Contacts of the helix formed by residues 101 - 115 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B THR* 3.5 8.0 + - - +
100B GLY* 1.3 77.7 - - - +
102B SER* 1.3 63.1 + - - +
103B GLU* 4.1 15.7 - - - -
104B ARG* 3.0 49.7 + - - +
105B GLU* 3.6 15.3 + - - +
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLY 3.5 4.4 + - - -
101B SER* 1.3 71.8 - - - +
103B GLU* 1.3 65.6 + - - +
105B GLU* 3.3 13.0 + - - +
106B VAL* 3.3 24.4 + - - +
133B GLU* 3.3 27.9 + - - +
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Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B SER* 4.1 15.0 - - - +
102B SER* 1.3 75.8 - - - +
104B ARG* 1.3 83.2 + - + +
105B GLU 3.1 2.3 + - - -
106B VAL* 3.3 17.5 + - - +
107B GLU* 3.5 16.8 + - - +
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Residues in contact with ARG 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ASN 5.1 3.2 + - - +
98B THR* 3.6 23.6 + - - +
99B GLY* 4.2 9.9 - - - -
100B GLY 4.3 2.4 - - - +
101B SER* 3.0 42.7 + - - +
102B SER 3.5 0.2 - - - -
103B GLU* 1.3 94.3 + - + +
105B GLU* 1.3 61.4 + - - +
107B GLU* 3.4 11.7 + - - +
108B ILE* 3.1 28.0 + - + +
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Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ILE* 4.7 2.9 - - + -
98B THR* 3.6 32.6 + - + +
101B SER 3.6 9.5 + - - +
102B SER* 3.3 17.4 + - - +
103B GLU 3.1 0.4 - - - -
104B ARG* 1.3 77.9 - - - +
106B VAL* 1.3 66.3 + - - +
108B ILE* 3.0 19.3 + - - +
109B TRP* 3.3 28.6 + - + +
122B TYR* 3.5 25.9 + - - -
131B ASP 5.4 0.3 - - - +
132B PRO 3.5 2.1 - - - -
133B GLU* 2.7 38.3 + - - +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B SER 3.3 17.0 - - - +
103B GLU* 3.3 10.7 + - - +
105B GLU* 1.3 76.4 - - - +
107B GLU* 1.3 67.6 + - - +
109B TRP* 3.2 7.7 + - - +
110B LYS* 3.2 36.5 + - + +
133B GLU* 3.6 32.7 + - + +
134B SER 4.2 14.5 - - - +
135B GLY* 5.1 4.9 - - - -
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLU 3.5 15.9 - - - +
104B ARG* 3.5 11.4 - - - +
105B GLU 3.2 0.4 - - - -
106B VAL* 1.3 81.2 - - - +
108B ILE* 1.3 55.1 + - + +
110B LYS* 3.0 35.5 + - - +
111B MSE 2.7 38.4 + - + +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ILE* 4.0 13.2 - - + -
96B ALA* 3.5 23.3 - - + -
97B ASN 5.4 5.4 - - - +
98B THR* 4.3 12.1 - - + -
104B ARG* 3.1 20.9 - - + +
105B GLU* 3.0 13.4 + - - +
107B GLU* 1.3 79.2 - - + +
109B TRP* 1.3 62.2 + - - +
111B MSE 3.0 21.2 + - + +
112B PHE* 2.8 52.9 + - + -
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Residues in contact with TRP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ILE* 3.4 19.7 - - + +
105B GLU* 3.3 43.2 + - + +
106B VAL* 3.2 6.4 + - - +
107B GLU 3.2 0.2 - - - -
108B ILE* 1.3 79.1 - - - +
110B LYS* 1.3 64.4 + - - +
112B PHE* 3.2 6.3 + + - +
113B GLN 3.1 17.5 + - - -
120B VAL* 3.8 28.3 - - + -
122B TYR* 3.9 17.5 - + - -
132B PRO* 3.9 12.1 - - + -
133B GLU 3.4 6.9 + - - -
134B SER* 3.4 34.6 - - - +
137B VAL* 3.5 40.0 - - + +
139B ILE* 4.5 14.1 - - + -
141B THR* 3.5 31.0 - - + -
154B LEU* 5.9 0.7 - - + -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 3.2 26.0 - - + +
107B GLU* 3.0 40.7 + - - +
109B TRP* 1.3 74.7 - - - +
111B MSE 1.3 64.0 + - - +
113B GLN* 3.1 15.0 + - - +
114B SER* 3.3 14.9 + - - -
137B VAL* 3.7 15.5 - - + +
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Residues in contact with MSE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU* 2.7 17.3 + - + +
108B ILE* 3.2 24.2 - - + +
110B LYS* 1.3 72.9 - - - +
112B PHE* 1.3 71.8 + - + +
114B SER* 3.3 4.8 + - - -
115B HIS* 2.6 55.0 + - + +
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Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLY* 4.5 7.0 - - - -
64B ILE 4.6 1.1 - - - -
65B ILE* 3.5 26.5 - - + -
94B LEU* 4.2 40.4 - - + -
95B ILE 4.8 1.3 - - - -
96B ALA* 3.7 22.2 - - + -
108B ILE* 2.8 42.8 + - + +
109B TRP* 3.9 4.9 - - - +
111B MSE 1.3 83.2 - - + +
113B GLN* 1.3 64.6 + - - +
115B HIS* 3.5 2.9 + + + -
116B ARG 3.4 1.7 + - - -
117B ILE* 3.1 55.3 + - + +
120B VAL* 4.5 8.1 - - + -
139B ILE* 4.1 11.2 - - + +
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B TRP 3.1 11.5 + - - +
110B LYS* 3.1 11.4 + - - +
112B PHE* 1.3 73.3 - - - +
114B SER* 1.3 60.1 + - - +
115B HIS 3.0 3.4 - - - -
116B ARG* 2.8 23.2 + - - -
136B ASP 4.4 4.0 - - - +
137B VAL* 3.7 33.9 - - + +
138B SER 4.5 3.5 + - - +
139B ILE* 4.1 10.7 - - + +
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LYS 3.3 7.7 + - - -
111B MSE 3.3 5.4 + - - -
113B GLN* 1.3 80.2 - - - +
115B HIS* 1.3 76.4 + - - +
116B ARG* 3.2 5.5 + - - +
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Residues in contact with HIS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B SER* 5.2 1.9 + - - -
94B LEU* 5.1 14.1 - - + -
111B MSE 2.6 47.3 + - + +
112B PHE* 3.8 9.6 - + + +
113B GLN 3.0 1.2 - - - -
114B SER* 1.3 87.3 + - - +
116B ARG* 1.3 71.6 + - - +
117B ILE* 3.3 14.9 + - + +
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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