Contacts of the helix formed by residues 95 - 113 (chain I) 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 ILE 95 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B ILE* 6.2 5.6 - - + -
96B GLU* 4.4 23.1 - - + +
99B MET* 3.3 28.7 - - + +
95G ILE* 4.9 7.4 - - + -
94I MET* 1.3 82.0 - - - +
96I GLU* 1.3 91.3 + - + +
97I GLN 2.9 1.6 - - - -
98I GLN* 2.8 16.2 + - - -
99I MET* 3.3 19.3 + - + +
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Residues in contact with GLU 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G MET* 2.8 29.6 + - - +
95G ILE* 3.1 26.7 + - + +
98G GLN* 2.7 43.8 + - - +
95I ILE* 1.3 88.0 - - + +
97I GLN* 1.3 59.2 - - - +
99I MET* 3.4 13.0 - - + +
100I ASP* 3.3 3.2 + - - +
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Residues in contact with GLN 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I MET* 4.4 18.4 - - + +
95I ILE 2.9 0.4 - - - -
96I GLU* 1.3 77.9 - - - +
98I GLN* 1.3 62.0 + - - +
99I MET 3.1 2.0 - - - -
100I ASP* 3.1 29.3 + - - +
101I ARG* 3.8 4.5 + - - +
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Residues in contact with GLN 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLU* 3.1 33.0 + - - +
99B MET* 3.0 27.8 + - + +
100B ASP* 2.8 53.4 + - - +
103B VAL* 4.4 8.8 - - + +
94I MET 3.8 9.6 + - - +
95I ILE 2.8 11.7 + - - +
97I GLN* 1.3 79.5 - - - +
99I MET* 1.3 61.5 + - - +
101I ARG* 3.4 23.7 + - - +
102I ILE* 3.6 13.4 + - - +
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Residues in contact with MET 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B MET* 4.3 16.6 - - + +
95E ILE* 5.7 2.9 - - + -
95G ILE* 3.5 31.6 - - + +
98G GLN* 3.0 40.6 - - + +
99G MET* 4.4 12.8 - - + -
102G ILE* 4.0 23.1 - - + -
95I ILE* 3.3 14.3 + - + +
96I GLU* 3.4 16.8 - - - +
97I GLN 3.1 0.4 - - - -
98I GLN* 1.3 75.7 - - - +
100I ASP* 1.3 56.6 + - - +
101I ARG 2.9 5.4 - - - -
102I ILE* 2.8 29.0 + - + +
103I VAL* 2.9 19.1 + - + +
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Residues in contact with ASP 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G GLN* 2.6 25.6 - - - +
96I GLU* 3.3 10.7 - - - +
97I GLN* 3.1 21.1 + - - +
99I MET* 1.3 78.3 - - - +
101I ARG* 1.3 56.3 + - - +
103I VAL* 4.2 9.8 - - - +
104I LYS* 3.6 16.6 + - - +
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Residues in contact with ARG 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ASP* 4.8 10.9 + - - -
103B VAL* 3.6 23.9 - - + +
107B ARG* 2.8 36.1 - - - +
97I GLN 3.8 4.0 + - - +
98I GLN* 3.4 19.4 + - - +
99I MET 2.9 0.8 - - - -
100I ASP* 1.3 77.8 - - - +
102I ILE* 1.3 68.3 + - - +
104I LYS* 3.0 23.6 - - + +
105I GLU* 2.9 26.7 + - - +
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Residues in contact with ILE 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B MET* 4.9 12.6 - - + +
102B ILE* 3.6 36.6 - - + -
103B VAL* 4.4 11.2 - - + -
106B MET* 3.8 11.3 - - + +
102G ILE* 3.9 33.4 - - + -
98I GLN 4.1 7.2 - - - +
99I MET* 2.8 20.2 + - + +
101I ARG* 1.3 79.0 - - - +
103I VAL* 1.3 55.1 + - - +
105I GLU* 2.9 4.8 + - - +
106I MET* 2.7 49.2 + - + +
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Residues in contact with VAL 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G GLN* 4.8 8.3 - - + +
101G ARG* 4.9 19.5 - - + -
102G ILE* 3.9 28.7 - - + +
105G GLU* 5.2 11.5 - - + +
99I MET* 2.9 20.3 + - + +
100I ASP* 4.5 7.9 - - - +
102I ILE* 1.3 76.7 - - - +
104I LYS* 1.3 62.1 + - - +
106I MET* 4.2 5.6 - - - +
107I ARG* 3.3 24.3 + - + +
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Residues in contact with LYS 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG* 5.2 1.6 - - - +
100I ASP 3.6 11.9 + - - +
101I ARG* 3.0 38.3 + - + +
102I ILE 3.0 0.8 - - - -
103I VAL* 1.3 81.3 - - - +
105I GLU* 1.3 70.2 + - + +
107I ARG* 3.6 4.9 + - - +
108I ARG* 3.1 22.9 + - + +
