Contacts of the helix formed by residues 58 - 69 (chain B) in PDB entry 1DOK
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 LYS 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B LYS 3.7 2.0 + - - -
57B GLN* 1.3 71.1 - - - +
59B TRP* 1.3 64.8 + - - +
60B VAL 3.0 0.5 + - - -
61B GLN* 3.0 23.5 + - - +
62B ASP* 3.0 47.0 + - - +
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Residues in contact with TRP 59 (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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16B THR* 4.1 13.0 - - + -
17B ASN 5.0 1.0 + - - -
18B ARG 3.8 13.1 - - - -
19B LYS* 3.6 44.2 - - + +
20B ILE* 3.5 47.8 - - + -
25B LEU* 4.9 1.8 - - + -
43B PHE* 3.9 30.1 - + - -
53B ALA* 4.0 4.9 - - + -
54B ASP 5.6 0.2 - - - -
57B GLN* 2.8 36.1 + - + -
58B LYS* 1.3 77.1 - - - +
60B VAL* 1.3 63.6 + - + +
62B ASP* 3.5 9.6 + - - +
63B SER* 2.6 47.2 + - - +
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Residues in contact with VAL 60 (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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41B VAL* 3.9 20.2 - - + -
43B PHE* 3.9 16.1 - - + -
53B ALA* 3.6 16.8 - - + -
54B ASP 3.2 24.5 - - - +
55B PRO* 3.7 21.5 - - + -
57B GLN* 3.1 5.3 + - + +
58B LYS 3.0 1.0 + - - -
59B TRP* 1.3 101.4 - - + +
61B GLN* 1.3 66.8 + - - +
63B SER* 3.1 5.2 + - - -
64B MET* 3.0 25.5 + - + +
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Residues in contact with GLN 61 (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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55B PRO 3.4 26.3 + - - +
56B LYS* 3.4 18.2 + - - +
57B GLN 3.5 8.0 + - - +
58B LYS* 3.0 18.8 + - - +
60B VAL* 1.3 75.5 - - - +
62B ASP* 1.3 68.4 + - - +
64B MET* 3.3 17.8 + - + +
65B ASP* 3.1 29.7 + - - +
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Residues in contact with ASP 62 (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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58B LYS* 3.0 52.6 + - - +
59B TRP* 3.8 9.9 - - - +
61B GLN* 1.3 80.0 - - - +
63B SER* 1.3 51.2 + - - +
65B ASP* 3.1 12.9 + - - +
66B HIS* 2.8 34.8 + - - +
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Residues in contact with SER 63 (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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20B ILE 4.7 1.9 + - - -
22B VAL* 4.0 24.3 - - - +
25B LEU* 4.3 5.5 - - - +
43B PHE* 3.8 22.7 - - - -
59B TRP* 2.6 35.8 + - - -
60B VAL 3.1 5.1 + - - -
62B ASP* 1.3 77.9 - - - +
64B MET* 1.3 56.1 + - - +
66B HIS* 3.3 0.7 + - - +
67B LEU* 2.8 36.1 + - - +
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Residues in contact with MET 64 (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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28B TYR* 3.6 48.8 - - + +
30B ARG* 4.2 22.9 - - - +
41B VAL* 3.6 33.9 - - + -
43B PHE* 4.7 2.2 - - + -
55B PRO* 4.3 6.1 - - + -
60B VAL* 3.0 16.7 + - + +
61B GLN* 3.7 25.4 - - + +
63B SER* 1.3 76.1 - - - +
65B ASP* 1.3 61.0 + - - +
67B LEU* 3.4 1.3 + - - -
68B ASP* 2.9 35.5 + - - +
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Residues in contact with ASP 65 (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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61B GLN* 3.1 16.7 + - - +
62B ASP* 3.1 14.7 + - - +
64B MET* 1.3 81.0 - - - +
66B HIS* 1.3 62.7 + - - +
68B ASP* 3.3 19.5 + - - +
69B LYS* 3.5 20.2 + - - +
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Residues in contact with HIS 66 (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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22B VAL* 3.4 44.8 - - + +
23B GLN* 4.1 14.9 + - - -
62B ASP 2.8 15.8 + - - +
63B SER* 3.6 7.4 - - - +
65B ASP* 1.3 74.2 - - - +
67B LEU* 1.3 70.9 + - + +
68B ASP 3.2 1.2 + - - -
69B LYS* 3.2 34.4 + - - +
70B GLN* 3.4 28.9 + - + +
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Residues in contact with LEU 67 (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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22B VAL* 3.6 25.6 - - + +
25B LEU* 4.4 13.2 - - + +
26B ALA 4.7 5.2 - - - +
27B SER* 3.7 32.1 - - - +
28B TYR* 3.6 31.6 - - + -
43B PHE* 4.2 12.6 - - + -
63B SER* 2.8 31.3 + - - +
64B MET 3.9 3.4 - - - +
66B HIS* 1.3 81.7 - - + +
68B ASP* 1.3 62.9 + - - +
70B GLN* 3.4 31.1 - - - +
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Residues in contact with ASP 68 (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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28B TYR* 2.7 30.5 + - - -
64B MET* 2.9 20.8 + - - +
65B ASP* 3.6 14.2 - - - +
66B HIS 3.2 0.8 + - - -
67B LEU* 1.3 77.6 - - - +
69B LYS* 1.3 60.2 + - - +
70B GLN 3.7 4.2 + - - +
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Residues in contact with LYS 69 (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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65B ASP* 3.5 10.5 - - - +
66B HIS* 3.2 42.8 + - - +
68B ASP* 1.3 73.3 - - - +
70B GLN* 1.3 64.8 + - - +
71B THR* 3.1 5.2 + - - -
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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