Contacts of the helix formed by residues 48 - 53 (chain G) in PDB entry 1DSX
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 LEU 48 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33G GLU* 3.0 38.6 + - - +
34G ARG 4.2 4.7 - - - +
35G VAL* 3.4 29.8 - - + -
46G VAL 3.5 2.9 + - - -
47G GLN* 1.3 70.7 - - - +
49G LYS* 1.3 58.1 + - + +
51G LEU* 3.3 9.4 + - + +
52G ALA* 3.0 29.1 + - - +
65G ARG* 4.4 23.6 + - - +
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Residues in contact with LYS 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G GLU 4.8 0.4 + - - -
47G GLN* 3.2 11.1 - - + +
48G LEU* 1.3 78.7 - - + +
50G THR* 1.3 59.9 + - - +
52G ALA* 3.4 7.6 + - + +
53G GLN* 3.0 33.4 + - - +
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Residues in contact with THR 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E ASP* 5.2 4.2 + - - +
46G VAL* 4.2 10.5 - - + -
47G GLN* 3.0 25.5 + - - +
49G LYS* 1.3 77.1 - - - +
51G LEU* 1.3 58.7 + - - +
53G GLN* 3.5 20.8 + - - +
54G PHE* 4.0 8.8 - - - -
92G TYR* 3.3 49.7 - - + +
93G GLN* 4.1 8.7 - - + +
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Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G VAL* 4.1 21.5 - - + -
37G ILE* 4.5 3.4 - - + -
46G VAL* 3.6 37.7 - - + -
47G GLN 3.3 10.4 + - - +
48G LEU* 3.3 8.2 + - - +
49G LYS 3.3 0.4 - - - -
50G THR* 1.3 75.2 - - - +
52G ALA* 1.3 59.9 + - - +
53G GLN 3.2 1.8 - - - -
54G PHE* 3.2 19.6 + - - +
59G LEU* 3.9 34.5 - - + +
60G GLY* 3.2 19.2 - - - -
65G ARG* 4.8 9.4 - - - +
89G LEU* 5.9 0.4 - - + -
92G TYR* 3.8 37.0 - - + -
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Residues in contact with ALA 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G LEU 3.0 17.7 + - - +
49G LYS* 3.4 10.3 + - + +
51G LEU* 1.3 74.0 - - - +
53G GLN* 1.3 59.4 + - - +
54G PHE 3.1 2.4 + - - -
55G PRO* 3.6 13.8 - - - +
60G GLY 4.6 10.1 - - - +
65G ARG* 5.8 2.4 - - - +
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Residues in contact with GLN 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G LYS* 3.0 20.8 + - - +
50G THR* 3.5 31.3 + - - +
51G LEU 3.2 0.8 - - - -
52G ALA* 1.3 74.8 - - - +
54G PHE* 1.3 82.3 + - + +
55G PRO* 3.4 7.5 - - - +
56G GLU* 4.4 0.5 - - - +
92G TYR 4.5 5.4 + - - +
95G GLY* 4.8 6.8 - - - -
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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