Contacts of the strand formed by residues 49 - 52 (chain E) in PDB entry 2X86
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 ASP 49 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D TYR* 2.6 30.2 + - - -
98D LYS* 2.9 29.3 + - - +
146D LEU* 4.8 1.8 - - - -
150D TYR* 4.7 8.6 - - + -
1E MET* 6.2 0.7 - - + -
27E ILE 3.3 3.5 + - - +
28E LEU* 3.6 21.1 - - + +
29E VAL 3.0 22.7 + - - -
47E ILE* 3.6 13.2 - - - +
48E ALA* 1.3 85.5 - - + +
50E TYR* 1.3 73.5 + - - +
51E MET* 4.4 7.8 - - - +
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Residues in contact with TYR 50 (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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87D LYS* 6.5 0.2 - - - -
90D MET* 4.2 34.8 - - + -
94D TYR* 3.8 12.9 + + + -
95D GLN* 4.2 8.7 - - - +
98D LYS* 4.3 0.9 + - - -
142D TYR* 5.8 1.3 - + - -
146D LEU* 3.7 22.4 - - + -
8E ALA* 4.9 1.6 - - + -
28E LEU* 4.1 1.6 - - - -
29E VAL* 3.4 23.8 - - + -
31E ASP* 3.2 42.4 + - + +
32E ASN 3.5 0.2 + - - -
33E LEU* 3.3 35.6 + - + +
42E LEU* 4.7 8.3 - - + -
47E ILE* 4.8 2.9 - - + -
49E ASP* 1.3 91.8 + - - +
51E MET* 1.3 82.2 + - - +
52E ASP* 3.9 7.2 + - + +
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Residues in contact with MET 51 (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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95D GLN* 5.6 4.3 - - - +
98D LYS* 5.4 4.0 - - - +
28E LEU* 4.0 16.4 - - + -
29E VAL 2.9 6.9 + - - +
30E VAL* 3.2 10.6 - - + -
31E ASP 3.1 22.7 + - - +
49E ASP* 4.4 15.7 - - - +
50E TYR* 1.3 82.2 - - - +
52E ASP* 1.3 73.2 + - - +
55E ASP* 4.0 8.1 - - + +
56E PHE* 4.0 32.5 - - - +
59E GLN* 4.1 30.7 - - - +
66E PHE* 4.3 10.5 - - + -
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Residues in contact with ASP 52 (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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87D LYS* 3.9 38.5 + - + +
91D ASP* 5.3 4.7 - - - +
30E VAL* 4.3 0.2 - - - -
31E ASP 3.3 11.8 - - - +
32E ASN* 3.8 13.9 - - - +
33E LEU 4.6 0.9 + - - -
50E TYR* 3.9 9.3 + - + +
51E MET* 1.3 76.5 - - - +
53E LYS* 1.3 70.6 + - - +
54E GLU* 2.9 33.1 + - - +
55E ASP* 3.1 21.3 + - - +
56E PHE* 3.0 20.3 + - - +
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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