Contacts of the helix formed by residues 58 - 68 (chain B) in PDB entry 1RLI
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 ASP 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B TYR 4.9 5.0 - - - +
34B LEU 4.9 6.6 - - - +
59B TYR* 1.3 70.3 + - - +
60B ASP 3.3 2.5 - - - -
61B SER* 3.1 18.1 + - - +
62B ILE* 3.1 44.6 + - - +
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Residues in contact with TYR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ASP* 1.3 77.0 + - - +
60B ASP* 1.3 77.1 + - - +
62B ILE* 3.1 12.7 + - + +
63B ILE* 3.0 36.7 + - + +
90B PHE* 3.6 39.0 - + - -
93B ARG* 3.2 83.1 + - + +
94B TRP* 3.4 12.5 - - - -
96B GLN* 6.0 0.2 - - + -
97B THR* 2.8 27.8 + - - -
103B PHE* 6.2 0.2 - + - -
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Residues in contact with ASP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ASP 3.3 1.0 - - - -
59B TYR* 1.3 92.6 - - - +
61B SER* 1.3 58.5 + - - +
63B ILE* 3.4 6.0 + - - +
64B GLU* 3.0 28.7 + - - +
93B ARG* 5.0 4.3 + - - -
100B ASP* 4.5 0.9 - - - +
102B ARG* 3.0 41.1 + - - +
103B PHE* 3.8 19.4 - - + -
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ASP* 3.1 21.0 + - - +
60B ASP* 1.3 75.1 - - - +
62B ILE* 1.3 62.3 + - - +
64B GLU* 3.3 11.3 + - - +
65B ARG* 2.9 34.6 + - - +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 5.7 0.7 - - + -
32B ILE* 3.7 30.1 - - + -
33B TYR 4.7 2.2 - - - +
34B LEU* 3.9 29.6 - - + +
58B ASP* 3.1 42.0 + - - +
59B TYR* 3.1 11.9 + - - +
61B SER* 1.3 77.4 - - - +
63B ILE* 1.3 63.0 + - - +
65B ARG* 3.1 7.6 + - - +
66B ILE* 2.9 28.7 + - + +
90B PHE* 3.7 29.2 - - + -
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR* 3.0 56.4 + - + +
60B ASP* 3.7 7.4 - - - +
62B ILE* 1.3 73.9 - - - +
64B GLU* 1.3 63.7 + - - +
66B ILE* 3.3 13.1 - - + +
67B LEU* 3.1 31.8 + - + +
90B PHE* 3.9 21.8 - - + -
94B TRP* 4.1 9.6 - - + +
97B THR* 4.2 7.2 - - + +
103B PHE* 3.8 28.0 - - + -
106B PHE* 4.1 20.0 - - + -
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASP 3.0 15.7 + - - +
61B SER* 3.5 14.2 - - - +
63B ILE* 1.3 79.1 - - - +
65B ARG* 1.3 61.0 + - + +
67B LEU* 3.6 8.8 + - - +
68B GLN* 3.2 30.2 + - - +
103B PHE* 4.2 18.5 - - + -
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLU* 3.0 43.8 + - - +
31B HIS 3.3 22.0 + - - +
32B ILE* 3.5 31.4 - - + +
33B TYR 5.2 0.4 - - - +
61B SER* 2.9 20.2 + - - +
62B ILE* 3.5 6.9 - - - +
64B GLU* 1.3 75.8 - - + +
66B ILE* 1.3 66.1 + - - +
68B GLN* 3.2 27.7 + - - +
69B CYS* 3.8 11.1 - - - -
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ALA* 4.6 1.3 - - + -
6B ILE* 3.9 24.0 - - + -
32B ILE* 3.3 27.8 - - + -
62B ILE* 2.9 19.9 + - + +
63B ILE* 3.3 24.5 - - + +
65B ARG* 1.3 71.2 - - - +
67B LEU* 1.3 64.2 + - + +
68B GLN 3.0 4.9 - - - -
69B CYS* 2.9 30.4 + - - +
72B LEU* 3.8 14.7 - - + +
90B PHE* 4.1 24.2 - - + -
94B TRP* 5.1 1.6 - - + +
106B PHE* 5.0 1.6 - - + -
110B MET* 4.6 23.6 - - + -
113B LYS* 3.5 5.6 + - - -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 3.1 27.0 + - + +
64B GLU* 3.8 7.2 - - - +
65B ARG 3.3 0.8 - - - -
66B ILE* 1.3 76.7 - - + +
68B GLN* 1.3 59.3 + - + +
69B CYS 3.3 0.2 - - - -
103B PHE* 3.9 28.3 - - + -
106B PHE* 3.9 24.2 - - + -
109B GLN* 3.6 57.2 + - + +
110B MET* 4.0 16.8 - - - -
113B LYS* 2.8 18.4 + - - +
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LYS* 5.0 5.5 + - - -
30B GLU* 6.0 1.1 - - - +
64B GLU* 3.2 29.2 + - + +
65B ARG* 3.2 19.1 + - - +
66B ILE 3.0 1.0 - - - -
67B LEU* 1.3 81.6 - - + +
69B CYS* 1.3 61.7 + - - +
70B HIS 4.2 0.7 + - - -
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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