Contacts of the helix formed by residues 80 - 90 (chain F) in PDB entry 4WYV
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 PRO 80 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20F ILE* 4.4 13.7 - - + -
79F PHE* 1.4 92.1 - - + +
81F ALA* 1.3 54.5 + - - +
82F GLU* 3.2 22.0 - - - +
83F GLN* 2.8 59.2 + - + +
87F PHE* 4.4 7.0 - - + -
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Residues in contact with ALA 81 (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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76F LYS 6.0 0.9 - - - +
79F PHE* 3.4 14.4 + - - -
80F PRO* 1.3 69.7 - - - +
82F GLU* 1.3 65.3 + - - +
83F GLN 3.1 1.5 + - - -
84F TYR* 3.3 17.0 + - - +
131F LYS* 3.4 15.8 + - + +
132F GLY* 4.3 22.8 - - - +
133F PHE 5.2 3.6 + - - +
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Residues in contact with GLU 82 (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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82B GLU* 3.2 34.3 - - + +
80F PRO* 3.0 24.1 + - - +
81F ALA* 1.3 80.0 + - - +
83F GLN* 1.3 67.2 + - + +
84F TYR* 3.3 4.0 + - - +
85F TYR 5.2 0.3 + - - -
131F LYS* 4.0 15.3 + - - +
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Residues in contact with GLN 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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85B TYR* 4.1 16.6 - - + -
134B HIS* 6.0 3.8 - - - -
20F ILE* 5.8 1.2 - - - +
79F PHE* 4.4 2.2 - - - -
80F PRO* 2.8 38.5 + - + +
82F GLU* 1.3 88.8 - - + +
84F TYR* 1.3 66.5 + - - +
85F TYR 3.2 3.1 - - - -
86F ARG* 2.9 53.0 + - + +
87F PHE* 3.8 20.0 + - + -
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Residues in contact with TYR 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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79F PHE* 3.6 13.9 - + + -
81F ALA 3.3 13.4 + - - +
82F GLU 3.3 3.9 + - - +
83F GLN* 1.3 76.8 - - - +
85F TYR* 1.3 95.2 + + + +
86F ARG 3.3 0.7 + - - -
87F PHE 3.5 0.5 + - - -
88F HIS* 3.3 43.3 + + - -
91F TRP* 3.4 43.1 + + - -
95F LEU* 4.9 2.6 - - - +
131F LYS* 5.3 4.3 - - - +
133F PHE* 3.9 36.2 - + - +
134F HIS* 2.9 45.4 + - + +
135F LEU* 4.8 0.3 - - - -
136F ASP* 4.6 4.0 + - + -
139F ASP* 4.4 4.7 + - - -
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Residues in contact with TYR 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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83B GLN* 4.7 11.2 - - + -
85B TYR* 3.8 15.0 - - + +
86B ARG* 3.5 64.1 + - + +
82F GLU 5.2 0.4 + - - -
83F GLN 3.2 1.6 - - - -
84F TYR* 1.3 110.4 - + + +
86F ARG* 1.3 61.3 + - - +
87F PHE 3.4 0.2 - - - -
88F HIS* 3.9 29.3 + + + +
89F GLU* 4.4 2.9 - - - +
134F HIS* 5.9 6.9 - - + +
136F ASP* 2.5 46.2 + - - +
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Residues in contact with ARG 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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85B TYR* 3.5 49.6 + - + +
136B ASP* 3.3 11.2 + - - +
137B VAL* 5.2 4.2 - - - +
138B GLU* 3.1 21.8 + - - -
17F GLU* 2.7 44.2 + - - +
21F ARG* 3.6 14.0 + - - +
83F GLN* 2.9 34.6 + - + +
85F TYR* 1.3 80.1 - - - +
87F PHE* 1.3 77.5 + - + +
88F HIS 3.5 0.2 - - - -
89F GLU* 3.3 18.1 - - - +
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Residues in contact with PHE 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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17F GLU* 4.2 15.9 - - + -
20F ILE* 3.5 33.9 - - + -
21F ARG* 3.6 41.5 - - + -
24F ILE* 3.6 19.5 - - + -
79F PHE* 3.9 23.1 - + + -
80F PRO* 4.4 5.4 - - + -
83F GLN* 3.8 31.6 - - + -
84F TYR 3.5 1.8 + - - -
86F ARG* 1.3 94.2 - - + +
88F HIS* 1.3 61.3 + - - +
89F GLU* 3.3 3.8 - - - -
90F HIS* 3.2 20.7 + + - +
91F TRP* 2.9 27.6 - - + -
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Residues in contact with HIS 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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84F TYR* 3.3 44.1 + + - +
85F TYR* 3.9 26.8 - + + +
86F ARG 3.5 0.2 - - - -
87F PHE* 1.3 75.9 - - - +
89F GLU* 1.3 63.2 + - - +
90F HIS 2.9 6.8 + - - -
91F TRP* 3.0 33.3 + - - -
92F ARG* 3.2 34.9 + - + +
136F ASP* 3.7 15.9 + - - -
139F ASP* 2.9 35.0 + - - -
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Residues in contact with GLU 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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21F ARG* 3.4 23.5 + - - -
85F TYR 4.4 2.3 - - - +
86F ARG 3.3 20.4 - - - +
87F PHE 4.4 1.8 - - - -
88F HIS* 1.3 78.1 + - - +
90F HIS* 1.3 68.1 + - + +
91F TRP 3.3 1.0 + - - -
92F ARG* 3.3 49.6 + - - +
93F PHE 5.0 0.7 + - - -
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Residues in contact with HIS 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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21F ARG* 3.0 49.9 + - + -
24F ILE* 3.8 24.7 - - + +
25F ARG* 3.0 47.9 + - - +
28F VAL* 3.5 20.8 - - + +
32F GLU* 5.0 1.9 - - - +
87F PHE* 3.2 27.5 + + - +
88F HIS 2.9 2.2 + - - -
89F GLU* 1.3 86.1 + - + +
91F TRP* 1.3 59.3 + - - +
93F PHE* 5.4 1.8 + - - +
94F VAL* 4.9 0.3 + - - +
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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