Contacts of the helix formed by residues 90 - 101 (chain B) in PDB entry 3OAX
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 GLY 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B PHE 3.6 1.6 + - - -
86B MET 3.0 8.0 + - - -
89B GLY* 1.3 78.4 - - - +
91B PHE* 1.3 59.5 + - - +
92B THR 3.0 2.7 - - - -
93B THR* 2.7 28.0 + - - -
94B THR* 2.9 15.5 + - - +
112B LEU 4.0 3.4 - - - -
113B GLU* 4.0 21.9 - - - +
116B PHE* 3.7 7.1 - - - +
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Residues in contact with PHE 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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44B MET* 3.5 18.0 - - + +
47B LEU* 4.2 21.8 - - + -
48B ILE* 3.6 17.0 - - + +
86B MET* 2.8 34.5 + - + -
87B VAL* 3.0 32.1 - - + +
90B GLY* 1.3 71.9 - - - +
92B THR* 1.3 55.6 + - - +
94B THR* 3.0 10.6 - - + +
95B LEU* 2.9 30.5 + - - +
113B GLU* 5.4 0.9 - - - -
117B ALA* 5.6 6.1 - - + -
296B LYS* 3.0 51.6 - - + -
299B ALA* 3.6 24.7 - - + -
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Residues in contact with THR 92 (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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1322A PLM 4.9 19.3 - - + -
48B ILE* 4.2 14.4 - - + -
87B VAL 3.3 9.8 + - - +
88B PHE* 2.6 41.8 + - + +
89B GLY 4.1 4.5 + - - -
91B PHE* 1.3 76.2 - - - +
93B THR* 1.3 63.8 + - - +
95B LEU* 3.3 4.2 + - - +
96B TYR* 3.1 23.7 + - - +
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Residues in contact with THR 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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89B GLY 4.4 1.9 + - - -
90B GLY 2.7 15.8 + - - -
92B THR* 1.3 75.7 + - - +
94B THR* 1.3 60.6 + - - +
96B TYR* 3.4 5.9 + - - +
97B THR* 2.8 45.3 + - - +
103B PHE* 3.8 5.8 - - + -
105B PHE* 4.4 16.9 - - + -
109B GLY* 3.3 36.7 - - - +
112B LEU* 3.8 23.6 - - - +
113B GLU* 4.2 6.3 - - + -
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Residues in contact with THR 94 (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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44B MET* 3.3 30.1 - - + +
90B GLY 2.9 7.9 + - - +
91B PHE* 3.0 36.8 - - + +
93B THR* 1.3 78.4 - - - +
95B LEU* 1.3 55.5 + - - +
97B THR* 3.8 1.8 - - - -
98B SER* 2.8 34.1 + - - -
113B GLU* 3.5 32.3 - - + +
185B CYS 3.9 10.6 - - - +
293B PHE* 3.9 11.8 - - - -
296B LYS* 4.2 0.7 - - - -
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Residues in contact with LEU 95 (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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308A MET* 4.5 4.0 - - + -
317A MET* 6.3 2.5 - - + -
41B ALA* 3.1 34.5 - - + +
44B MET* 4.2 7.4 - - + +
45B PHE* 4.0 25.8 - - + +
48B ILE* 3.9 22.2 - - + -
91B PHE 2.9 17.2 + - - +
92B THR* 3.6 5.4 - - - +
93B THR 3.2 0.2 - - - -
94B THR* 1.3 74.7 + - - +
96B TYR* 1.3 65.8 + - - +
98B SER* 3.4 2.6 + - - -
99B LEU* 3.0 46.1 + - + +
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Residues in contact with TYR 96 (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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327A PRO 5.6 2.9 - - - -
328A LEU* 5.4 4.5 - - + -
329A GLY* 3.9 19.6 + - - -
330A ASP* 3.8 16.3 + - - -
959A ZN 4.1 4.7 - - - -
92B THR 3.1 14.2 + - - +
93B THR 3.7 3.6 - - - +
95B LEU* 1.3 79.8 - - - +
97B THR* 1.3 61.6 + - - +
99B LEU* 3.2 15.3 + - + +
100B HIS* 2.7 53.3 + + - -
104B VAL* 3.4 30.5 - - + +
105B PHE* 3.1 51.2 - + + -
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Residues in contact with THR 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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93B THR* 2.8 26.5 + - - +
94B THR* 3.8 4.7 - - - -
95B LEU 3.2 0.2 - - - -
96B TYR* 1.3 75.5 - - - +
98B SER* 1.3 59.1 + - - +
100B HIS* 3.0 2.8 + - - -
101B GLY* 2.8 25.1 + - - -
102B TYR 3.3 31.9 + - - +
103B PHE* 3.4 33.5 - - + +
104B VAL* 4.9 3.1 + - - +
105B PHE* 5.6 1.4 + - - -
185B CYS* 3.5 34.5 - - - +
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Residues in contact with SER 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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29B TYR* 5.1 0.3 + - - -
37B PHE* 3.5 26.3 - - - +
40B LEU* 4.0 12.0 + - - +
41B ALA* 3.8 25.9 + - - -
44B MET* 4.8 0.2 - - - +
94B THR* 2.8 22.7 + - - -
95B LEU 3.8 4.0 - - - -
97B THR* 1.3 77.9 - - - +
99B LEU* 1.3 62.0 + - - +
100B HIS 3.2 0.7 + - - -
101B GLY 3.4 7.6 + - - -
185B CYS* 3.6 26.6 - - - +
293B PHE* 4.1 6.9 - - - -
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Residues in contact with LEU 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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308A MET* 3.1 36.1 - - + +
314A ARG* 3.6 54.8 + - - +
29B TYR* 4.1 7.2 + - - -
38B SER* 6.1 1.8 - - - +
41B ALA* 3.9 3.6 - - + -
95B LEU* 3.0 43.5 + - + +
96B TYR* 3.4 15.0 - - + +
97B THR 3.2 0.2 - - - -
98B SER* 1.3 77.0 - - - +
100B HIS* 1.3 68.5 + - + +
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Residues in contact with HIS 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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311A LYS* 3.8 1.8 - - - -
314A ARG* 5.9 1.7 + - - -
330A ASP* 2.9 17.9 + - - -
959A ZN 2.4 36.9 - - - -
27B PRO* 3.7 9.4 - - - +
29B TYR* 3.4 13.9 + - - -
96B TYR* 2.7 58.6 + + - +
97B THR 3.0 4.0 + - - +
99B LEU* 1.3 86.8 + - + +
101B GLY* 1.3 60.5 + - - +
102B TYR* 3.4 19.6 - - + +
104B VAL* 3.6 22.7 - - + +
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Residues in contact with GLY 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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28B GLN* 2.7 36.7 + - - +
29B TYR* 3.9 13.2 + - - -
37B PHE* 3.7 28.2 - - - -
97B THR 2.8 6.1 + - - -
98B SER 3.4 4.8 + - - -
99B LEU 3.6 0.2 - - - -
100B HIS* 1.3 78.3 - - - +
102B TYR* 1.3 58.8 + - - +
185B CYS* 4.3 3.0 - - - -
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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