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Residues in contact with GLU 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 4.3 2.8 - - - +
106B MET* 3.5 30.9 - - + +
107B ARG* 2.7 59.6 + - - +
110B LEU* 4.1 9.0 - - + +
101I ARG* 2.9 16.5 + - - +
102I ILE* 2.9 4.9 + - - +
104I LYS* 1.3 86.3 - - + +
106I MET* 1.3 60.6 + - - +
107I ARG 2.9 1.8 - - - -
108I ARG* 3.4 12.3 - - + -
109I GLN* 2.8 32.9 + - - +
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Residues in contact with MET 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B MET* 3.2 29.1 - - + +
109E GLN* 6.5 0.2 - - - -
102G ILE* 4.1 29.8 - - + +
105G GLU* 4.1 26.9 - - + +
106G MET* 4.3 24.2 - - + -
109G GLN* 3.0 40.0 - - - +
102I ILE* 2.7 28.0 + - + +
103I VAL* 4.2 5.4 - - - +
105I GLU* 1.3 73.2 - - - +
107I ARG* 1.3 56.6 + - - +
109I GLN* 4.0 7.4 - - - +
110I LEU* 3.0 29.8 + - - +
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Residues in contact with ARG 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G GLU* 4.6 15.5 + - - +
103I VAL* 3.3 17.8 + - + +
104I LYS* 3.7 4.7 - - - +
105I GLU 2.9 0.4 - - - -
106I MET* 1.3 80.0 - - - +
108I ARG* 1.3 60.6 + - - +
110I LEU* 4.0 7.4 - - + +
111I GLU* 2.8 37.0 + - + +
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Residues in contact with ARG 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.7 13.2 - - + -
104I LYS* 3.1 17.4 + - + +
105I GLU* 3.1 15.6 + - + +
107I ARG* 1.3 76.0 - - - +
109I GLN* 1.3 68.1 + - - +
111I GLU* 2.9 20.2 + - - +
112I MET* 3.2 12.7 + - - +
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Residues in contact with GLN 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B MET* 4.3 21.8 - - + +
109B GLN* 2.7 39.7 + - - +
110B LEU* 3.0 32.3 - - + +
113B ILE* 4.1 22.0 - - + +
109G GLN* 3.5 29.5 + - - +
105I GLU 2.8 18.7 + - - +
106I MET* 4.0 5.6 - - - +
108I ARG* 1.3 71.5 - - - +
110I LEU* 1.3 55.6 + - - +
112I MET* 2.6 28.8 + - - +
113I ILE* 2.9 11.8 + - + +
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Residues in contact with LEU 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G GLU* 3.9 23.6 - - - +
108G ARG* 3.9 22.4 - - + +
109G GLN* 3.9 15.3 - - + +
112G MET* 3.2 32.3 - - + -
106I MET 3.0 18.1 + - - +
107I ARG* 4.0 8.1 - - + +
109I GLN* 1.3 81.2 - - - +
111I GLU* 1.3 63.1 + - + +
112I MET 3.1 0.4 - - - -
113I ILE* 2.8 28.6 - - + +
114I ASP* 3.6 7.1 + - - +
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Residues in contact with GLU 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I ARG* 2.8 26.7 + - + +
108I ARG* 2.9 12.4 + - - +
110I LEU* 1.3 80.9 - - + +
112I MET* 1.3 56.9 + - - +
114I ASP* 3.5 7.8 - - - +
115I LYS* 2.9 39.4 + - - +
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Residues in contact with MET 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 3.9 27.6 - - + +
113B ILE* 3.6 14.3 - - + +
114B ASP* 3.9 39.3 - - + +
117B THR* 4.1 6.1 + - + +
108I ARG 3.2 7.7 + - - +
109I GLN* 2.6 21.3 + - - +
111I GLU* 1.3 71.0 - - - +
113I ILE* 1.3 54.6 + - - +
114I ASP 2.8 7.6 + - - -
115I LYS* 3.3 10.4 + - + +
116I LEU* 3.3 19.9 + - - +
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Residues in contact with ILE 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ILE* 4.7 21.0 - - + +
109G GLN* 4.5 14.1 - - + +
112G MET* 3.5 28.8 - - + +
113G ILE* 3.2 39.3 - - + +
116G LEU* 4.8 13.2 - - + +
109I GLN* 2.9 9.2 + - + +
110I LEU* 2.8 33.2 - - + +
112I MET* 1.3 75.5 - - - +
114I ASP* 1.3 59.9 + - - +
115I LYS 3.5 0.2 - - - -
116I LEU* 4.1 12.3 - - + +
117I THR* 3.5 20.4 + - - -
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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
------------------------------------------------------------
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