Contacts of the helix formed by residues 82 - 95 (chain F) in PDB entry 4RHW
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 GLN 82 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19F GLU 4.1 2.3 - - - +
20F LEU* 3.6 11.1 - - - +
21F GLN* 2.9 58.2 + - + +
24F GLN* 4.1 9.1 - - - +
25F LEU* 4.1 11.1 - - - +
77F LEU* 2.9 25.8 + - + +
80F THR* 3.2 27.8 + - - +
81F GLY* 1.3 79.2 - - - +
83F ASP* 1.3 61.9 + - - +
84F MET 3.3 3.1 - - - -
85F LEU* 3.3 12.3 + - + +
86F ALA* 3.1 20.8 + - - +
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Residues in contact with ASP 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F GLU* 3.4 38.5 - - - +
81F GLY* 3.2 7.6 + - - +
82F GLN* 1.3 73.9 - - - +
84F MET* 1.3 59.2 - - - +
86F ALA* 4.1 5.0 - - - +
87F SER* 2.8 36.0 + - - -
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Residues in contact with MET 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ARG* 5.8 0.2 + - - -
19F GLU* 5.5 4.3 - - - +
82F GLN 3.3 0.8 - - - -
83F ASP* 1.3 78.5 - - - +
85F LEU* 1.3 56.5 + - - +
87F SER* 3.2 9.9 + - - +
88F PHE* 3.1 25.5 + - - +
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ARG* 3.6 35.2 - - + +
16F LEU* 4.2 22.0 - - + +
19F GLU* 3.9 19.0 + - + +
20F LEU* 3.7 51.6 - - + +
77F LEU* 4.4 8.5 - - + -
82F GLN* 3.3 15.9 + - + +
83F ASP 3.3 0.4 - - - -
84F MET* 1.3 75.9 - - - +
86F ALA* 1.3 66.9 + - - +
88F PHE* 3.3 10.7 + - + +
89F LEU* 3.0 25.6 + - - +
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Residues in contact with ALA 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ILE* 4.0 9.0 - - + +
77F LEU* 3.6 32.8 - - + +
78F GLU* 3.8 29.6 - - + +
82F GLN 3.1 11.9 + - - +
83F ASP* 3.7 4.9 - - - +
85F LEU* 1.3 76.7 - - - +
87F SER* 1.3 56.8 + - - +
89F LEU* 3.3 3.9 + - - +
90F ARG* 2.8 32.1 + - - +
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Residues in contact with SER 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ASP* 2.8 24.3 + - - -
84F MET* 3.2 13.1 + - - +
86F ALA* 1.3 70.0 - - - +
88F PHE* 1.3 69.6 + - - +
90F ARG* 3.9 10.5 - - - +
91F THR* 2.9 37.8 + - - +
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Residues in contact with PHE 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F CYS* 3.6 36.1 - - + -
15F ARG* 3.1 74.5 - - + +
84F MET 3.1 10.6 + - - +
85F LEU* 3.3 17.9 - - + +
87F SER* 1.3 85.6 + - - +
89F LEU* 1.3 65.0 + - + +
91F THR* 3.4 15.1 + - - -
92F ASN* 3.6 21.1 + - - +
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 3.9 16.4 - - + +
9F LEU* 4.9 5.8 - - + -
12F CYS* 3.9 32.8 - - + -
16F LEU* 4.2 19.1 - - + -
70F LEU* 4.6 5.4 - - + -
73F PHE* 3.9 17.9 - - + -
74F ILE* 3.9 22.4 - - + -
77F LEU* 3.6 29.4 - - + -
85F LEU 3.0 13.5 + - - +
86F ALA 3.7 5.6 - - - +
88F PHE* 1.3 77.7 - - + +
90F ARG* 1.3 66.3 + - - +
92F ASN* 3.1 8.0 + - - +
93F ARG* 3.1 19.2 + - - +
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Residues in contact with ARG 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F PRO 5.8 0.2 + - - -
74F ILE* 3.5 27.3 - - + +
75F SER* 5.0 5.1 + - - -
78F GLU* 2.7 41.4 + - - -
86F ALA 2.8 18.8 + - - +
87F SER* 3.2 12.5 + - - +
89F LEU* 1.3 71.2 - - - +
91F THR* 1.3 66.0 + - + +
93F ARG* 3.1 15.3 + - - +
94F GLN* 3.5 22.0 + - + +
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Residues in contact with THR 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F SER* 2.9 21.6 + - - +
88F PHE* 3.4 12.9 + - - -
90F ARG* 1.3 78.6 - - + +
92F ASN* 1.3 71.9 + - - +
94F GLN* 3.5 10.0 + - - +
95F ALA* 3.2 23.1 + - - +
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Residues in contact with ASN 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 3.6 18.0 - - + +
11F ARG* 4.5 20.7 + - - +
12F CYS* 3.5 20.2 - - - -
88F PHE* 3.6 25.3 + - - +
89F LEU* 3.1 10.6 + - - +
91F THR* 1.3 86.5 + - - +
93F ARG* 1.3 64.4 + - - +
94F GLN 3.4 0.5 + - - -
95F ALA* 3.4 22.3 + - - +
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Residues in contact with ARG 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ASP* 5.2 2.8 + - - -
5F ASP* 2.9 42.5 + - - +
8F LEU* 3.8 17.2 - - + +
67F SER 5.2 2.2 + - - -
68F GLN* 5.6 2.0 + - - +
70F LEU* 3.6 15.4 - - - +
71F PRO* 3.8 31.5 - - - +
74F ILE* 4.6 12.3 - - - -
89F LEU 3.1 8.0 + - - +
90F ARG* 3.1 10.3 + - - +
92F ASN* 1.3 77.7 - - - +
94F GLN* 1.3 64.0 + - + +
95F ALA 4.4 2.4 - - - -
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Residues in contact with GLN 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ARG* 3.5 20.0 + - + +
91F THR* 3.5 9.9 + - - +
92F ASN 3.3 0.6 - - - -
93F ARG* 1.3 78.2 - - + +
95F ALA* 1.3 68.8 + - - +
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F THR 3.2 15.8 + - - +
92F ASN* 3.4 17.4 + - - +
93F ARG 4.4 2.2 - - - -
94F GLN* 1.3 85.8 - - - +
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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