Contacts of the helix formed by residues 61 - 70 (chain A) in PDB entry 1RGW
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLY* 5.0 0.9 - - - -
21A LYS* 4.2 12.8 - - + +
22A ASP* 4.1 29.6 - - + +
27A LEU* 5.1 1.1 - - - -
59A THR 4.4 8.1 - - - +
60A MET* 1.3 73.0 - - - +
62A HIS* 1.3 58.6 + - - +
63A LEU* 3.7 9.0 + - - +
64A GLU* 3.2 27.1 + - - +
65A ALA* 2.8 31.8 + - - +
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.4 50.9 + - + +
18A GLN* 5.3 0.7 - - - -
19A GLY 3.6 24.8 + - - +
20A GLY* 4.4 7.8 - - - -
21A LYS 4.5 0.4 - - - +
22A ASP* 4.9 3.5 - - + +
23A PHE* 4.2 21.1 - + + -
27A LEU* 5.5 2.7 - - - -
61A THR* 1.3 72.6 - - - +
63A LEU* 1.3 64.9 + - + +
65A ALA* 4.0 4.0 - - - +
66A GLN* 3.1 29.3 + - + +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A THR* 3.7 7.8 + - - +
62A HIS* 1.3 82.3 - - + +
64A GLU* 1.3 64.2 + - - +
66A GLN* 3.4 10.6 - - + +
67A ASN* 3.0 46.1 + - - +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR 3.7 16.2 - - - +
60A MET* 3.8 11.6 - - + +
61A THR* 3.2 26.1 + - - +
63A LEU* 1.3 78.8 - - - +
65A ALA* 1.3 52.5 + - - +
67A ASN* 3.1 10.9 + - + +
68A LYS* 2.7 74.0 + - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 5.0 4.9 - - + -
27A LEU* 3.6 37.9 - - + -
29A ILE* 6.5 0.4 - - + -
52A ILE* 3.8 6.8 - - + +
60A MET* 3.8 13.9 - - - +
61A THR 2.8 22.1 + - - +
62A HIS* 4.0 3.4 - - - +
64A GLU* 1.3 70.0 - - - +
66A GLN* 1.3 62.2 + - - +
68A LYS* 4.2 1.3 - - - -
69A ILE* 3.2 30.9 + - + +
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Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 4.7 2.4 - - - -
17A LEU* 3.4 38.8 - - + +
62A HIS* 3.1 24.0 + - + +
63A LEU* 3.4 13.2 - - + +
65A ALA* 1.3 76.4 - - - +
67A ASN* 1.3 62.3 + - - +
69A ILE* 3.6 3.5 + - - +
70A LYS* 3.1 62.1 + - + +
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Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.0 38.1 + - - +
64A GLU* 3.3 13.2 - - + +
66A GLN* 1.3 78.9 - - - +
68A LYS* 1.3 65.1 + - + +
70A LYS* 3.3 8.1 + - - +
71A SER* 2.8 29.8 + - - +
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ILE* 3.5 22.2 - - + -
53A ASP* 5.9 1.3 - - - +
55A VAL* 5.7 4.5 - - - -
60A MET* 3.7 28.0 - - - -
64A GLU* 2.7 59.9 + - - +
65A ALA* 3.9 4.5 - - - +
67A ASN* 1.3 73.5 - - + +
69A ILE* 1.3 61.6 + - - +
71A SER* 3.1 22.0 + - - +
72A ALA* 3.8 6.4 + - - +
76A LEU* 4.7 2.7 - - - +
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TRP* 3.2 40.8 + - + -
15A PHE* 3.2 35.9 - - + -
17A LEU* 5.8 0.2 - - + -
29A ILE* 4.6 6.1 - - + -
45A GLN* 3.4 21.3 - - - +
52A ILE* 3.9 19.9 - - + +
65A ALA* 3.2 18.0 + - + +
66A GLN 3.7 2.7 - - - +
68A LYS* 1.3 75.4 - - - +
70A LYS* 1.3 63.4 + - + +
71A SER 3.2 4.5 + - - -
72A ALA* 3.3 14.7 + - - +
76A LEU* 3.7 20.6 - - + +
78A LEU* 4.4 2.5 - - + -
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Residues in contact with LYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PRO* 4.7 17.4 - - - +
13A TRP* 4.9 7.5 - - + +
15A PHE* 4.9 9.2 - - + -
66A GLN* 3.1 49.5 + - + +
67A ASN* 3.7 9.4 - - - +
68A LYS 3.3 0.6 - - - -
69A ILE* 1.3 86.6 - - + +
71A SER* 1.3 58.1 + - - +
72A ALA 3.4 4.9 + - - +
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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