Contacts of the helix formed by residues 76 - 86 (chain A) in PDB entry 2DOS
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 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASP* 3.9 13.0 - - - -
64A GLN 4.6 0.7 + - - -
65A PRO 3.9 0.3 - - - -
66A SER* 3.5 26.7 + - - -
75A PHE* 1.3 78.6 + - - +
77A ILE* 1.3 65.7 + - - +
78A GLN* 3.0 31.6 + - - -
79A VAL* 3.0 20.6 + - - +
80A ILE* 3.2 16.2 + - - +
120A TRP* 5.0 4.7 - - - -
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLN* 4.7 22.0 - - + +
64A GLN 5.7 0.9 + - - +
76A SER* 1.3 73.6 + - - +
78A GLN* 1.3 62.5 + - - +
80A ILE* 4.5 1.1 - - + -
81A SER* 2.7 42.2 + - - -
91A LEU* 4.8 15.9 - - + -
113A ILE* 5.9 0.7 - - + -
115A ASN* 5.8 1.3 - - - +
120A TRP* 3.2 37.5 - - + -
163A PHE* 4.4 34.8 - - + -
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Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.3 14.4 - - + +
41A ASP* 4.3 5.5 + - - -
44A GLU* 3.7 21.8 + - + +
60A THR* 5.6 2.5 - - + +
63A GLN* 3.7 32.7 - - + +
64A GLN 3.5 9.4 - - - +
65A PRO* 3.3 37.0 - - + +
66A SER 4.1 1.2 - - - +
76A SER* 3.0 26.8 + - - -
77A ILE* 1.3 82.3 + - - +
79A VAL* 1.3 57.3 + - - +
81A SER* 4.2 3.0 - - - -
82A ASN* 3.0 30.3 + - - +
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 4.6 5.2 - - + -
36A ILE* 3.8 26.7 - - + -
37A ALA* 3.6 24.7 - - + +
40A LEU* 3.6 22.4 - - + -
75A PHE* 3.1 32.5 - - + -
76A SER* 3.0 22.6 + - - +
78A GLN* 1.3 74.6 - - + +
80A ILE* 1.3 64.8 - - - +
82A ASN* 3.3 3.9 + - + +
83A ALA* 3.0 23.7 + - - +
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 6.0 1.8 - - + -
15A ALA* 4.5 8.5 - - - -
18A CYS* 4.9 11.0 - - + -
19A LEU* 3.9 23.8 - - + -
75A PHE* 3.3 31.2 - - + -
76A SER 3.2 12.6 + - - +
77A ILE* 3.9 4.7 - - - +
79A VAL* 1.3 75.7 - - - +
81A SER* 1.3 62.4 + - - +
83A ALA* 3.1 7.6 + - - +
84A LEU* 3.0 44.9 + - + +
91A LEU* 4.5 6.5 - - + -
113A ILE* 6.0 3.6 - - + -
120A TRP* 3.8 36.8 - - + -
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLN* 6.5 0.2 - - - -
77A ILE* 2.7 30.9 + - - -
78A GLN* 4.2 3.4 - - - -
80A ILE* 1.3 73.1 - - - +
82A ASN* 1.3 51.7 + - - +
84A LEU* 3.2 3.5 + - - +
85A LYS* 2.7 45.2 + - - +
89A LEU 4.5 0.9 - - - +
90A GLU* 6.0 0.2 - - - -
91A LEU* 3.7 30.2 + - - +
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Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 5.9 5.0 - - + +
40A LEU* 5.2 7.6 - - + -
78A GLN 3.0 20.9 + - - +
79A VAL* 3.5 7.2 - - - +
81A SER* 1.3 77.7 + - - +
83A ALA* 1.3 64.8 + - - +
85A LYS* 3.2 20.1 + - - +
86A VAL* 3.1 37.6 + - - +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.6 34.3 - - + -
28A PHE* 5.0 6.7 - - + -
33A LEU* 5.1 4.9 - - + -
75A PHE* 6.5 0.2 - - + -
79A VAL 3.0 16.5 + - - +
80A ILE 3.1 5.4 + - - +
82A ASN* 1.3 80.0 - - - +
84A LEU* 1.3 56.8 + - - +
86A VAL* 2.8 23.8 - - - +
87A TRP* 2.9 24.7 - - + -
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 5.6 2.2 - - + -
22A LEU* 3.3 33.9 - - + -
80A ILE* 3.0 45.9 + - + +
81A SER* 3.6 3.1 - - - +
83A ALA* 1.3 78.7 - - + +
85A LYS* 1.3 55.7 + - - +
87A TRP* 2.9 14.0 + - + +
88A GLY 2.8 10.2 + - - -
89A LEU* 2.7 61.0 + - + +
90A GLU* 5.4 0.9 - - - -
91A LEU* 3.8 22.4 - - + -
113A ILE* 5.7 2.2 - - + -
165A VAL* 3.8 12.6 - - + -
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A SER* 2.7 30.3 + - - +
82A ASN* 3.2 22.9 + - - +
84A LEU* 1.3 73.6 - - - +
86A VAL* 1.3 61.9 + - + +
88A GLY* 2.9 19.0 + - - +
89A LEU 3.1 10.7 + - - +
90A GLU* 6.0 1.8 - - + -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 6.2 0.9 - - + -
82A ASN* 3.1 27.9 + - - +
83A ALA* 2.8 32.3 - - - +
85A LYS* 1.3 79.0 - - + +
87A TRP* 1.3 75.3 + - + +
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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