Contacts of the helix formed by residues 83 - 94 (chain F) in PDB entry 6R90
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 THR 83 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86E GLN* 3.9 20.0 - - + +
89E ALA* 4.1 3.6 - - - -
79F ARG* 3.8 23.3 + - - +
81F THR* 3.9 7.9 - - + +
82F VAL* 1.3 78.4 - - - +
84F ALA* 1.3 64.3 + - - +
85F MET* 3.6 11.6 + - - +
86F ASP* 2.8 46.5 + - - +
87F VAL* 3.5 10.2 + - - +
101I A 6.1 5.4 - - - -
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Residues in contact with ALA 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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86E GLN* 3.5 13.7 + - - +
88E SER* 4.6 8.5 - - - +
89E ALA* 3.8 28.1 - - - +
92E ALA* 5.2 3.4 - - + -
83F THR* 1.3 74.1 - - - +
85F MET* 1.3 64.8 + - + +
87F VAL* 3.0 7.9 + - - +
88F VAL* 2.9 26.3 + - - +
101F PHE* 4.5 21.5 - - + +
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Residues in contact with MET 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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83F THR* 3.2 10.7 - - - +
84F ALA* 1.3 77.5 - - + +
86F ASP* 1.3 64.7 + - - +
88F VAL* 3.2 9.9 + - + +
89F TYR* 3.0 69.0 + - + +
101F PHE 3.6 14.4 - - - +
102F GLY* 3.7 7.2 - - - -
103F GLY* 3.2 47.6 - - - +
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Residues in contact with ASP 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ALA* 4.3 9.4 - - - +
73F TYR* 3.7 30.6 - - + +
74F THR* 3.9 14.0 + - - +
79F ARG* 3.5 25.0 + - - -
82F VAL* 4.2 3.7 - - + -
83F THR* 2.8 36.8 + - - +
84F ALA 3.2 0.2 - - - -
85F MET* 1.3 79.0 - - - +
87F VAL* 1.3 62.4 + - - +
89F TYR* 3.3 11.0 + - - +
90F ALA* 3.0 24.9 + - - +
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Residues in contact with VAL 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E PHE* 5.4 0.4 - - + -
89E ALA* 4.6 5.4 - - + +
92E ALA* 4.9 7.2 - - + -
93E LEU* 3.5 46.7 - - + +
66F VAL* 5.2 1.3 - - + -
70F ALA* 4.4 15.5 - - + -
82F VAL* 4.6 9.2 - - + -
83F THR 3.5 11.9 + - - +
84F ALA* 3.0 12.6 + - - +
86F ASP* 1.3 77.1 - - - +
88F VAL* 1.3 57.6 + - + +
90F ALA* 3.3 5.7 + - - +
91F LEU* 2.9 57.2 + - + +
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Residues in contact with VAL 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ALA* 5.6 2.0 - - + -
84F ALA* 2.9 20.4 + - + +
85F MET* 3.2 16.8 + - + +
87F VAL* 1.3 77.9 - - + +
89F TYR* 1.3 71.4 + - + +
91F LEU* 3.2 8.6 + - - +
92F LYS* 2.9 32.7 + - + +
97F THR* 5.9 2.2 - - + -
98F LEU* 4.3 34.6 + - + +
101F PHE* 4.5 25.8 - - + +
102F GLY* 4.9 4.5 - - - +
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Residues in contact with TYR 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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73F TYR* 4.0 19.1 + + + +
85F MET* 3.0 57.1 + - + +
86F ASP* 3.8 12.3 - - - +
88F VAL* 1.3 85.1 - - + +
90F ALA* 1.3 62.5 + - - +
92F LYS* 3.1 14.8 + - - +
93F ARG* 3.0 24.1 + - - +
84H TYR* 3.3 74.1 - + + +
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Residues in contact with ALA 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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66F VAL* 4.3 9.6 - - + +
69F ASP* 4.1 8.3 - - + -
70F ALA* 4.0 19.5 - - + +
73F TYR* 3.4 25.9 - - + -
86F ASP 3.0 14.1 + - - +
87F VAL* 3.8 5.4 - - - +
89F TYR* 1.3 76.8 - - - +
91F LEU* 1.3 60.9 + - - +
93F ARG* 3.3 20.4 - - - +
94F GLN* 3.4 16.2 + - - -
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Residues in contact with LEU 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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92E ALA 5.3 0.2 - - - +
93E LEU* 5.2 1.6 - - + -
96E ALA* 4.3 28.7 - - + -
62F PHE* 5.0 5.6 - - + -
66F VAL* 3.7 31.4 - - + -
87F VAL* 2.9 47.1 + - + +
88F VAL* 3.7 5.6 - - - +
90F ALA* 1.3 76.5 - - - +
92F LYS* 1.3 62.8 + - - +
94F GLN* 3.3 10.9 + - + +
95F GLY 3.4 0.2 + - - -
96F ARG* 2.9 47.8 + - + +
97F THR* 4.9 1.8 - - - -
98F LEU* 4.4 20.4 - - + +
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Residues in contact with LYS 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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69D ASP* 5.4 8.1 - - - +
72D GLU* 4.2 20.8 + - - +
88F VAL* 2.9 20.8 + - + +
89F TYR* 3.1 12.2 + - - +
91F LEU* 1.3 78.5 - - - +
93F ARG* 1.3 61.5 + - - +
95F GLY* 2.9 19.2 + - - -
97F THR* 3.4 34.9 + - + +
80H ARG* 4.1 23.6 - - - +
84H TYR* 4.3 13.2 + - - -
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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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69F ASP* 3.6 11.2 + - - +
73F TYR* 3.6 20.0 - - - +
89F TYR 3.0 13.0 + - - +
90F ALA* 3.3 16.4 - - - +
92F LYS* 1.3 80.2 - - - +
94F GLN* 1.3 68.0 + - + +
95F GLY 3.2 1.0 + - - -
77H GLU* 4.0 15.8 + - - +
80H ARG* 5.8 2.9 - - - +
101H LEU* 2.9 51.2 + - - +
102H LEU* 3.1 36.0 + - - +
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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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62F PHE* 4.9 6.8 - - - -
65F ASN* 3.8 20.8 + - - +
66F VAL* 3.4 31.8 + - - +
69F ASP* 3.2 25.7 + - - +
90F ALA 3.4 16.5 + - - +
91F LEU* 3.3 10.0 + - + +
92F LYS 3.2 0.8 - - - -
93F ARG* 1.3 87.3 - - - +
95F GLY* 1.3 61.7 + - - +
96F ARG* 3.3 18.3 + - + +
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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