -
145A ILE* 3.8 28.0 - - + -
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Residues in contact with GLY 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLU* 2.6 35.2 + - - +
107A LYS 4.4 1.9 + - - -
108A ASP 3.7 0.8 - - - -
109A PHE* 1.3 70.7 - - - +
111A SER* 1.3 61.1 + - - +
114A ARG* 5.0 0.2 - - - -
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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