Contacts of the strand formed by residues 47 - 54 (chain R) in PDB entry 2A3W
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 TYR 47 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39R ALA* 6.1 0.9 - - - +
41R SER* 4.1 18.2 + - - -
43R LEU* 3.7 38.6 + - + -
44R SER 5.6 0.2 - - - -
45R ARG* 3.2 24.7 - - - +
46R ALA* 1.3 75.2 - - - +
48R SER* 1.3 60.1 + - - +
49R LEU* 3.7 33.2 - - + -
64R TYR* 3.6 8.1 - - - -
65R LYS* 2.9 65.2 + - + +
148R GLN* 3.5 7.4 - - - +
149R SER 3.5 23.8 - - - +
150R PHE* 3.5 20.4 - + - -
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Residues in contact with SER 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R TYR* 1.3 75.4 - - - +
49R LEU* 1.3 62.6 + - - +
50R PHE 3.5 10.9 + - - -
51R SER* 3.8 6.8 + - - -
62R LEU* 3.3 20.7 - - - +
63R VAL 3.7 3.8 - - - -
64R TYR* 3.9 6.1 - - - -
134R GLY 5.0 3.6 + - - -
135R GLN 3.8 5.8 + - - +
136R GLU* 3.6 35.7 - - - -
148R GLN 3.2 8.6 + - - +
150R PHE* 3.5 24.4 + - - +
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Residues in contact with LEU 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R PHE* 3.6 30.7 - - + -
39R ALA* 4.1 16.6 - - + -
47R TYR* 3.7 33.9 + - + -
48R SER* 1.3 74.5 - - - +
50R PHE* 1.3 61.8 + - - +
63R VAL* 2.8 21.0 + - + +
64R TYR 4.9 0.2 - - - -
65R LYS* 3.9 24.5 - - + +
71R TYR* 4.7 3.1 - - + -
94R ILE* 4.4 14.1 - - + -
132R VAL 5.2 0.7 - - - -
133R LEU* 3.8 19.4 - - - +
134R GLY 5.2 0.2 + - - -
150R PHE* 3.7 19.5 - - + -
154R ILE* 4.1 16.7 - - + +
157R LEU* 5.8 0.7 - - - +
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Residues in contact with PHE 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R LEU* 4.2 4.9 - - + -
35R LEU* 3.5 42.0 - - + -
37R PHE* 4.6 3.1 - - + -
48R SER* 3.5 2.4 + - - -
49R LEU* 1.3 81.3 - - + +
51R SER* 1.3 58.3 + - - +
52R TYR* 3.9 28.3 - + + -
61R LEU* 4.4 10.3 - - + -
62R LEU* 3.3 8.3 - - - +
63R VAL* 3.0 36.1 + - + -
131R ILE* 3.4 29.8 - - + -
132R VAL 4.2 2.7 - - - -
133R LEU* 4.0 14.6 - - + -
157R LEU* 4.1 7.9 - - + -
159R MET* 3.8 24.5 - - - -
183R LEU* 3.9 12.1 - - + -
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Residues in contact with SER 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R SER* 3.8 6.9 + - - -
50R PHE* 1.3 73.8 - - - +
52R TYR* 1.3 59.8 + - - +
53R ASN* 4.3 3.6 + - - -
62R LEU* 3.8 11.2 - - - +
131R ILE* 3.3 3.6 - - - +
132R VAL* 2.9 40.2 + - - -
135R GLN 3.7 22.9 - - - -
136R GLU* 4.2 2.1 + - - -
137R GLN* 2.9 42.1 + - - +
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Residues in contact with TYR 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26R LEU* 3.7 18.2 - - + +
30R LEU* 4.3 2.9 - - + +
50R PHE* 3.9 11.2 - + + -
51R SER* 1.3 73.0 + - - +
53R ASN* 1.3 68.1 + - - +
54R THR* 3.9 7.0 - - + -
59R ASN* 4.6 0.2 - - - -
60R GLU* 3.3 7.8 + - + -
61R LEU* 2.9 72.7 + - + +
62R LEU* 5.0 0.6 - - - +
125R VAL* 3.7 20.6 - - + +
126R GLU 2.7 30.3 + - - -
129R PRO* 3.4 31.4 - - + +
130R LYS 3.8 3.4 - - - -
131R ILE* 3.7 24.2 - - + -
159R MET* 4.5 9.6 - - + -
182R ILE* 6.1 0.4 - - + -
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Residues in contact with ASN 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51R SER* 4.3 3.5 + - - -
52R TYR* 1.3 79.3 - - - +
54R THR* 1.3 66.0 + - - +
57R ARG 3.6 9.5 + - - +
58R ASP* 3.0 29.4 + - - +
59R ASN* 2.9 21.8 + - - +
60R GLU* 4.4 0.9 - - - -
62R LEU* 6.0 0.3 - - - +
129R PRO* 3.3 1.9 - - - +
130R LYS 2.8 32.7 + - - -
137R GLN* 3.6 34.6 + - - +
139R SER 3.2 27.0 + - - +
140R TYR* 3.5 5.0 - - - -
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Residues in contact with THR 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52R TYR* 3.9 9.0 - - + -
53R ASN* 1.3 78.9 - - - +
55R GLN* 1.3 66.7 + - - +
56R GLY 3.2 1.2 + - - -
57R ARG* 2.9 45.4 + - - +
60R GLU* 3.7 9.8 - - + +
126R GLU* 3.4 27.1 - - + +
127R ALA 3.3 25.8 - - - +
128R GLN 4.5 0.4 - - - -
129R PRO* 3.9 9.9 - - + -
139R SER 5.6 0.2 - - - -
140R TYR* 3.4 16.0 + - - +
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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