Contacts of the helix formed by residues 30 - 37 (chain B) in PDB entry 1DSB
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 CYS 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B SER* 3.3 9.8 + - - +
28B PHE 3.4 0.2 - - - -
29B PHE* 1.3 76.7 - - - +
31B PRO* 1.4 70.0 - - - +
32B HIS* 4.0 3.6 - - - -
33B CYS* 2.0 64.5 + - - +
34B TYR 3.2 9.9 + - - -
64B MET* 3.9 21.3 - - - -
97B GLN* 3.3 7.2 + - - -
150B VAL* 3.7 12.6 - - + -
151B PRO* 3.7 11.9 - - - -
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Residues in contact with PRO 31 (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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34A TYR* 3.4 53.2 - - + +
35A GLN* 4.5 5.2 - - - +
97A GLN* 4.3 8.7 - - + +
98A LYS* 3.5 22.6 - - + +
29B PHE 3.2 10.5 - - - +
30B CYS* 1.4 83.6 - - + +
32B HIS* 1.3 63.5 + - - +
34B TYR* 3.1 8.0 + - - +
35B GLN 3.1 16.1 + - - -
64B MET* 4.8 3.8 - - + -
97B GLN* 3.4 13.0 - - - +
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Residues in contact with HIS 32 (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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97A GLN 3.6 10.9 + - - +
98A LYS 2.7 29.7 + - - -
99A THR 4.4 6.5 - - - -
100A GLN* 3.8 36.3 + - + +
30B CYS* 3.4 2.6 - - - -
31B PRO* 1.3 81.5 - - - +
33B CYS* 1.3 56.2 + - - +
35B GLN* 3.3 8.8 + - + +
36B PHE* 2.9 62.0 + + - -
40B LEU* 5.2 2.9 - - + -
151B PRO* 3.8 25.4 - - + -
163B PRO* 6.2 2.9 - - + +
171B MET* 6.1 3.4 - - + -
174B PHE* 6.1 0.6 - - - -
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Residues in contact with CYS 33 (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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26B PHE* 4.0 11.0 - - + -
27B SER 3.9 14.8 - - - +
30B CYS* 2.0 56.0 - - + +
32B HIS* 1.3 73.4 - - - +
34B TYR* 1.3 64.6 + - - +
36B PHE* 3.3 9.8 - - - +
37B GLU* 3.0 25.6 + - - +
93B PHE* 3.8 9.4 - - + -
150B VAL* 4.0 7.4 - - - -
151B PRO* 3.5 28.3 - - + -
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Residues in contact with TYR 34 (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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98A LYS* 3.3 23.6 - - - +
30B CYS 3.2 5.4 + - - +
31B PRO 3.1 11.1 + - - +
33B CYS* 1.3 79.5 - - - +
35B GLN* 1.3 55.7 + - - +
37B GLU* 3.8 0.2 - - - -
38B GLU* 3.0 57.9 + - + +
90B VAL* 5.1 0.2 - - + -
93B PHE* 3.6 52.4 - + + -
94B GLU* 3.4 26.6 + - + +
97B GLN* 3.4 28.9 - - + +
98B LYS* 4.1 18.6 - - + +
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Residues in contact with GLN 35 (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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98A LYS* 3.4 41.6 - - + +
99A THR* 3.6 32.1 + - - +
31B PRO 3.1 8.7 + - - +
32B HIS* 3.3 14.8 - - + +
34B TYR* 1.3 76.1 - - - +
36B PHE* 1.3 61.7 + - - +
38B GLU* 5.5 0.2 - - - -
39B VAL* 3.0 55.6 + - - +
40B LEU* 3.1 26.8 + - + +
171B MET* 6.1 0.8 - - - +
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Residues in contact with PHE 36 (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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24B GLU* 4.7 11.4 - - - +
32B HIS* 2.9 42.9 + + - +
33B CYS* 3.3 12.1 - - - +
35B GLN* 1.3 77.5 - - - +
37B GLU* 1.3 59.6 + - - +
40B LEU* 3.9 22.0 - - + -
41B HIS 2.9 22.5 + - - -
42B ILE* 3.0 38.9 + - + +
43B SER 4.9 0.7 + - - -
151B PRO* 3.8 32.5 - - + -
153B MET* 5.9 0.9 - - + -
163B PRO* 5.1 8.5 - - + -
174B PHE* 4.8 11.9 - + - -
178B TYR* 4.1 31.0 - + - -
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Residues in contact with GLU 37 (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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24B GLU* 4.8 2.6 - - - +
26B PHE* 5.1 4.2 - - - +
33B CYS 3.0 15.5 + - - +
34B TYR 3.8 2.9 - - - +
36B PHE* 1.3 81.4 - - - +
38B GLU* 1.3 61.7 + - + +
41B HIS* 3.2 29.2 + - - +
43B SER* 3.8 11.0 + - - -
44B ASP* 6.1 0.9 - - - -
58B LYS* 2.9 36.4 + - - +
89B THR* 3.9 26.0 - - + +
90B VAL* 5.1 8.3 - - + -
93B PHE* 3.9 20.7 - - + -
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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