Contacts of the helix formed by residues 84 - 94 (chain F) in PDB entry 5A31
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 LYS 84 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58F TYR* 3.0 40.8 + - + +
59F ARG* 6.0 2.6 - - - +
79F CYS* 2.9 16.5 + - + +
82F LEU* 3.8 28.8 - - + +
83F SER* 1.3 75.9 - - - +
85F LEU* 1.3 63.9 + - - +
86F ALA* 3.3 3.4 - - - -
87F GLU* 3.1 29.7 + - + +
88F GLY 3.1 17.5 + - - -
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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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79F CYS 5.2 0.2 - - - -
80F VAL* 5.0 11.4 - - + +
83F SER 3.1 11.3 + - - +
84F LYS* 1.3 73.9 - - - +
86F ALA* 1.3 70.6 + - + +
88F GLY* 3.4 1.1 + - - +
89F GLU* 3.1 20.3 + - - +
124F VAL* 3.7 22.5 - - + +
127F LYS* 4.2 40.4 - - + +
128F THR* 3.9 36.8 - - + +
130F ARG* 5.5 0.7 - - - +
538Y LEU* 6.3 3.6 - - + -
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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
----------------------------------------------------------
84F LYS* 3.3 1.3 - - - -
85F LEU* 1.3 90.8 - - + +
87F GLU* 1.3 60.8 + - - +
89F GLU* 3.5 13.5 + - - +
90F GLN* 3.6 14.0 + - - +
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Residues in contact with GLU 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F TYR* 2.4 48.4 + - - -
62F LYS* 3.2 25.5 + - - +
75F LEU* 4.5 3.8 - - - +
79F CYS* 3.6 8.9 - - - -
84F LYS* 3.1 30.0 + - + +
86F ALA* 1.3 77.3 - - - +
88F GLY* 1.3 64.9 + - - +
90F GLN* 3.3 16.6 - - - +
91F ILE* 3.3 19.5 - - + +
292Y LEU* 4.0 14.0 - - + +
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Residues in contact with GLY 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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76F ALA* 3.8 19.7 - - - +
79F CYS* 3.4 25.2 - - - +
80F VAL* 5.0 5.4 - - - -
84F LYS 3.1 11.6 + - - -
85F LEU 3.9 3.4 - - - -
86F ALA 3.4 0.2 - - - -
87F GLU* 1.3 78.7 - - - +
89F GLU* 1.3 61.6 + - - +
91F ILE* 3.6 8.4 + - - +
92F LEU* 3.7 12.1 + - - +
124F VAL* 5.2 3.8 - - - -
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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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85F LEU* 3.1 17.1 + - - +
86F ALA* 3.8 8.3 - - - +
87F GLU 3.3 0.2 - - - -
88F GLY* 1.3 75.9 - - - +
90F GLN* 1.3 58.6 + - - +
91F ILE 3.2 0.2 + - - -
92F LEU* 3.4 3.1 + - - +
93F SER* 2.5 51.2 + - - +
121F LEU* 4.9 4.9 - - + +
124F VAL* 4.1 14.6 - - + +
125F TYR* 2.8 29.8 + - + -
130F ARG* 2.2 39.4 + - - -
133F LYS* 4.6 4.2 + - - -
505Y ASN 5.4 0.5 - - - +
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Residues in contact with GLN 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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86F ALA 3.6 8.3 + - - +
87F GLU* 3.3 20.0 - - - +
89F GLU* 1.3 80.9 - - - +
91F ILE* 1.3 67.2 + - - +
93F SER* 3.7 5.4 - - - -
94F GLY* 2.7 33.5 + - - +
95F GLY 4.6 10.5 - - - +
288Y LYS* 4.1 21.4 + - + +
289Y ASN* 3.6 23.1 + - - +
292Y LEU* 3.1 42.9 - - - +
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Residues in contact with ILE 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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72F LYS* 3.5 52.4 - - + +
75F LEU* 3.4 38.4 - - + -
76F ALA* 4.2 5.2 - - + +
79F CYS* 3.8 13.2 - - - -
87F GLU* 3.3 24.7 - - + +
88F GLY 3.9 7.0 - - - +
89F GLU 3.2 1.0 - - - -
90F GLN* 1.3 91.1 - - - +
92F LEU* 1.3 64.4 + - - +
94F GLY* 3.8 3.6 + - - -
101F LYS* 4.2 5.9 + - - -
110F PHE* 5.2 0.3 - - - -
292Y LEU* 5.4 5.8 - - + -
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Residues in contact with LEU 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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72F LYS 4.4 6.1 - - - +
73F TYR* 4.4 2.9 - - + -
76F ALA* 3.4 33.0 - - + -
88F GLY 3.7 6.9 + - - +
89F GLU* 3.4 5.3 + - - +
91F ILE* 1.3 79.4 - - - +
93F SER* 1.3 63.6 + - - +
101F LYS* 3.4 16.8 + - - +
106F ILE* 4.4 5.7 - - + +
110F PHE* 3.4 45.3 - - + -
117F THR* 4.1 24.2 - - + +
120F LEU* 3.8 24.0 - - + -
121F LEU* 4.4 20.9 - - + +
124F VAL* 5.5 2.2 - - + -
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Residues in contact with SER 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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89F GLU* 2.5 40.9 + - - +
90F GLN* 3.7 0.7 - - - -
92F LEU* 1.3 80.1 - - - +
94F GLY* 1.3 62.0 + - - +
95F GLY* 3.1 19.1 + - - -
101F LYS* 3.2 29.0 + - - +
106F ILE* 4.9 4.3 - - - -
121F LEU* 4.5 11.4 - - - -
125F TYR* 4.2 19.3 - - - -
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Residues in contact with GLY 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 GLN* 2.7 25.4 + - - -
91F ILE 3.8 2.3 + - - -
92F LEU 3.3 2.6 + - - -
93F SER* 1.3 71.1 - - - +
95F GLY* 1.3 57.0 + - - +
98F ASN* 2.9 38.8 + - - +
101F LYS* 3.9 14.5 - - - -
289Y ASN* 5.2 2.6 - - - +
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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