Contacts of the helix formed by residues 77 - 92 (chain F) in PDB entry 5AN5
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 ASN 77 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-1F MET* 3.0 25.8 + - - +
0F ALA 3.5 0.4 + - - -
76F THR* 1.3 76.9 - - - +
78F PHE* 1.3 64.2 + - - +
79F ASP* 3.2 13.2 + - - +
80F ILE* 3.0 39.5 + - + +
81F LEU* 3.1 25.0 + - - +
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Residues in contact with PHE 78 (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 THR 3.5 5.2 + - - +
77F ASN* 1.3 73.8 + - - +
79F ASP* 1.3 73.1 + - - +
81F LEU* 3.3 8.8 + - + -
82F LYS* 2.8 66.0 + - + +
0J ALA* 4.9 1.6 - - + -
76J THR* 6.2 3.4 - - + -
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Residues in contact with ASP 79 (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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77F ASN* 3.2 10.2 + - - +
78F PHE* 1.3 92.8 - - - +
80F ILE* 1.3 60.8 + - + +
82F LYS* 3.8 1.0 - - - +
83F ARG* 2.9 43.6 + - - +
-1J MET 6.2 0.7 - - - -
0J ALA* 3.9 20.7 - - + +
76J THR* 5.8 2.4 - - - +
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Residues in contact with ILE 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E ILE* 5.1 3.4 - - + -
81E LEU* 3.8 17.9 - - + -
84E LEU* 4.3 13.9 - - + -
-1F MET* 3.4 47.6 - - + +
77F ASN* 3.0 28.8 + - + +
79F ASP* 1.3 76.0 - - + +
81F LEU* 1.3 64.3 + - - +
83F ARG* 3.3 12.4 + - - +
84F LEU* 3.0 34.5 + - + +
80G ILE* 4.2 26.2 - - + -
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Residues in contact with LEU 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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-1F MET 5.0 0.9 - - - +
0F ALA 3.6 26.9 - - - +
76F THR* 4.2 6.3 - - - -
77F ASN 3.1 22.4 + - - +
78F PHE* 3.8 8.7 - - + +
80F ILE* 1.3 75.2 - - - +
82F LYS* 1.3 57.4 + - - +
84F LEU* 3.4 6.1 + - + +
85F SER* 3.0 32.0 + - - -
79G ASP* 6.1 0.4 - - - +
80G ILE* 4.6 18.8 - - + -
83G ARG* 3.7 21.7 + - - +
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Residues in contact with LYS 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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78F PHE* 2.8 53.7 + - + +
79F ASP 3.8 3.1 - - - +
81F LEU* 1.3 74.8 - - - +
83F ARG* 1.3 59.6 + - - +
85F SER* 3.3 6.1 + - - -
86F ASN* 2.8 50.9 + - - +
0J ALA* 3.9 24.5 - - + +
76J THR* 5.8 1.8 - - + -
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Residues in contact with ARG 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LEU* 4.6 13.9 + - - +
84E LEU* 3.5 29.8 - - + +
85E SER* 3.5 18.2 + - - +
88E GLU* 2.7 45.1 + - - +
79F ASP* 2.9 30.9 + - - +
80F ILE* 3.6 8.2 - - - +
82F LYS* 1.3 77.1 - - - +
84F LEU* 1.3 61.8 + - - +
86F ASN* 3.5 7.9 + - - +
87F LEU* 3.1 29.3 + - - +
-1J MET* 3.6 23.2 - - - +
0J ALA* 3.8 19.5 - - - +
78J PHE* 4.8 2.3 - - + -
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Residues in contact with LEU 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E LEU* 3.8 21.5 - - + -
80F ILE* 3.0 26.7 + - + +
81F LEU* 3.6 2.7 - - - +
83F ARG* 1.3 74.3 - - - +
85F SER* 1.3 60.0 + - - +
87F LEU* 3.3 5.4 + - - +
88F GLU* 2.9 33.1 + - - +
80G ILE* 4.1 31.6 - - + -
83G ARG* 3.5 43.3 - - + +
84G LEU* 3.8 22.9 - - + -
87G LEU* 4.0 16.7 - - + +
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Residues in contact with SER 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F LEU* 3.0 18.8 + - - +
82F LYS* 3.8 7.4 - - - -
84F LEU* 1.3 75.4 - - - +
86F ASN* 1.3 59.3 + - - +
88F GLU* 3.3 12.1 + - - +
89F LYS* 3.0 30.4 + - - +
83G ARG* 3.1 12.5 + - - -
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Residues in contact with ASN 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F LYS* 2.8 32.3 + - - +
83F ARG* 3.7 4.4 - - - +
85F SER* 1.3 78.7 - - - +
87F LEU* 1.3 62.4 + - - +
89F LYS* 3.4 6.5 + - - +
90F HIS* 3.0 17.7 + - - +
0J ALA* 3.4 19.8 + - - +
78J PHE* 3.2 59.9 - - + +
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Residues in contact with LEU 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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84E LEU* 3.7 29.8 - - + -
87E LEU* 4.0 20.0 - - + +
88E GLU* 4.1 24.0 - - + +
91E VAL* 4.1 32.3 - - + -
92E PHE* 4.8 0.4 - - + -
83F ARG 3.1 15.9 + - - +
84F LEU* 3.6 6.3 - - - +
86F ASN* 1.3 76.0 - - - +
88F GLU* 1.3 58.5 + - - +
90F HIS* 3.2 0.8 + - - +
91F VAL* 2.9 36.8 + - + +
87G LEU* 4.1 22.9 - - + -
78J PHE* 4.1 15.3 - - + -
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Residues in contact with GLU 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 LEU* 2.9 15.8 + - - +
85F SER* 3.6 7.7 + - - +
87F LEU* 1.3 75.5 - - - +
89F LYS* 1.3 62.7 + - - +
92F PHE* 3.2 46.4 + - + +
83G ARG* 2.8 59.8 + - - +
87G LEU* 4.1 18.0 - - + +
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Residues in contact with LYS 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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85F SER 3.0 17.0 + - - +
86F ASN* 3.7 7.4 - - - +
88F GLU* 1.3 77.3 - - - +
90F HIS* 1.3 61.9 + - - +
92F PHE 4.4 7.4 + - - -
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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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91E VAL* 3.3 35.4 + - + +
92E PHE* 4.6 5.0 - + - -
86F ASN 3.0 17.4 + - - +
87F LEU* 3.2 4.2 + - - +
89F LYS* 1.3 81.5 - - - +
91F VAL* 1.3 64.8 + - + +
92F PHE 4.9 1.4 - - - -
78J PHE* 3.7 20.8 - + + -
82J LYS* 4.2 26.0 - - + +
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Residues in contact with VAL 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E VAL* 3.9 21.8 - - + -
87F LEU* 2.9 24.4 + - + +
90F HIS* 1.3 87.6 - - + +
92F PHE* 1.3 76.5 + - + +
87G LEU* 3.4 25.4 - - + -
90G HIS* 3.2 23.7 + - + -
91G VAL* 3.8 28.0 - - + -
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Residues in contact with PHE 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F GLU* 3.2 39.0 + - + +
89F LYS 4.7 7.0 - - - -
90F HIS 3.6 1.8 - - - -
91F VAL* 1.3 80.9 - - + +
86G ASN* 3.9 30.5 - - + -
87G LEU* 3.9 21.5 - - + -
90G HIS* 3.4 42.3 + + + -
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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