Contacts of the helix formed by residues 90 - 104 (chain F) in PDB entry 4OA5
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 ASP 90 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88F GLU* 3.1 15.3 + - - +
89F LYS* 1.3 84.6 - - + +
91F TYR* 1.3 62.2 + - - +
92F GLU* 2.8 28.7 + - - +
93F ASN* 3.0 33.1 + - - +
94F VAL* 3.1 13.5 + - - +
114F HIS* 4.2 0.9 - - - -
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Residues in contact with TYR 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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89F LYS 3.4 5.1 + - - -
90F ASP* 1.3 72.9 + - - +
92F GLU* 1.3 75.7 + - + +
94F VAL* 3.1 13.3 + - + +
95F VAL* 3.0 47.7 + - + +
114F HIS* 3.5 38.3 + + + +
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Residues in contact with GLU 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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90F ASP* 2.8 17.4 + - - +
91F TYR* 1.3 86.0 - - + +
93F ASN* 1.3 64.6 + - - +
95F VAL* 3.4 8.6 + - + +
96F THR* 3.0 29.6 + - - -
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Residues in contact with ASN 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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32F PRO* 3.4 27.3 - - - +
35F LEU* 3.7 25.9 - - - +
66F CYS* 3.4 25.8 - - - +
67F VAL* 4.2 2.5 - - - +
88F GLU* 3.3 24.5 + - + -
90F ASP* 3.0 25.6 + - - +
92F GLU* 1.3 77.8 - - - +
94F VAL* 1.3 58.6 + - - +
96F THR* 3.4 6.1 + - - -
97F ALA* 2.8 32.4 + - - +
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Residues in contact with VAL 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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88F GLU* 3.7 30.5 - - + +
90F ASP 3.1 14.5 + - - +
91F TYR* 3.1 18.4 + - + +
93F ASN* 1.3 77.5 - - - +
95F VAL* 1.3 56.3 + - - +
97F ALA* 3.6 5.0 - - - +
98F ASN* 2.9 47.2 + - - +
112F VAL* 3.9 18.1 - - + +
114F HIS* 3.8 26.7 - - + -
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Residues in contact with VAL 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 TYR* 3.0 52.9 + - + +
92F GLU* 3.7 10.8 - - + +
93F ASN 3.3 0.4 - - - -
94F VAL* 1.3 76.2 - - + +
96F THR* 1.3 64.8 + - - +
98F ASN* 3.3 6.9 + - - +
99F GLN* 3.0 44.8 + - + +
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Residues in contact with THR 96 (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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30F THR* 3.5 37.9 - - + +
67F VAL* 3.7 16.7 - - + +
92F GLU 3.0 17.6 + - - -
93F ASN* 3.8 4.2 + - - -
95F VAL* 1.3 76.1 - - - +
97F ALA* 1.3 64.3 - - - +
99F GLN* 3.1 19.7 + - - +
100F ASN* 2.9 29.9 + - - +
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Residues in contact with ALA 97 (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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65F THR* 3.9 16.2 - - + -
66F CYS 3.9 5.6 - - - +
67F VAL* 3.3 29.8 + - - +
68F GLY* 4.0 1.6 - - - +
93F ASN 2.8 22.0 + - - +
94F VAL* 3.6 5.2 - - - +
96F THR* 1.3 72.7 - - - +
98F ASN* 1.3 57.9 + - - +
100F ASN* 3.2 3.5 + - - +
101F ILE* 2.9 36.3 + - + +
112F VAL* 4.3 9.2 - - + -
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Residues in contact with ASN 98 (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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94F VAL* 2.9 37.3 + - - +
95F VAL* 3.6 6.3 - - - +
97F ALA* 1.3 77.1 - - - +
99F GLN* 1.3 60.8 + - - +
101F ILE* 3.8 7.3 - - - +
102F VAL* 3.0 32.2 + - + +
110F ILE 5.7 0.5 - - - +
112F VAL* 3.5 27.6 + - - +
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Residues in contact with GLN 99 (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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95F VAL* 3.0 37.9 + - + +
96F THR* 3.1 20.9 + - - +
98F ASN* 1.3 74.4 - - - +
100F ASN* 1.3 62.0 + - - +
102F VAL* 3.3 6.9 + - - +
103F ASN* 2.8 41.1 + - - +
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Residues in contact with ASN 100 (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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23F GLY 5.7 0.2 - - - +
26F LYS* 5.3 0.3 - - - +
27F ALA* 3.7 25.4 + - + +
30F THR* 2.8 40.0 + - - +
67F VAL* 2.9 26.1 + - - +
72F ILE* 4.1 5.4 - - + -
96F THR* 2.9 18.5 + - - +
97F ALA 3.6 5.8 - - - +
99F GLN* 1.3 78.8 - - - +
101F ILE* 1.3 59.0 + - - +
103F ASN* 3.3 14.2 + - - +
104F CYS* 3.0 33.7 + - - -
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Residues in contact with ILE 101 (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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68F GLY* 5.3 6.7 - - - -
71F ALA* 5.6 0.2 - - + -
72F ILE* 4.4 11.4 - - + -
86F THR* 5.4 0.7 - - + -
97F ALA* 2.9 25.0 + - + +
98F ASN* 3.8 9.2 - - - +
100F ASN* 1.3 77.1 - - - +
102F VAL* 1.3 60.8 + - - +
104F CYS* 3.2 6.6 + - - +
105F LYS 3.0 4.3 + - - -
106F LEU* 3.0 57.0 + - + +
107F GLU* 3.6 12.3 - - + +
110F ILE* 3.7 36.8 - - + +
112F VAL* 3.6 30.1 - - + -
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Residues in contact with VAL 102 (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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98F ASN* 3.0 23.7 + - + +
99F GLN* 3.5 6.7 - - - +
101F ILE* 1.3 75.5 - - + +
103F ASN* 1.3 64.1 + - - +
105F LYS* 2.9 24.9 + - - +
107F GLU* 3.9 33.0 - - + +
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Residues in contact with ASN 103 (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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23F GLY* 6.1 0.7 - - - -
26F LYS* 6.4 0.6 - - - +
99F GLN* 2.8 32.1 + - - +
100F ASN* 3.6 15.8 + - - +
102F VAL* 1.3 76.5 - - - +
104F CYS* 1.3 62.0 + - - +
105F LYS* 3.5 9.4 + - - +
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Residues in contact with CYS 104 (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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23F GLY* 3.5 40.8 - - - -
72F ILE* 3.9 20.0 - - - -
76F HIS* 5.1 6.6 + - - +
100F ASN 3.0 20.4 + - - +
101F ILE* 3.2 6.2 + - - +
103F ASN* 1.3 76.6 - - - +
105F LYS* 1.3 70.0 + - - +
106F LEU* 3.4 25.7 + - + +
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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