Contacts of the strand formed by residues 48 - 53 (chain E) in PDB entry 2W3S
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 THR 48 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E THR* 4.9 1.4 - - - +
45E GLY* 2.4 26.4 + - - -
46E ALA 3.3 2.0 + - - -
47E CYS* 1.3 77.4 - - - +
49E VAL* 1.3 62.8 + - - +
59E ALA* 3.9 15.0 - - + -
60E VAL 3.3 12.8 - - - +
61E ASN* 4.0 4.2 + - - +
78E ILE 5.3 0.3 + - - -
108E PRO 4.5 2.3 - - - +
109E GLY* 3.6 14.2 - - - +
112E VAL* 3.3 33.6 - - + +
113E SER* 3.4 20.2 - - - +
132E ASN* 3.7 1.2 + - - -
274E GLN* 3.2 21.3 + - + +
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Residues in contact with VAL 49 (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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23E LEU* 4.0 15.7 - - + -
27E LEU* 4.2 3.8 - - + -
35E THR* 4.0 14.4 - - + +
47E CYS 2.9 10.2 + - - +
48E THR* 1.3 76.4 - - - +
50E MET* 1.3 58.9 + - - +
51E ILE* 5.5 0.2 - - + -
59E ALA* 3.3 4.3 - - - -
60E VAL* 2.6 56.8 + - + +
62E ALA* 3.5 27.1 - - + +
75E LEU* 4.5 7.6 - - + -
76E ARG 3.7 4.3 - - - +
77E THR* 3.6 30.7 - - + -
78E ILE 5.4 0.2 - - - +
112E VAL* 3.6 6.0 - - - +
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Residues in contact with MET 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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49E VAL* 1.3 73.4 - - - +
51E ILE* 1.3 65.5 + - - +
52E ARG* 4.6 4.9 - - + +
57E SER* 3.0 33.7 - - - +
58E ARG 3.2 15.5 - - - +
59E ALA* 4.9 0.7 - - - -
75E LEU* 3.6 3.8 - - - +
76E ARG* 2.7 64.1 + - + +
81E ILE* 5.2 4.0 - - + -
112E VAL* 3.7 13.9 - - + +
115E ALA* 4.8 6.1 - - - +
116E ALA* 3.5 35.2 - - + -
119E ASP* 3.8 16.2 - - + +
158E LEU* 5.4 8.7 - - + -
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Residues in contact with ILE 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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23E LEU* 5.3 0.4 - - + -
49E VAL 4.2 0.2 - - - -
50E MET* 1.3 74.3 - - - +
52E ARG* 1.3 59.2 + - - +
53E ASP 4.3 0.2 - - - -
56E GLY 4.0 0.3 - - - +
57E SER* 3.1 2.2 - - - -
58E ARG* 2.7 74.7 + - + +
60E VAL* 4.0 32.3 - - + -
65E MET* 4.5 14.4 - - + -
70E ILE* 4.6 17.9 - - + -
73E LYS* 4.7 19.7 - - + -
74E ALA 3.4 6.3 - - - +
75E LEU* 3.6 27.8 - - + -
278E VAL* 5.0 2.0 - - + -
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Residues in contact with ARG 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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50E MET* 4.6 3.7 - - + +
51E ILE* 1.3 74.1 - - - +
53E ASP* 1.3 68.7 + - - +
56E GLY* 3.1 14.9 - - - +
57E SER* 3.5 18.2 + - - +
73E LYS* 4.0 1.7 - - - -
74E ALA* 2.8 41.5 + - + +
119E ASP* 2.6 36.6 + - - -
158E LEU* 2.9 34.6 + - - +
159E GLN* 3.7 14.5 + - - +
161E ASP* 3.5 35.5 - - - +
162E ALA* 3.8 10.6 - - - +
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Residues in contact with ASP 53 (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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52E ARG* 1.3 83.4 - - - +
54E ALA* 1.3 66.9 + - - +
55E ALA* 2.8 16.6 + - - +
56E GLY* 2.8 17.0 + - - +
58E ARG* 2.6 33.7 + - - +
72E GLY 4.9 3.4 - - - +
73E LYS* 3.3 46.5 + - + +
162E ALA* 5.9 1.4 - - - -
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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