Contacts of the strand formed by residues 70 - 75 (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 GLU 70 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R LYS* 3.8 7.1 - - - +
66R GLU* 3.5 24.3 + - + +
67R ARG* 3.0 64.6 + - + +
68R VAL 4.4 1.6 - - - +
69R GLY* 1.3 83.5 - - - +
71R TYR* 1.3 65.1 + - - +
81R THR* 4.2 15.7 - - + +
82R SER 3.6 3.1 - - - -
83R LYS* 3.6 36.2 + - + -
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Residues in contact with TYR 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R LEU* 4.7 6.3 - - + -
63R VAL* 5.3 1.8 - - + -
64R TYR 4.0 2.7 - - - -
65R LYS* 3.7 33.3 + - + +
70R GLU* 1.3 76.4 - - - +
72R SER* 1.3 62.3 + - - +
81R THR* 3.3 2.2 - - - -
82R SER 2.9 38.9 + - - +
84R VAL* 3.7 19.1 - - + -
86R GLU* 2.7 34.6 + - - -
92R VAL* 3.7 19.8 - - - +
94R ILE* 3.7 24.9 - - + -
107R PHE* 3.9 33.8 - + + -
109R ILE* 3.6 28.0 - - + -
114R LEU* 4.5 1.3 - - + -
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Residues in contact with SER 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R VAL* 3.6 4.9 - - - -
64R TYR* 2.9 44.4 + - - -
66R GLU* 2.8 31.6 + - - +
70R GLU 4.3 0.2 - - - -
71R TYR* 1.3 73.5 - - - +
73R LEU* 1.3 58.7 + - - +
74R TYR* 4.2 10.5 - - - -
79R LYS* 4.5 2.0 - - - -
80R VAL 3.2 6.3 - - - -
81R THR* 2.6 25.4 + - - +
107R PHE* 3.6 7.4 - - - -
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Residues in contact with LEU 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R PHE* 4.2 3.8 - - + -
61R LEU* 3.9 20.6 - - + -
62R LEU 3.4 15.0 - - - +
63R VAL* 4.4 6.7 - - + -
72R SER* 1.3 73.1 - - - +
74R TYR* 1.3 73.9 + - - +
75R ILE* 3.8 21.1 - - + -
78R HIS 3.8 0.2 - - - +
79R LYS* 3.6 2.3 - - - -
80R VAL* 2.9 40.6 + - + +
96R VAL* 3.9 21.5 - - + -
98R TRP* 4.2 9.4 - - + -
105R ALA* 3.8 27.1 - - + -
107R PHE* 3.7 16.6 - - + -
119R LEU* 4.0 3.0 - - + +
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Residues in contact with TYR 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349N CPJ 3.1 37.3 + - + -
59R ASN* 4.1 23.1 - - + +
61R LEU* 3.3 7.0 - - - -
62R LEU* 2.9 64.3 + - + +
64R TYR* 4.1 19.1 - + + -
66R GLU* 4.1 4.0 + - - -
72R SER* 4.3 5.8 - - - -
73R LEU* 1.3 77.9 - - - +
75R ILE* 1.3 66.7 + - - +
76R GLY 4.2 0.4 - - - -
77R ARG 3.9 16.4 - - - +
78R HIS 3.1 13.5 - - - +
79R LYS* 3.3 41.0 + - + -
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Residues in contact with ILE 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R PHE* 3.6 35.9 - - + -
60R GLU 3.5 3.6 - - - +
61R LEU* 4.5 3.8 - - + -
73R LEU* 3.8 17.9 - - + -
74R TYR* 1.3 80.9 - - - +
76R GLY* 1.3 68.4 + - - +
78R HIS* 2.9 17.2 + - - +
98R TRP* 3.7 42.0 - - + -
119R LEU* 3.6 16.4 - - + +
120R ARG* 3.2 17.3 - - + +
123R TYR* 3.9 19.3 - - + -
125R VAL* 4.3 9.6 - - + -
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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
------------------------------------------------------------
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