Contacts of the helix formed by residues 90 - 104 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88E GLU* 3.0 15.5 + - - +
89E LYS* 1.3 82.9 - - + +
91E TYR* 1.3 65.2 + - - +
92E GLU* 2.8 25.3 + - - +
93E ASN* 3.0 33.3 + - - +
94E VAL* 3.1 13.2 + - - +
114E HIS* 4.2 1.6 - - - -
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Residues in contact with TYR 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E LYS 3.4 5.3 + - - -
90E ASP* 1.3 72.6 + - - +
92E GLU* 1.3 76.0 + - + +
94E VAL* 3.1 13.3 + - + +
95E VAL* 3.0 47.4 + - + +
114E HIS* 3.6 38.8 - + + +
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Residues in contact with GLU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E ASP* 2.8 16.0 + - - +
91E TYR* 1.3 84.8 - - + +
93E ASN* 1.3 63.1 + - - +
95E VAL* 3.4 15.7 + - - +
96E THR* 3.0 29.1 + - - +
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Residues in contact with ASN 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E PRO* 3.4 26.7 - - - +
35E LEU* 3.7 25.7 - - - +
66E CYS* 3.4 26.3 - - - +
67E VAL* 4.2 3.1 - - - +
88E GLU* 3.3 23.0 + - + -
90E ASP* 3.0 25.0 + - - +
92E GLU* 1.3 77.7 - - - +
94E VAL* 1.3 59.5 + - - +
96E THR* 3.4 5.6 + - - -
97E ALA* 2.8 32.6 + - - +
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Residues in contact with VAL 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E GLU* 3.7 30.1 - - + +
90E ASP 3.1 14.1 + - - +
91E TYR* 3.1 18.6 + - + +
93E ASN* 1.3 77.2 - - - +
95E VAL* 1.3 58.1 + - + +
97E ALA* 3.6 5.0 - - - +
98E ASN* 2.9 47.1 + - - +
112E VAL* 3.9 18.6 - - + +
114E HIS* 3.8 27.6 - - + -
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Residues in contact with VAL 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E TYR* 3.0 53.3 + - + +
92E GLU* 3.6 17.5 - - - +
93E ASN 3.3 0.2 - - - -
94E VAL* 1.3 77.0 - - + +
96E THR* 1.3 63.5 + - - +
98E ASN* 3.3 6.8 + - - +
99E GLN* 3.0 43.6 + - + +
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Residues in contact with THR 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E THR* 3.5 37.9 - - + +
67E VAL* 3.7 17.9 - - + +
92E GLU* 3.0 16.6 + - - +
93E ASN* 3.8 4.2 + - - -
95E VAL* 1.3 79.1 - - - +
97E ALA* 1.3 62.1 + - - +
99E GLN* 3.1 19.6 + - - +
100E ASN* 2.9 30.1 + - - +
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Residues in contact with ALA 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E THR* 4.0 16.2 - - + -
66E CYS 3.9 5.2 - - - +
67E VAL* 3.4 28.0 + - - +
68E GLY* 4.0 2.0 - - - +
93E ASN 2.8 22.4 + - - +
94E VAL* 3.6 5.6 - - - +
96E THR* 1.3 73.2 - - - +
98E ASN* 1.3 58.5 - - - +
100E ASN* 3.2 3.5 + - - +
101E ILE* 2.9 35.4 + - + +
112E VAL* 4.3 9.2 - - + -
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Residues in contact with ASN 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E VAL* 2.9 37.5 + - - +
95E VAL* 3.6 7.0 - - - +
97E ALA* 1.3 77.4 - - - +
99E GLN* 1.3 54.8 + - - +
101E ILE* 3.4 8.2 + - - +
102E VAL* 3.0 37.1 + - + +
110E ILE 5.7 0.3 - - - +
112E VAL* 3.5 26.2 + - - +
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Residues in contact with GLN 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E VAL* 3.0 37.4 + - + +
96E THR* 3.1 20.5 + - - +
98E ASN* 1.3 74.4 - - - +
100E ASN* 1.3 61.3 + - - +
102E VAL* 3.3 7.9 + - - +
103E ASN* 2.8 41.1 + - - +
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Residues in contact with ASN 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLY 5.7 0.2 - - - +
26E LYS 5.3 0.2 - - - -
27E ALA* 3.7 24.6 + - + +
30E THR* 2.9 39.8 + - - +
67E VAL* 2.9 26.3 + - - +
72E ILE* 4.1 5.2 - - + -
96E THR* 2.9 18.1 + - - +
97E ALA 3.6 5.8 - - - +
99E GLN* 1.3 76.4 - - - +
101E ILE* 1.3 61.4 + - - +
103E ASN* 3.3 14.2 + - - +
104E CYS* 3.0 32.9 + - - -
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Residues in contact with ILE 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E GLY* 5.2 6.7 - - - -
72E ILE* 4.4 12.3 - - + -
86E THR* 5.4 0.7 - - + -
97E ALA* 2.9 25.1 + - + +
98E ASN* 3.8 8.7 - - - +
100E ASN* 1.3 73.9 - - - +
102E VAL* 1.3 66.0 + - + +
104E CYS* 3.2 6.2 + - - +
105E LYS 3.0 3.6 + - - -
106E LEU* 3.0 55.3 + - + +
107E GLU* 3.5 12.1 - - + +
110E ILE* 3.7 36.1 - - + +
112E VAL* 3.6 29.8 - - + -
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ASN* 3.0 23.5 + - + +
99E GLN* 3.5 7.4 - - - +
101E ILE* 1.3 76.8 - - + +
103E ASN* 1.3 64.5 + - - +
105E LYS* 2.9 25.1 + - - +
107E GLU* 3.5 31.3 - - + +
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Residues in contact with ASN 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLY* 6.0 1.3 - - - -
99E GLN* 2.8 28.9 + - - +
100E ASN* 3.5 15.0 + - - +
101E ILE 3.3 0.2 - - - -
102E VAL* 1.3 80.0 - - - +
104E CYS* 1.3 61.7 + - - +
105E LYS* 3.5 8.5 + - - +
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Residues in contact with CYS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLY* 3.5 41.7 - - - -
72E ILE* 3.8 19.7 - - - -
76E HIS* 5.1 7.0 + - - +
100E ASN 3.0 21.2 + - - +
101E ILE* 3.7 5.8 - - - +
102E VAL 3.2 0.2 - - - -
103E ASN* 1.3 77.2 - - - +
105E LYS* 1.3 68.9 + - - +
106E LEU* 3.3 25.6 + - + +
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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