Contacts of the strand formed by residues 42 - 47 (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 42 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E LEU* 5.1 8.1 - - + -
82E ARG* 3.9 18.4 - - - +
42F LEU* 6.0 2.0 - - + -
38G ASN* 4.3 0.7 - - - -
39G ILE 2.9 34.9 + - - +
40G SER 3.5 0.4 - - - -
41G GLY* 1.3 75.9 - - - +
43G ARG* 1.3 59.8 + - - +
44G PHE* 3.4 35.5 - - + -
82G ARG* 3.7 46.4 - - + +
86G ASP* 5.2 4.0 - - - +
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Residues in contact with ARG 43 (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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41E GLY* 3.6 17.6 - - - +
43E ARG* 6.1 2.7 - - - +
82E ARG* 3.0 21.5 + - - -
45F GLU* 4.0 6.5 + - - -
36G VAL* 3.5 24.0 - - + -
37G ILE 3.5 4.0 - - - +
38G ASN* 4.0 11.4 + - + -
41G GLY 3.8 7.1 + - - +
42G LEU* 1.3 76.4 - - - +
44G PHE* 1.3 60.5 + - - +
45G GLU* 5.7 1.1 - - + -
73G ARG* 3.4 26.7 - - - +
75G GLU* 2.5 39.6 + - - -
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Residues in contact with PHE 44 (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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40E SER 3.6 4.0 - - - +
82E ARG* 3.4 37.5 - - - -
35G VAL 3.7 0.3 - - - +
36G VAL* 3.3 4.0 - - - +
37G ILE* 2.7 45.2 + - + +
39G ILE* 3.8 13.0 - - + -
42G LEU* 3.4 46.0 - - + -
43G ARG* 1.3 74.3 - - - +
45G GLU* 1.3 62.3 + - - +
46G VAL* 4.2 0.7 - - + -
82G ARG 4.5 1.3 - - - -
85G PHE* 3.6 48.7 - + + -
86G ASP* 3.6 22.9 - - - -
89G LEU* 4.0 14.1 - - + -
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Residues in contact with GLU 45 (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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38E ASN* 3.0 22.2 + - - -
40E SER* 3.0 29.7 + - - +
41E GLY* 3.8 17.0 - - - +
43E ARG* 4.0 6.2 + - - -
73E ARG* 3.2 20.4 + - - -
77E PHE* 3.8 18.6 - - + -
79E ASP* 4.5 3.1 - - - +
34G ARG* 3.0 32.1 + - + +
35G VAL 3.4 3.8 - - - +
36G VAL* 3.7 28.2 - - + +
43G ARG* 5.5 1.6 - - + -
44G PHE* 1.3 74.1 - - - +
46G VAL* 1.3 61.9 + - - +
89G LEU* 5.0 2.4 - - - +
93G GLN* 5.5 0.2 + - - -
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Residues in contact with VAL 46 (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* 4.4 5.8 - - - +
34G ARG* 3.3 4.8 - - - +
35G VAL* 2.8 33.8 + - + +
37G ILE* 3.5 32.3 - - + -
44G PHE 5.5 0.2 - - - -
45G GLU* 1.3 75.1 - - - +
47G GLN* 1.3 75.3 + - - +
50G THR* 4.2 16.2 - - + -
51G LEU* 3.6 32.8 - - + -
89G LEU* 3.9 26.0 - - + -
92G TYR* 4.9 0.7 - - + -
93G GLN* 5.7 0.9 - - + +
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Residues in contact with GLN 47 (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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77E PHE* 5.5 2.6 - - - -
79E ASP* 3.1 31.6 + - - +
33G GLU* 3.5 19.8 - - - +
34G ARG* 4.2 16.7 - - + +
46G VAL* 1.3 81.1 - - - +
48G LEU* 1.3 65.6 + - - +
49G LYS* 4.3 10.0 - - + +
50G THR* 3.0 31.1 + - - +
51G LEU* 3.3 10.3 + - - +
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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