Contacts of the strand formed by residues 104 - 109 (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 ILE 104 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10Q VAL* 3.8 28.3 - - + -
12Q PRO* 3.9 17.3 - - + -
195Q TYR* 4.5 1.6 - - - +
197Q ILE* 4.2 17.7 - - + -
199Q LYS* 4.2 13.5 - - + -
97R SER* 3.9 0.9 + - - +
98R TRP* 3.4 4.4 - - - -
99R GLU* 3.2 27.1 + - + +
102R SER* 3.2 26.3 + - - +
103R GLY* 1.3 75.9 - - - +
105R ALA* 1.3 63.2 + - - +
106R GLU* 4.7 5.6 - - + +
116R LYS* 3.9 33.0 - - + -
117R LYS 3.3 10.5 - - - +
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Residues in contact with ALA 105 (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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73R LEU* 3.8 28.7 - - + -
80R VAL* 3.9 13.0 - - + -
96R VAL* 5.4 0.7 - - + -
97R SER 3.3 4.9 - - - -
98R TRP* 4.0 1.3 - - + -
103R GLY 3.4 0.6 + - - -
104R ILE* 1.3 74.1 - - - +
106R GLU* 1.3 60.1 + - - +
107R PHE* 4.2 5.0 + - + -
115R VAL 4.8 1.0 - - - +
116R LYS* 3.7 6.6 - - - -
117R LYS* 2.7 33.9 + - - +
119R LEU* 3.8 16.8 - - + -
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Residues in contact with GLU 106 (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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199Q LYS* 5.5 2.9 - - - +
202Q VAL* 5.2 2.9 - - + +
95R CYS 3.7 0.7 - - - +
96R VAL* 3.2 6.3 - - - +
97R SER* 2.8 50.4 + - - +
104R ILE* 4.7 6.7 - - + +
105R ALA* 1.3 70.9 - - - +
107R PHE* 1.3 64.0 + - - +
108R TRP* 2.8 39.0 + - + +
113R PRO* 6.2 1.3 - - + -
114R LEU 5.6 3.1 - - - +
116R LYS* 3.2 48.4 + - + +
163R VAL* 4.9 7.5 - - - +
164R LEU 4.7 8.7 - - - +
166R PRO* 5.9 0.5 - - - +
169R ILE* 5.8 0.2 - - - +
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Residues in contact with PHE 107 (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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63R VAL* 4.1 17.0 - - + -
71R TYR* 3.9 34.5 - + + -
72R SER 3.6 20.4 - - - -
73R LEU* 3.7 28.3 - - + -
80R VAL* 5.0 6.1 - - + -
82R SER* 4.6 10.5 - - - -
94R ILE* 4.3 13.5 - - + -
95R CYS 3.4 11.0 - - - -
96R VAL* 3.7 25.8 - - + -
105R ALA* 4.2 4.3 + - + -
106R GLU* 1.3 74.4 - - - +
108R TRP* 1.3 62.7 + - - +
109R ILE* 4.6 4.7 - - + -
113R PRO* 3.6 3.1 - - - +
114R LEU* 2.8 53.4 + - + +
115R VAL 5.6 2.4 + - - -
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Residues in contact with TRP 108 (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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202Q VAL* 4.1 20.0 - - + -
93R HIS* 3.5 5.8 + - - +
94R ILE* 3.5 1.9 - - - -
95R CYS* 2.7 44.3 + - + +
97R SER* 5.2 1.5 + - - -
106R GLU* 2.8 43.0 + - + +
107R PHE* 1.3 77.9 - - - +
109R ILE* 1.3 63.4 + - - +
110R ASN 4.0 0.2 - - - -
111R GLY* 3.7 16.9 + - - +
112R THR 3.2 6.7 - - - +
113R PRO* 3.5 45.1 - - + -
166R PRO* 3.7 41.1 - - + -
169R ILE* 3.6 44.2 - - + +
170R LEU* 5.4 4.5 - - + -
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Residues in contact with ILE 109 (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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71R TYR* 3.6 35.4 - - + -
84R VAL* 4.1 21.5 - - + +
85R ILE 5.5 0.4 - - - +
86R GLU* 4.4 7.4 - - + +
92R VAL* 3.7 19.3 - - + -
93R HIS 3.5 1.1 - - - -
94R ILE* 3.9 20.2 - - + -
107R PHE* 4.6 6.1 - - + -
108R TRP* 1.3 78.6 - - - +
110R ASN* 1.3 80.6 + - - +
111R GLY 3.2 0.2 - - - -
112R THR* 2.8 28.6 + - - -
114R LEU* 3.8 31.9 - - + -
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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