Contacts of the helix formed by residues 81 - 94 (chain B) in PDB entry 1DXO
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 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B LYS 4.0 7.7 + - - -
54B ASP* 2.6 34.1 + - - -
56B THR* 3.8 6.7 - - - +
79B HIS 3.7 0.4 + - - -
80B LEU* 1.3 72.3 - - - +
82B PRO* 1.3 74.9 - - - +
83B ASP* 2.6 24.9 + - - -
84B ILE* 3.0 23.9 + - - +
85B VAL* 3.1 9.9 + - - +
118B ARG* 4.1 3.1 + - - -
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Residues in contact with PRO 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 3.8 15.5 - - + -
80B LEU 3.2 6.5 - - - +
81B SER* 1.3 86.7 - - - +
83B ASP* 1.3 57.0 + - - +
85B VAL* 3.4 7.9 + - + +
86B ALA* 3.0 28.9 + - - +
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Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B MET* 5.9 1.0 - - + +
46B PHE* 4.5 11.2 - - + -
47B ASN* 4.3 7.6 + - - +
81B SER* 2.6 30.5 + - - -
82B PRO* 1.3 75.5 - - - +
84B ILE* 1.3 63.8 + - - +
86B ALA* 3.5 8.4 - - - +
87B GLU* 3.4 26.0 + - - +
118B ARG* 2.4 31.9 + - - -
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Residues in contact with ILE 84 (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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46B PHE* 5.7 1.8 - - + -
54B ASP* 3.6 26.0 - - + +
67B TYR* 4.5 1.8 - - - +
80B LEU* 4.3 15.3 - - + -
81B SER* 3.0 15.6 + - - +
83B ASP* 1.3 78.2 + - - +
85B VAL* 1.3 66.3 + - - +
86B ALA 3.2 0.2 - - - -
87B GLU* 3.2 5.0 + - - +
88B GLN* 3.1 45.8 + - + +
118B ARG* 3.2 69.8 - - + +
119B VAL* 4.4 9.1 - - + +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLY* 6.2 1.8 - - - -
80B LEU* 3.7 38.8 - - + +
81B SER 3.1 6.0 + - - +
82B PRO* 3.8 10.1 - - + +
84B ILE* 1.3 77.6 - - - +
86B ALA* 1.3 55.8 + - - +
88B GLN* 3.3 16.4 + - + +
89B LYS* 2.9 54.0 + - - +
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Residues in contact with ALA 86 (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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82B PRO 3.0 17.3 + - - +
83B ASP* 3.5 10.1 - - - +
85B VAL* 1.3 78.8 - - - +
87B GLU* 1.3 66.5 + - - +
89B LYS* 3.3 12.4 - - - +
90B LYS* 3.3 26.2 + - - +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 5.1 0.7 - - - +
39B SER* 2.7 22.4 + - - -
44B MET* 3.4 17.9 - - + +
46B PHE* 4.2 9.6 - - + -
83B ASP 3.4 12.7 + - - +
84B ILE 3.2 4.5 + - - +
86B ALA* 1.3 81.6 - - - +
88B GLN* 1.3 60.2 + - - +
89B LYS 3.1 0.2 - - - -
90B LYS* 2.7 50.8 + - - +
91B LEU* 3.0 17.5 + - - +
115B TRP* 2.9 33.1 + - + +
119B VAL* 3.5 24.7 - - + -
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Residues in contact with GLN 88 (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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75B TYR* 3.6 21.1 - - - -
80B LEU* 3.5 25.8 - - - +
84B ILE* 3.1 21.6 + - + +
85B VAL* 3.5 14.6 - - + +
87B GLU* 1.3 75.2 - - - +
89B LYS* 1.3 56.8 + - - +
91B LEU* 3.2 4.7 + - - +
92B GLU* 2.9 38.5 + - - +
119B VAL* 3.2 24.8 + - + +
121B ILE* 4.0 6.9 - - - +
124B PHE* 3.2 41.1 - - + +
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Residues in contact with LYS 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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85B VAL* 2.9 38.0 + - - +
86B ALA* 3.3 12.5 - - - +
88B GLN* 1.3 79.3 - - - +
90B LYS* 1.3 59.1 + - + +
92B GLU* 3.4 16.6 + - - +
93B ALA* 3.4 21.1 + - - +
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Residues in contact with LYS 90 (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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6B LEU* 3.7 26.3 - - + +
37B VAL* 4.0 16.4 - - + -
38B GLU 2.9 15.5 + - - +
39B SER* 2.8 26.3 + - - +
44B MET* 4.3 6.5 - - - +
86B ALA* 3.3 15.0 + - - +
87B GLU* 2.7 35.0 + - - +
89B LYS* 1.3 79.3 - - + +
91B LEU* 1.3 57.4 + - - +
93B ALA* 3.2 6.8 + - - +
94B ALA* 3.0 28.6 + - - +
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Residues in contact with LEU 91 (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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6B LEU* 4.3 7.2 - - + -
87B GLU 3.0 13.0 + - - +
88B GLN 3.2 6.7 + - - +
90B LYS* 1.3 72.1 - - - +
92B GLU* 1.3 54.0 + - - +
93B ALA 3.1 2.5 + - - -
94B ALA* 3.3 8.5 + - - +
97B VAL* 4.1 25.4 - - + -
99B PHE* 5.7 0.4 - - + -
115B TRP* 3.9 20.0 - - + -
119B VAL* 3.3 34.1 - - + -
120B PHE* 3.7 18.8 - - + -
124B PHE* 4.1 14.8 - - + -
137B PHE* 4.7 9.6 - - + -
140B LYS* 2.6 37.8 + - + +
181B PHE* 4.4 15.0 - - + -
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Residues in contact with GLU 92 (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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4B ARG* 5.1 0.9 + - - -
75B TYR* 4.4 9.7 + - - -
88B GLN* 2.9 25.0 + - - +
89B LYS* 3.4 21.3 + - - +
90B LYS 3.4 0.2 - - - -
91B LEU* 1.3 75.2 - - - +
93B ALA* 1.3 56.7 + - - +
124B PHE* 3.6 26.5 - - + -
137B PHE* 5.8 2.0 - - + -
140B LYS* 3.3 15.7 + - - +
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Residues in contact with ALA 93 (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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4B ARG* 2.9 58.5 + - + +
89B LYS 3.4 14.0 + - - +
90B LYS* 3.2 7.0 + - - +
91B LEU 3.1 0.6 - - - -
92B GLU* 1.3 80.4 - - - +
94B ALA* 1.3 62.3 + - - +
95B ASP* 3.7 1.2 + - - +
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Residues in contact with ALA 94 (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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4B ARG* 3.8 7.2 - - - -
5B ALA 4.5 0.4 - - - -
6B LEU* 3.8 19.3 - - + +
90B LYS 3.0 16.2 + - - +
91B LEU* 3.3 5.0 + - - +
93B ALA* 1.3 77.0 - - - +
95B ASP* 1.3 59.5 + - - +
96B LEU 3.8 4.5 - - - +
97B VAL* 3.7 27.4 - - + -
140B LYS* 2.5 35.9 + - - +
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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