Contacts of the helix formed by residues 98 - 110 (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 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D GLU 5.2 0.9 - - - -
97D PRO* 1.3 76.6 - - - +
99D GLY* 1.3 69.5 + - - +
100D LYS 3.8 0.3 + - - -
101D LEU 3.9 0.9 + - - -
102D ALA* 3.4 13.9 + - - -
194D LYS* 5.4 3.1 + - - -
197D GLU* 3.0 33.9 + - - +
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Residues in contact with GLY 99 (chain D).
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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98D SER* 1.3 75.9 + - - +
100D LYS* 1.3 66.8 + - - -
102D ALA* 3.0 13.2 + - - +
103D GLU* 3.1 19.6 + - - +
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Residues in contact with LYS 100 (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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98D SER 3.8 0.2 + - - -
99D GLY* 1.3 70.5 - - - -
101D LEU* 1.3 51.7 + - - +
103D GLU* 2.9 23.2 + - - +
104D TYR* 2.8 44.5 + - + -
200D PHE* 3.9 16.6 - - + -
201D GLU* 4.7 26.6 + - + +
204D LEU* 5.1 16.7 + - - +
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Residues in contact with LEU 101 (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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97D PRO* 3.8 20.2 - - + -
98D SER 3.9 8.9 + - - +
99D GLY 3.2 0.4 - - - -
100D LYS* 1.3 77.0 - - - +
102D ALA* 1.3 57.8 + - - +
104D TYR* 3.2 1.0 + - - -
105D ILE* 2.9 45.5 + - + +
134D LEU* 4.6 11.7 - - + -
143D LEU* 4.4 16.6 - - + -
162D LEU* 5.0 0.9 - - + -
193D TRP* 3.8 10.5 - - + -
196D VAL* 3.6 28.3 - - + -
197D GLU* 4.0 20.2 - - + +
200D PHE* 3.7 36.0 - - + -
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Residues in contact with ALA 102 (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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97D PRO* 3.5 18.5 - - + +
98D SER* 3.4 26.0 + - - -
99D GLY 3.0 12.0 + - - +
101D LEU* 1.3 79.8 - - - +
103D GLU* 1.3 62.4 + - + +
105D ILE* 3.4 4.7 + - - +
106D GLU* 3.1 27.4 + - - +
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Residues in contact with GLU 103 (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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99D GLY 3.1 12.9 + - - +
100D LYS* 2.9 29.3 + - - +
102D ALA* 1.3 76.9 - - + +
104D TYR* 1.3 64.8 + - + +
106D GLU* 3.4 12.4 + - - +
107D LYS* 3.1 23.3 + - - +
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Residues in contact with TYR 104 (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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100D LYS* 2.8 36.6 + - + +
101D LEU 3.8 2.2 - - - +
103D GLU* 1.3 75.1 - - + +
105D ILE* 1.3 60.4 + - - +
107D LYS* 3.7 17.5 - - - -
108D ASP* 2.9 50.7 + - - +
136D TYR* 3.9 12.9 + + - -
141D ASP* 2.7 46.7 + - - -
143D LEU* 3.6 17.7 - - + -
200D PHE* 3.5 27.1 - + + -
204D LEU 4.7 8.7 + - - -
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Residues in contact with ILE 105 (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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97D PRO* 3.8 28.7 - - + -
101D LEU* 2.9 29.3 + - + +
102D ALA* 3.8 5.4 - - - +
104D TYR* 1.3 74.6 - - - +
106D GLU* 1.3 59.1 + - + +
109D PHE* 2.9 32.7 + - + +
110D GLY 3.6 0.5 + - - -
111D SER 3.8 9.0 - - - +
112D PHE* 3.9 15.3 - - + +
115D PHE* 3.6 52.0 - - + -
134D LEU* 5.2 2.0 - - + -
143D LEU* 3.8 18.6 - - + -
193D TRP* 4.8 2.0 - - + -
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Residues in contact with GLU 106 (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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102D ALA 3.1 15.7 + - - +
103D GLU* 3.5 14.3 - - - +
105D ILE* 1.3 78.3 - - + +
107D LYS* 1.3 58.6 + - - +
110D GLY* 2.6 48.5 + - - +
111D SER* 4.3 8.0 - - - +
112D PHE 5.2 2.0 - - - +
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Residues in contact with LYS 107 (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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103D GLU 3.1 13.4 + - - +
104D TYR* 3.7 27.6 - - + +
106D GLU* 1.3 80.5 - - - +
108D ASP* 1.3 89.3 + - - +
110D GLY* 4.5 1.2 + - - -
140D THR 5.1 0.2 + - - -
141D ASP* 2.8 36.5 + - - +
142D ARG* 4.3 3.8 - - - +
5F LYS* 2.9 26.6 + - + +
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Residues in contact with ASP 108 (chain D).
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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104D TYR* 2.9 26.5 + - - +
107D LYS* 1.3 112.0 + - - +
109D PHE* 1.3 74.4 + - + +
142D ARG* 3.6 13.6 + - - +
143D LEU* 2.9 34.3 + - + +
5F LYS* 4.1 12.9 + - - +
55F ARG* 2.8 31.4 + - - +
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Residues in contact with PHE 109 (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* 2.9 25.6 + - - +
108D ASP* 1.3 81.9 - - + +
110D GLY* 1.3 58.0 + - - +
111D SER 3.2 13.7 - - - +
114D ARG* 3.0 24.8 - - + +
115D PHE* 3.7 43.1 - + + +
118D GLU* 3.6 15.3 - - - -
134D LEU* 4.6 0.4 - - + -
143D LEU* 4.0 40.6 - - + -
145D ILE* 3.8 28.7 - - + -
55F ARG* 3.4 44.7 - - - +
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Residues in contact with GLY 110 (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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106D GLU* 2.6 36.1 + - - +
107D LYS 4.4 1.7 + - - -
108D ASP 3.7 1.0 - - - -
109D PHE* 1.3 72.8 - - - +
111D SER* 1.3 60.4 + - - +
114D ARG* 5.1 0.2 - - - -
55F ARG* 5.7 3.6 - - - -
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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