Contacts of the helix formed by residues 88 - 110 (chain B) in PDB entry 1DM9
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 THR 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B THR* 5.5 0.4 - - + -
65B THR* 2.9 35.6 + - + +
67B ILE* 3.9 33.2 - - + -
87B GLU* 1.3 75.3 - - - +
89B ALA* 1.3 65.0 + - - +
90B GLU* 3.7 8.5 + - - +
91B SER* 3.0 26.5 + - - -
92B VAL* 3.0 24.3 + - - +
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Residues in contact with ALA 89 (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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87B GLU 3.9 1.4 + - - -
88B THR* 1.3 71.9 - - - +
90B GLU* 1.3 63.7 + - - +
92B VAL* 3.1 10.7 + - - +
93B GLU* 2.9 29.5 + - - +
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B THR* 6.4 0.7 - - - -
88B THR* 3.2 9.3 + - - +
89B ALA* 1.3 79.5 - - - +
91B SER* 1.3 57.7 + - - +
93B GLU* 2.9 26.4 - - - +
94B LYS* 2.9 33.7 + - + +
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Residues in contact with SER 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU 4.1 1.9 + - - +
64B ARG* 3.3 6.6 - - - -
65B THR* 2.8 40.5 + - - -
87B GLU* 2.7 20.8 + - - -
88B THR* 3.0 23.7 + - - -
90B GLU* 1.3 74.5 - - - +
92B VAL* 1.3 66.2 + - - +
94B LYS* 3.3 7.5 + - - +
95B ARG* 3.0 26.3 + - - +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 3.5 27.8 + - + +
88B THR 3.0 18.6 + - - +
89B ALA* 3.5 9.6 - - - +
91B SER* 1.3 76.9 - - - +
93B GLU* 1.3 58.4 + - - +
95B ARG* 3.1 18.4 + - - +
96B GLU* 2.9 48.8 + - + +
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Residues in contact with GLU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 2.9 17.3 + - - +
90B GLU* 2.9 46.5 - - + +
92B VAL* 1.3 74.5 - - - +
94B LYS* 1.3 66.7 + - - +
96B GLU* 3.6 12.4 - - - +
97B LYS* 2.9 51.1 + - + +
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Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 3.2 37.2 + - + +
90B GLU* 2.9 23.8 + - + +
91B SER* 3.6 8.7 - - - +
92B VAL 3.3 0.2 - - - -
93B GLU* 1.3 77.3 - - - +
95B ARG* 1.3 64.0 + - + +
97B LYS* 3.4 9.8 + - - +
98B MET* 3.1 35.3 + - + +
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Residues in contact with ARG 95 (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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62B ASP* 6.3 0.9 - - - +
63B GLU 3.5 26.2 - - - +
64B ARG* 3.3 40.9 - - - +
87B GLU* 2.9 35.4 + - - -
91B SER 3.0 12.9 + - - +
92B VAL* 3.5 23.0 - - - +
94B LYS* 1.3 77.9 - - + +
96B GLU* 1.3 63.6 + - + +
98B MET* 3.2 11.6 + - + +
99B ALA* 3.1 22.2 + - - +
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Residues in contact with GLU 96 (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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92B VAL* 2.9 38.2 + - + +
93B GLU* 3.1 13.1 + - - +
95B ARG* 1.3 77.1 - - + +
97B LYS* 1.3 57.1 + - + +
99B ALA* 3.1 8.6 + - - +
100B LEU* 2.8 29.3 + - - +
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Residues in contact with LYS 97 (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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93B GLU* 2.9 42.4 + - + +
94B LYS* 3.9 7.4 - - - +
96B GLU* 1.3 76.8 - - + +
98B MET* 1.3 57.2 + - - +
100B LEU* 3.6 14.0 - - + +
101B ALA* 2.8 29.8 + - - +
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Residues in contact with MET 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASN* 3.0 47.1 - - + +
62B ASP* 5.5 0.7 - - - +
63B GLU* 5.5 3.1 - - + +
94B LYS* 3.1 26.7 + - + +
95B ARG* 3.6 13.7 - - + +
97B LYS* 1.3 74.7 - - - +
99B ALA* 1.3 66.4 + - - +
101B ALA* 3.4 6.7 + - + +
102B ARG* 3.0 25.0 + - + +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ARG 3.1 12.8 + - - +
