Contacts of the helix formed by residues 103 - 111 (chain H) in PDB entry 3MIW
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 VAL 103 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98F GLN* 4.4 11.2 - - + +
101F ARG* 4.9 14.4 - - + -
102F ILE* 3.4 28.7 - - + +
105F GLU* 4.8 13.8 - - + +
99H MET* 3.0 26.2 + - + +
100H ASP* 4.4 10.1 - - - +
101H ARG 3.2 0.2 - - - -
102H ILE* 1.3 79.5 - - - +
104H LYS* 1.3 62.3 + - - +
106H MET* 3.6 8.0 - - - +
107H ARG* 3.5 19.1 + - - +
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Residues in contact with LYS 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H ASP 3.7 14.6 + - - +
101H ARG* 3.4 11.4 + - + +
103H VAL* 1.3 75.8 - - - +
105H GLU* 1.3 59.0 + - + +
106H MET 3.0 4.0 - - - -
107H ARG* 3.0 9.7 + - - +
108H ARG* 2.9 41.5 + - - +
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Residues in contact with GLU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H ARG* 3.2 46.8 + - + +
104H LYS* 1.3 74.1 - - + +
106H MET* 1.3 62.9 + - - +
107H ARG 3.2 0.2 - - - -
108H ARG* 2.5 47.7 + - + +
109H GLN* 3.3 26.5 + - - +
103J VAL* 5.0 8.2 - - + +
106J MET* 3.3 25.2 - - + +
107J ARG* 4.4 15.6 + - - +
110J LEU* 3.7 18.3 - - + +
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Residues in contact with MET 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 4.7 11.4 - - + -
106D MET* 5.6 5.8 - - + -
102F ILE* 5.0 18.6 - - + +
105F GLU* 4.0 27.9 - - + +
106F MET* 5.5 4.0 - - - -
109F GLN* 3.8 24.5 + - - +
102H ILE* 2.8 29.5 + - + +
103H VAL* 3.6 10.5 - - - +
104H LYS 3.0 0.4 - - - -
105H GLU* 1.3 81.4 - - - +
107H ARG* 1.3 58.9 + - - +
109H GLN* 3.2 32.3 - - - +
110H LEU* 3.4 16.6 + - - +
106J MET* 3.2 27.8 - - + +
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Residues in contact with ARG 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F GLU* 4.3 13.0 - - - +
103H VAL 3.5 9.4 + - - +
104H LYS* 3.0 9.6 + - - +
106H MET* 1.3 77.7 - - - +
108H ARG* 1.3 61.9 + - - +
109H GLN 2.9 4.5 - - - -
110H LEU* 2.8 22.2 + - + +
111H GLU* 2.9 18.0 + - + +
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Residues in contact with ARG 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H ARG* 5.4 3.8 - - - +
104H LYS* 2.9 29.4 + - - +
105H GLU* 2.5 38.5 + - - +
107H ARG* 1.3 76.4 - - - +
109H GLN* 1.3 49.8 + - - +
111H GLU* 5.1 2.8 - - - +
112H MET* 2.6 32.3 + - - +
110J LEU* 3.2 27.0 - - + +
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Residues in contact with GLN 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 6.2 0.8 - - - +
109F GLN* 2.8 32.8 + - - +
105H GLU 3.3 13.3 + - - +
106H MET* 3.2 26.2 - - - +
107H ARG 2.9 0.6 - - - -
108H ARG* 1.3 77.9 - - - +
110H LEU* 1.3 54.3 + - - +
112H MET* 2.8 3.1 + - - +
113H ILE* 2.6 48.8 + - + +
106J MET* 3.7 12.9 + - - +
109J GLN* 3.2 34.8 - - - +
110J LEU* 3.4 21.5 - - + -
113J ILE* 4.5 7.2 - - + +
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Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F GLU* 3.4 23.1 - - - +
108F ARG* 4.3 33.4 - - + +
109F GLN* 4.4 12.1 - - + +
112F MET* 4.1 34.5 - - + -
106H MET 3.4 10.9 + - - +
107H ARG* 2.8 12.2 + - + +
109H GLN* 1.3 74.3 - - - +
111H GLU* 1.3 57.4 + - + +
112H MET 2.8 3.8 - - - -
113H ILE* 2.7 28.9 + - + +
114H ASP* 2.9 11.3 + - - +
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Residues in contact with GLU 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H EDO 5.5 6.7 - - - -
107H ARG* 2.9 14.8 + - + +
108H ARG* 5.1 2.5 - - - +
110H LEU* 1.3 77.5 - - + +
112H MET* 1.3 58.7 + - - +
114H ASP* 3.6 20.0 + - - +
115H LYS* 3.8 10.0 + - - +
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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