Contacts of the helix formed by residues 62 - 74 (chain R) in PDB entry 3RWR
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 62 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61R MET* 1.3 76.7 - - - +
63R LYS* 1.3 59.5 + - - +
64R GLY* 2.9 24.0 - - - +
65R LYS* 2.7 35.8 + - + +
66R TYR* 2.8 13.0 + - - +
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Residues in contact with LYS 63 (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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29R GLU* 3.8 23.2 + - - +
49R GLU* 3.9 16.2 + - - -
52R ILE* 3.7 26.2 - - + +
53R SER* 4.2 27.1 - - - +
56R ALA* 4.7 8.1 - - + -
61R MET 3.4 3.9 + - - -
62R GLU* 1.3 75.3 - - + +
64R GLY* 1.3 56.7 + - - +
66R TYR* 3.9 6.5 - - + -
67R VAL* 2.9 43.3 + - + +
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Residues in contact with GLY 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R GLU* 2.9 22.5 - - - +
63R LYS* 1.3 78.9 - - - +
65R LYS* 1.3 60.4 + - - +
66R TYR 3.5 0.2 - - - -
67R VAL* 5.0 0.9 - - - -
68R GLY* 3.6 18.8 + - - -
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Residues in contact with LYS 65 (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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61R MET* 3.4 34.6 - - + +
62R GLU* 2.7 25.9 + - + +
64R GLY* 1.3 79.5 - - - +
66R TYR* 1.3 58.1 + - - +
68R GLY* 4.5 0.4 - - - -
69R GLU* 3.1 33.8 + - + +
611W GLU* 5.8 3.8 - - - +
614W GLY* 2.8 38.3 + - - -
615W LEU* 5.5 0.2 - - - -
616W PRO* 4.9 4.8 - - - +
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Residues in contact with TYR 66 (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 GLU 5.4 0.2 - - - -
52R ILE* 4.4 9.0 - - + -
55R GLU* 3.5 35.1 - - + +
56R ALA* 4.3 23.6 - - + -
59R MET* 3.5 37.7 - - + -
61R MET* 4.6 9.2 - - + -
62R GLU 2.8 13.2 + - - +
63R LYS* 4.3 3.4 - - + +
65R LYS* 1.3 76.9 - - - +
67R VAL* 1.3 68.0 + - + +
69R GLU* 2.8 21.0 + - + +
70R LEU* 3.0 46.2 + - + +
97R PHE* 5.0 1.7 - - - -
108R LEU* 2.6 32.1 + - + -
109R GLY* 4.4 0.5 - - - -
564W ARG* 3.8 1.7 + - - -
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Residues in contact with VAL 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R LEU* 4.5 9.2 - - + +
29R GLU* 3.4 44.2 - - + +
52R ILE* 5.2 3.6 - - + -
63R LYS* 2.9 32.2 + - + +
64R GLY* 5.0 1.3 - - - -
66R TYR* 1.3 80.6 - - + +
68R GLY* 1.3 66.0 + - - +
69R GLU 2.8 1.7 + - - -
70R LEU* 3.0 20.2 + - - +
71R ARG* 3.1 40.4 + - - +
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Residues in contact with GLY 68 (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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64R GLY 3.6 18.9 + - - -
65R LYS* 4.5 0.4 - - - -
66R TYR 3.3 0.6 - - - -
67R VAL* 1.3 78.9 - - - +
69R GLU* 1.3 57.1 + - - +
71R ARG* 3.6 22.7 - - - +
72R LYS* 3.0 24.6 - - - +
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Residues in contact with GLU 69 (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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61R MET* 5.5 4.7 - - - -
65R LYS* 3.1 23.4 + - + +
66R TYR* 2.8 18.0 + - + +
68R GLY* 1.3 75.8 - - - +
70R LEU* 1.3 60.8 + - + +
71R ARG 3.1 1.6 - - - -
72R LYS* 2.8 59.2 + - - +
73R ALA* 3.2 7.5 + - - +
84R TYR* 3.1 22.2 + - - -
99R LYS* 3.1 35.3 + - + +
108R LEU* 4.6 10.6 - - + +
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Residues in contact with LEU 70 (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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28R LEU* 4.0 13.2 - - + +
32R PHE* 4.3 16.2 - - + -
66R TYR* 3.0 69.6 + - + +
67R VAL* 3.0 8.6 + - - +
69R GLU* 1.3 72.9 - - + +
71R ARG* 1.3 54.7 + - - +
72R LYS 2.7 7.6 + - - -
73R ALA* 2.6 12.9 + - - +
74R LEU* 2.6 60.8 + - + +
75R LEU 3.1 3.4 + - - -
97R PHE* 3.9 15.7 - - + -
108R LEU* 4.9 2.5 - - + -
111R PHE* 5.5 2.2 - - + -
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Residues in contact with ARG 71 (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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24R TRP* 6.3 1.0 - - - -
27R THR* 3.6 22.4 + - - -
28R LEU* 3.6 14.2 - - + +
29R GLU* 5.1 2.0 - - - +
67R VAL* 3.1 33.0 + - - +
68R GLY* 3.6 23.8 - - - +
69R GLU 3.1 0.2 - - - -
70R LEU* 1.3 75.4 - - - +
72R LYS* 1.3 58.1 + - + +
75R LEU* 3.4 41.1 - - + +
76R SER 3.5 0.2 - - - -
77R GLY* 3.0 18.9 + - - -
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Residues in contact with LYS 72 (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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68R GLY 3.0 25.6 - - - +
69R GLU* 3.0 33.4 + - - +
70R LEU 2.7 0.6 + - - -
71R ARG* 1.3 83.2 - - + +
73R ALA* 1.3 55.8 + - - +
76R SER* 3.5 6.3 + - - -
77R GLY 3.2 37.3 + - - +
78R ALA* 4.0 4.5 + - - +
82R ASP* 3.2 26.2 + - - -
84R TYR* 3.0 39.8 + - + +
99R LYS* 5.3 0.2 - - - +
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Residues in contact with ALA 73 (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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8R ILE* 5.6 0.2 - - - +
20R LEU* 5.1 0.5 - - - +
69R GLU 3.2 8.5 + - - +
70R LEU* 2.6 9.3 + - - +
72R LYS* 1.3 73.5 - - - +
74R LEU* 1.3 61.9 + - - +
75R LEU 3.4 0.7 - - - -
76R SER* 3.8 8.1 + - - -
84R TYR* 3.9 26.0 - - + -
86R PHE* 3.2 27.7 - - + -
97R PHE* 3.5 32.8 - - + -
108R LEU* 4.2 4.9 - - + -
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Residues in contact with LEU 74 (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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6R SER* 5.1 3.3 - - - -
20R LEU* 3.4 19.2 - - + +
22R VAL* 3.0 29.4 - - + +
28R LEU* 5.7 0.9 - - + -
32R PHE* 3.6 24.9 - - + -
34R ILE* 4.9 4.5 - - + -
70R LEU* 2.6 44.5 + - + +
73R ALA* 1.3 76.2 - - - +
75R LEU* 1.3 61.1 + - + +
76R SER* 3.4 0.4 - - - -
86R PHE* 5.1 0.4 - - + -
95R PHE* 3.8 23.6 - - + -
97R PHE* 3.5 43.1 - - + -
111R PHE* 4.0 6.3 - - + -
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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