96B GLU* 3.4 10.5 - - - +
98B MET* 1.3 74.9 - - - +
100B LEU* 1.3 65.0 + - - +
102B ARG* 3.0 14.2 - - - +
103B LYS* 2.9 25.3 + - - +
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Residues in contact with LEU 100 (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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96B GLU 2.8 16.9 + - - +
97B LYS* 3.6 13.7 - - + +
99B ALA* 1.3 76.0 - - - +
101B ALA* 1.3 56.7 + - - +
103B LYS* 3.2 8.6 + - + +
104B LEU* 2.9 60.1 + - + +
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Residues in contact with ALA 101 (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 LYS 2.8 18.8 + - - +
98B MET* 3.7 7.9 - - + +
99B ALA 3.2 0.2 - - - -
100B LEU* 1.3 78.5 - - - +
102B ARG* 1.3 60.7 + - - +
104B LEU* 3.4 11.0 + - - +
105B ASN* 3.2 21.1 + - - +
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Residues in contact with ARG 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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98B MET* 3.0 16.7 + - + +
99B ALA* 3.0 23.6 - - - +
101B ALA* 1.3 76.0 - - - +
103B LYS* 1.3 69.7 + - - +
105B ASN* 3.1 22.1 + - - +
106B ALA* 3.2 38.6 + - - +
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Residues in contact with LYS 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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99B ALA 2.9 16.5 + - - +
100B LEU* 3.5 9.9 - - + +
102B ARG* 1.3 91.2 - - - +
104B LEU* 1.3 65.5 + - + +
106B ALA* 3.1 5.7 + - - +
107B LEU* 3.1 22.5 + - - +
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Residues in contact with LEU 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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100B LEU* 2.9 46.6 + - + +
101B ALA* 3.7 9.4 - - - +
102B ARG 3.3 0.2 - - - -
103B LYS* 1.3 77.4 - - + +
105B ASN* 1.3 56.2 + - - +
107B LEU* 3.6 16.3 - - + +
108B THR* 3.0 42.9 + - + +
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Residues in contact with ASN 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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101B ALA 3.2 11.0 + - - +
102B ARG* 3.1 18.7 + - - +
104B LEU* 1.3 80.4 - - - +
106B ALA* 1.3 55.9 + - - +
108B THR* 3.8 6.2 + - - -
109B MET* 3.2 27.9 + - - +
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Residues in contact with ALA 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 ARG* 3.2 31.8 + - - +
103B LYS 3.1 6.1 + - - +
105B ASN* 1.3 79.5 - - - +
107B LEU* 1.3 54.8 + - - +
109B MET* 4.6 2.2 - - - -
110B PRO* 2.7 38.7 - - + +
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Residues in contact with LEU 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 LYS 3.1 12.3 + - - +
104B LEU* 3.6 22.0 - - + +
105B ASN 3.3 0.2 - - - -
106B ALA* 1.3 75.1 - - - +
108B THR* 1.3 68.0 - - + +
109B MET 3.0 4.6 + - - -
110B PRO 2.8 30.3 - - - +
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 3.0 24.1 + - + +
105B ASN* 3.8 7.1 + - - -
107B LEU* 1.3 82.1 - - + +
109B MET* 1.3 61.0 + - - +
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Residues in contact with MET 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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105B ASN 3.2 18.8 + - - +
106B ALA* 4.1 3.1 - - - +
107B LEU 3.0 1.0 - - - -
108B THR* 1.3 84.3 + - - +
110B PRO* 1.3 61.8 - - + +
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Residues in contact with PRO 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 ALA* 2.7 25.0 - - + +
107B LEU* 2.8 25.6 - - - +
109B MET* 1.3 77.6 - - + +
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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