Contacts of the helix formed by residues 60 - 68 (chain A) in PDB entry 1DOM
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A VAL* 4.2 6.5 - - + -
43A PHE* 3.2 33.0 - - + -
53A ALA* 3.7 7.9 - - + -
54A ASP 3.5 27.4 - - - +
55A PRO* 4.0 13.5 - - + -
57A GLN* 4.1 2.8 + - + +
59A TRP* 1.3 117.4 - - + +
61A GLN* 1.3 56.0 + - - +
62A ASP 3.2 0.4 - - - -
64A MET* 2.7 45.7 + - + +
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Residues in contact with GLN 61 (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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55A PRO 4.0 14.1 + - - +
56A LYS* 5.7 2.2 - - - +
57A GLN 3.2 23.3 + - - +
58A LYS* 4.0 26.2 + - + +
59A TRP 3.1 0.8 - - - -
60A VAL* 1.3 81.5 - - - +
62A ASP* 1.3 60.7 + - - +
64A MET* 4.4 8.7 - - + -
65A ASP* 3.4 24.9 + - - +
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Residues in contact with ASP 62 (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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58A LYS* 3.9 22.4 + - - +
59A TRP* 3.4 8.4 + - - +
60A VAL 3.2 0.4 - - - -
61A GLN* 1.3 81.0 - - - +
63A SER* 1.3 65.7 + - - +
65A ASP* 3.3 5.1 + - - +
66A HIS* 3.0 20.8 + - - +
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Residues in contact with SER 63 (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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20A ILE 4.3 3.3 + - - -
22A VAL* 4.3 12.1 + - - +
25A LEU* 3.4 29.3 - - - +
43A PHE* 3.7 7.6 - - - -
59A TRP* 2.4 35.6 + - - -
62A ASP* 1.3 74.8 - - - +
64A MET* 1.3 57.6 + - - +
65A ASP 2.9 4.7 - - - -
66A HIS* 2.7 28.7 + - - +
67A LEU* 3.0 14.8 + - - +
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Residues in contact with MET 64 (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 TYR* 3.2 45.3 - - + -
30A ARG* 4.7 13.0 - - - +
41A VAL* 3.9 3.1 - - + -
43A PHE* 3.5 18.0 - - + -
55A PRO* 4.3 25.1 - - + +
60A VAL* 2.7 43.2 + - + +
61A GLN* 4.4 8.5 - - + -
63A SER* 1.3 79.1 - - - +
65A ASP* 1.3 63.9 + - - +
67A LEU* 4.3 2.0 - - - -
68A ASP* 2.9 30.7 + - - +
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Residues in contact with ASP 65 (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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61A GLN 3.4 20.4 + - - +
62A ASP* 3.3 6.9 + - - +
63A SER 2.9 0.6 - - - -
64A MET* 1.3 85.0 - - - +
66A HIS* 1.3 67.6 + - - +
67A LEU 3.0 1.8 - - - -
68A ASP* 3.4 13.6 - - - +
69A LYS* 2.8 41.6 + - + +
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Residues in contact with HIS 66 (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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22A VAL* 2.9 39.9 + - + +
62A ASP 3.0 12.6 + - - +
63A SER 2.7 9.8 + - - +
65A ASP* 1.3 76.6 - - - +
67A LEU* 1.3 67.4 + - + +
69A LYS* 3.4 20.0 - - - +
70A GLN* 3.2 30.8 + - + +
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Residues in contact with LEU 67 (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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22A VAL* 4.5 0.9 - - + +
25A LEU* 3.3 34.5 - - + +
26A ALA 4.7 0.7 - - - -
27A SER* 3.6 12.1 - - - +
28A TYR* 3.1 46.6 - - + +
43A PHE* 3.1 30.5 - - + -
63A SER 3.0 8.9 + - - +
65A ASP 3.0 0.4 - - - -
66A HIS* 1.3 91.1 - - + +
68A ASP* 1.3 62.6 + - - +
69A LYS 2.9 5.1 + - - -
70A GLN* 3.0 29.1 + - + +
71A THR* 4.3 5.9 + - - +
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Residues in contact with ASP 68 (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 TYR* 2.9 37.0 + - - -
64A MET* 2.9 23.0 + - - +
65A ASP* 3.4 17.3 - - - +
67A LEU* 1.3 77.0 - - - +
69A LYS* 1.3 58.1 + - + +
71A THR* 5.4 1.8 - - - +
72A GLN* 3.5 21.4 + - - +
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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
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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