Contacts of the helix formed by residues 101 - 115 (chain A) in PDB entry 3MIZ
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A THR* 3.1 7.2 + - - -
99A GLY 3.3 1.0 + - - -
100A GLY* 1.3 76.7 - - - +
102A SER* 1.3 58.1 + - - +
103A GLU* 3.3 13.0 + - - +
104A ARG* 3.1 53.1 + - - +
105A GLU* 2.9 30.7 + - - +
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Residues in contact with SER 102 (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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100A GLY 3.8 4.4 + - - -
101A SER* 1.3 71.4 + - - +
103A GLU* 1.3 81.1 + - - +
105A GLU* 3.3 8.5 + - - +
106A VAL* 3.0 30.1 + - - +
133A GLU* 3.9 28.1 - - - +
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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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101A SER* 3.2 12.3 + - - +
102A SER* 1.3 94.0 + - - +
104A ARG* 1.3 64.4 + - + +
106A VAL* 3.2 15.0 + - - +
107A GLU* 3.3 12.4 + - - +
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Residues in contact with ARG 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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97A ASN 5.5 2.5 - - - +
98A THR* 3.1 32.0 + - - +
99A GLY* 4.3 9.3 + - - -
101A SER* 3.1 28.8 + - - +
103A GLU* 1.3 77.4 - - + +
105A GLU* 1.3 56.2 + - - +
107A GLU* 3.3 18.8 + - - +
108A ILE* 2.9 37.3 + - + +
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Residues in contact with GLU 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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65A ILE* 4.6 3.6 - - + -
98A THR* 3.8 27.6 + - + +
101A SER 2.9 19.1 + - - +
102A SER* 3.5 8.0 + - - +
103A GLU 3.2 0.2 - - - -
104A ARG* 1.3 73.9 - - - +
106A VAL* 1.3 66.6 + - - +
108A ILE* 2.9 13.1 + - - +
109A TRP* 3.0 40.2 + - + +
122A TYR* 3.0 32.1 + - - -
131A ASP 5.3 0.3 - - - +
133A GLU* 2.7 39.3 + - - +
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Residues in contact with VAL 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 SER 3.0 18.6 + - - +
103A GLU* 3.2 9.4 + - - +
105A GLU* 1.3 75.7 - - - +
107A GLU* 1.3 63.5 + - - +
109A TRP* 3.3 5.2 + - - +
110A LYS* 3.2 40.1 + - - +
133A GLU* 3.5 30.1 - - + +
134A SER* 4.9 1.4 - - - +
135A GLY* 4.5 19.3 - - - +
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Residues in contact with GLU 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 3.3 8.3 + - - +
104A ARG* 3.3 21.7 + - - +
105A GLU 3.2 0.2 - - - -
106A VAL* 1.3 81.0 - - - +
108A ILE* 1.3 58.8 + - + +
110A LYS* 3.3 13.0 + - + +
111A MSE 2.9 29.7 + - + +
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Residues in contact with ILE 108 (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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65A ILE* 3.9 12.6 - - + -
96A ALA* 3.7 30.1 - - + -
97A ASN 3.6 32.3 - - - +
98A THR* 4.0 16.2 - - + -
104A ARG* 2.9 22.3 + - + +
105A GLU* 2.9 7.8 + - - +
107A GLU* 1.3 78.4 - - + +
109A TRP* 1.3 61.5 + - - +
111A MSE 3.2 13.5 + - + +
112A PHE* 2.9 42.0 + - + +
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Residues in contact with TRP 109 (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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65A ILE* 3.5 21.4 - - + +
105A GLU* 3.0 49.8 + - + +
106A VAL 3.3 6.5 + - - +
108A ILE* 1.3 76.5 - - - +
110A LYS* 1.3 63.2 + - - +
112A PHE* 3.2 6.4 + + - +
113A GLN* 3.0 22.5 + - - +
120A VAL* 3.8 28.5 - - + -
122A TYR* 3.9 9.0 - + - -
132A PRO* 3.8 21.3 - - + -
133A GLU 3.2 18.0 + - - -
134A SER* 3.4 26.5 - - - +
137A VAL* 3.8 29.4 - - + +
139A ILE* 4.4 13.0 - - + +
141A THR* 3.4 31.9 - - + -
154A LEU* 5.9 0.7 - - + -
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Residues in contact with LYS 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 VAL* 3.2 30.0 + - - +
107A GLU* 3.4 13.9 - - - +
109A TRP* 1.3 79.8 - - - +
111A MSE 1.3 61.8 + - - +
113A GLN* 3.3 7.7 + - - +
114A SER* 3.0 23.7 + - - -
134A SER 5.4 0.4 + - - -
135A GLY* 5.6 0.2 - - - -
136A ASP* 5.1 11.5 + - - +
137A VAL* 3.9 20.3 - - + +
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Residues in contact with MSE 111 (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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107A GLU* 2.9 19.3 + - + +
108A ILE* 3.2 17.9 + - + +
110A LYS* 1.3 76.6 - - - +
112A PHE* 1.3 72.3 + - + +
114A SER* 3.2 7.9 + - - -
115A HIS* 3.0 53.5 + - + +
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Residues in contact with PHE 112 (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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63A GLY* 3.9 22.2 - - - -
64A ILE 4.2 2.0 - - - -
65A ILE* 3.3 42.4 - - + -
94A LEU* 4.0 20.9 - - + -
95A ILE 5.6 0.2 - - - -
96A ALA* 3.9 20.0 - - + -
108A ILE* 2.9 20.5 + - + -
109A TRP* 3.2 8.2 + - - +
111A MSE 1.3 83.0 - - + +
113A GLN* 1.3 66.6 + - - +
115A HIS* 3.2 4.9 + + + +
116A ARG 3.2 15.6 + - - -
117A ILE* 3.2 42.5 + - + +
120A VAL* 4.1 9.4 - - + -
139A ILE* 4.2 13.2 - - + +
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Residues in contact with GLN 113 (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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109A TRP 3.0 13.7 + - - +
110A LYS* 3.6 12.7 - - - +
112A PHE* 1.3 75.4 - - - +
114A SER* 1.3 64.2 + - - +
116A ARG* 3.0 31.9 + - - +
117A ILE 5.2 0.2 - - - +
136A ASP 5.1 1.6 + - - -
137A VAL* 4.1 35.7 - - + +
138A SER* 4.4 9.5 + - - +
139A ILE* 3.9 11.2 - - + +
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Residues in contact with SER 114 (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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110A LYS 3.0 13.1 + - - -
111A MSE 3.2 13.7 + - - -
113A GLN* 1.3 79.2 - - - +
115A HIS* 1.3 65.1 + - - +
116A ARG* 3.2 23.2 + - - +
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Residues in contact with HIS 115 (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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59A SER* 5.1 3.8 - - - -
94A LEU* 5.7 6.9 - - + +
111A MSE 3.0 55.0 + - + +
112A PHE* 3.9 7.4 - + + +
113A GLN 3.2 0.8 - - - -
114A SER* 1.3 80.6 + - - +
116A ARG* 1.3 72.9 + - - +
117A ILE* 3.3 17.8 + - + +
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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