Contacts of the strand formed by residues 42 - 47 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ILE 2.8 40.1 + - - +
41E GLY* 1.3 75.5 - - - +
43E ARG* 1.3 62.4 + - - +
44E PHE* 3.4 35.7 - - + -
82E ARG* 3.4 51.9 - - + +
86E ASP* 5.8 2.0 - - - +
42G LEU* 5.1 8.3 - - + -
42H LEU* 6.1 2.2 - - + -
82H ARG* 4.2 15.7 - - - +
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Residues in contact with ARG 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E VAL* 3.9 15.7 - - + +
37E ILE 3.7 2.5 - - - -
38E ASN* 3.5 20.4 - - + +
41E GLY 3.6 9.0 + - - +
42E LEU* 1.3 79.1 - - - +
44E PHE* 1.3 52.9 - - - +
45E GLU* 5.5 2.7 - - + +
73E ARG* 3.3 33.5 - - - +
75E GLU* 2.6 30.0 + - - -
43G ARG* 6.1 2.6 - - - +
45G GLU* 4.0 4.4 + - - -
41H GLY* 4.1 8.4 - - - +
82H ARG* 2.2 33.6 + - - -
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Residues in contact with PHE 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E VAL* 3.3 7.4 - - - +
37E ILE* 2.8 43.7 + - + +
39E ILE* 3.9 10.3 - - + -
42E LEU* 3.4 48.5 - - + -
43E ARG* 1.3 74.1 - - - +
45E GLU* 1.3 64.2 + - - +
46E VAL* 6.1 0.4 - - + -
82E ARG 4.7 1.1 - - - -
85E PHE* 3.6 48.0 - + + -
86E ASP* 3.5 33.7 - - - -
89E LEU* 3.9 16.2 - - + -
40H SER 3.4 5.6 - - - +
82H ARG* 3.4 25.6 - - - -
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Residues in contact with GLU 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ARG* 2.9 32.8 + - - -
35E VAL 3.4 6.1 - - - +
36E VAL* 4.0 22.4 - - + +
43E ARG* 5.5 2.7 - - + +
44E PHE* 1.3 80.9 - - - +
46E VAL* 1.3 62.9 + - - +
89E LEU* 4.8 1.2 - - - +
38H ASN* 3.4 19.1 + - - -
40H SER* 3.0 33.3 + - - -
41H GLY* 3.7 19.3 - - - +
43H ARG* 3.8 12.6 + - - -
73H ARG* 5.1 6.3 + - - -
77H PHE* 3.8 12.5 - - + -
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Residues in contact with VAL 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ARG* 3.5 5.7 - - - +
35E VAL* 2.9 40.7 + - + +
37E ILE* 3.7 30.5 - - + -
44E PHE* 5.7 0.9 - - + -
45E GLU* 1.3 77.1 - - - +
47E GLN* 1.3 74.3 + - - +
48E LEU 3.6 0.2 + - - -
50E THR* 3.9 14.1 - - + -
51E LEU* 4.0 17.0 - - + -
89E LEU* 3.7 27.4 - - + -
77H PHE* 4.4 1.3 - - - -
79H ASP* 3.5 13.5 - - - +
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Residues in contact with GLN 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E GLU* 3.4 26.0 + - + +
34E ARG* 4.0 15.2 - - + +
46E VAL* 1.3 77.2 - - - +
48E LEU* 1.3 64.8 + - - +
49E LYS* 4.2 12.0 - - + +
50E THR* 3.0 29.2 + - - +
51E LEU* 3.4 5.9 + - - +
77H PHE* 4.0 19.7 + - + -
79H ASP* 3.0 30.1 + - - +
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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