Contacts of the helix formed by residues 90 - 104 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B GLU* 3.0 16.5 + - - +
89B LYS* 1.3 80.4 - - + +
91B TYR* 1.3 64.0 + - - +
92B GLU* 2.8 24.6 + - - +
93B ASN* 3.1 25.3 + - - +
94B VAL* 3.0 21.1 + - - +
114B HIS* 4.2 1.3 - - - -
301B SAH 4.2 4.5 - - - +
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Residues in contact with TYR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LYS 3.4 5.7 + - - -
90B ASP* 1.3 73.4 + - - +
92B GLU* 1.3 66.5 + - + +
94B VAL* 3.1 16.6 + - + +
95B VAL* 3.0 47.0 + - + +
114B HIS* 3.5 40.1 + + + +
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Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ASP* 2.8 15.7 + - - +
91B TYR* 1.3 78.6 - - + +
93B ASN* 1.3 63.4 + - - +
95B VAL* 3.4 8.8 + - + +
96B THR* 3.0 29.1 + - - +
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Residues in contact with ASN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PRO* 3.4 26.5 - - - +
35B LEU* 3.7 17.0 - - - +
66B CYS* 3.4 22.8 - - - +
67B VAL* 4.2 2.7 - - - +
88B GLU* 3.3 22.1 + - + -
90B ASP* 3.1 24.9 + - - +
92B GLU* 1.3 77.8 - - - +
94B VAL* 1.3 58.6 + - - +
96B THR* 3.4 6.3 + - - -
97B ALA* 2.8 32.1 + - - +
301B SAH 3.3 15.2 + - - -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU* 3.7 31.2 - - + +
90B ASP 3.0 14.1 + - - +
91B TYR* 3.1 21.1 + - + +
93B ASN* 1.3 76.9 - - - +
95B VAL* 1.3 57.4 + - - +
97B ALA* 3.4 6.1 + - - +
98B ASN* 2.9 47.2 + - - +
112B VAL* 3.9 19.1 - - + +
114B HIS* 3.8 25.6 - - + -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 3.0 51.0 + - + +
92B GLU* 3.6 10.8 - - + +
93B ASN 3.3 0.2 - - - -
94B VAL* 1.3 77.0 - - + +
96B THR* 1.3 65.7 + - - +
98B ASN* 3.3 6.7 + - - +
99B GLN* 3.0 45.0 + - + +
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Residues in contact with THR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 3.5 38.1 - - + +
67B VAL* 3.7 16.9 - - + +
92B GLU* 3.0 17.8 + - - +
93B ASN* 3.8 4.2 + - - -
95B VAL* 1.3 78.1 - - - +
97B ALA* 1.3 63.7 + - - +
99B GLN* 3.1 19.8 + - - +
100B ASN* 2.9 24.9 + - - +
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B THR* 3.9 16.8 - - + -
66B CYS 3.9 5.2 - - - +
67B VAL* 3.3 29.5 - - - +
68B GLY* 4.3 1.3 - - - -
93B ASN 2.8 23.0 + - - +
94B VAL* 3.6 5.6 - - - +
96B THR* 1.3 72.3 - - - +
98B ASN* 1.3 57.6 + - - +
100B ASN* 3.2 3.6 + - - +
101B ILE* 2.9 35.5 + - + +
112B VAL* 4.3 8.5 - - + -
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Residues in contact with ASN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 2.9 36.9 + - - +
95B VAL* 3.6 7.2 - - - +
97B ALA* 1.3 76.9 - - - +
99B GLN* 1.3 55.9 + - - +
101B ILE* 3.4 7.8 + - - +
102B VAL* 2.9 36.0 + - + +
110B ILE 5.7 0.5 - - - +
112B VAL* 3.5 26.2 + - - +
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B VAL* 3.0 36.1 + - + +
96B THR* 3.4 21.4 + - - +
98B ASN* 1.3 74.8 - - - +
100B ASN* 1.3 62.5 + - - +
102B VAL* 3.3 6.9 + - - +
103B ASN* 2.8 41.2 + - - +
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Residues in contact with ASN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LYS* 5.3 0.3 - - - +
27B ALA* 3.7 25.4 + - + +
30B THR* 2.9 41.2 + - - +
67B VAL* 2.9 25.8 + - - +
72B ILE* 4.1 5.4 - - + -
96B THR* 2.9 17.0 + - - +
97B ALA 3.6 6.5 - - - +
99B GLN* 1.3 79.1 - - - +
101B ILE* 1.3 57.2 + - - +
103B ASN* 3.3 14.2 + - - +
104B CYS* 3.0 34.4 + - - -
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Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B THR* 5.6 0.2 - - + -
68B GLY* 5.3 7.0 - - - -
71B ALA* 5.6 0.2 - - + -
72B ILE* 4.4 10.5 - - + -
86B THR* 5.4 0.2 - - + -
97B ALA* 2.9 23.8 + - + +
98B ASN* 3.8 9.0 - - - +
100B ASN* 1.3 76.9 - - - +
102B VAL* 1.3 62.6 - - + +
104B CYS* 3.2 6.5 + - - +
105B LYS 3.0 4.2 + - - -
106B LEU* 3.0 56.8 + - + +
107B GLU* 3.5 11.4 - - + +
110B ILE* 3.7 36.3 - - + +
112B VAL* 3.6 30.5 - - + -
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASN* 2.9 23.4 + - + +
99B GLN* 3.5 6.5 - - - +
101B ILE* 1.3 77.0 - - + +
103B ASN* 1.3 64.2 + - - +
105B LYS* 2.9 17.5 + - - +
107B GLU* 3.2 33.0 - - + +
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Residues in contact with ASN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLY* 6.1 1.1 - - - -
26B LYS* 6.3 1.4 - - + +
99B GLN* 2.8 32.6 + - - +
100B ASN* 3.5 15.2 + - - +
102B VAL* 1.3 77.9 - - - +
104B CYS* 1.3 61.9 - - - +
105B LYS* 3.5 1.9 + - - +
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Residues in contact with CYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLY* 3.5 41.3 - - - -
72B ILE* 3.9 20.0 - - + -
76B HIS* 5.1 7.8 - - + -
100B ASN 3.0 19.6 + - - +
101B ILE* 3.2 5.8 + - - +
102B VAL 3.2 0.2 - - - -
103B ASN* 1.3 77.2 - - - +
105B LYS* 1.3 69.8 + - - +
106B LEU* 3.4 25.4 + - + +
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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