Contacts of the helix formed by residues 87 - 100 (chain B) in PDB entry 3OLJ
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 TYR 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B PRO* 3.6 26.2 + - + +
72B LEU* 4.8 4.9 - - + -
74B ARG* 5.1 3.3 + - - -
85B ILE* 4.1 1.8 - - - -
86B GLU* 1.3 87.2 - - + +
88B HIS* 1.3 60.2 + - - +
89B ASP* 3.3 5.8 - - - +
90B ILE* 3.4 31.4 + - + -
91B TRP* 3.0 27.9 + - - +
155B ILE* 3.7 26.2 - - + +
157B GLU* 3.1 28.2 + - - +
279B HIS* 4.0 25.1 - + - -
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Residues in contact with HIS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 3.4 43.2 + - + +
86B GLU* 3.6 16.0 + - - -
87B TYR* 1.3 69.9 - - - +
89B ASP* 1.3 60.7 + - - +
91B TRP* 4.2 0.9 - + - -
92B GLN* 2.9 50.1 + - + +
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Residues in contact with ASP 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TYR* 3.8 11.8 - - - -
88B HIS* 1.3 72.7 + - - +
90B ILE* 1.3 70.5 + - - +
92B GLN* 3.4 7.7 + - - +
93B MET* 3.4 18.7 + - - +
275B LEU* 3.4 25.5 - - + +
278B LYS* 5.1 2.1 - - - -
279B HIS* 2.6 39.0 + - - -
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Residues in contact with ILE 90 (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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72B LEU* 4.6 1.1 - - + -
87B TYR* 3.4 27.3 + - + +
88B HIS 3.4 0.2 - - - -
89B ASP* 1.3 80.3 + - - +
91B TRP* 1.3 65.5 + - - +
93B MET* 3.3 6.6 + - - +
94B TYR* 3.3 17.5 + - - +
155B ILE* 3.2 26.5 - - + -
157B GLU* 3.6 6.3 - - + -
158B ALA* 3.6 28.5 - - - +
272B PHE* 3.6 20.9 - - + -
275B LEU* 3.7 13.0 - - + -
276B MET* 3.5 20.9 - - + -
279B HIS* 4.3 13.5 - - + +
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Residues in contact with TRP 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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82B ILE* 4.0 21.1 - - + -
83B PHE* 4.4 7.7 - + - -
85B ILE* 3.5 50.1 - - + +
87B TYR 3.0 18.6 + - - +
88B HIS* 3.8 3.8 - + - +
90B ILE* 1.3 78.4 - - - +
92B GLN* 1.3 72.9 + - - +
94B TYR* 3.1 35.4 + + - +
95B LYS* 2.9 50.4 + - + +
156B THR* 5.6 0.7 - - + -
157B GLU* 3.9 18.6 - - + +
160B CYS* 4.0 17.9 - - - -
174C GLU* 3.6 26.4 + - - -
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Residues in contact with GLN 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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88B HIS* 2.9 45.0 + - + +
89B ASP* 3.8 7.9 - - - +
90B ILE 3.3 0.4 - - - -
91B TRP* 1.3 93.6 - - - +
93B MET* 1.3 57.5 + - + +
95B LYS* 3.3 14.4 + - - +
96B LYS* 2.9 28.6 + - - +
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Residues in contact with MET 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 ASP 3.4 11.6 + - - +
90B ILE* 3.3 10.0 + - - +
91B TRP 3.2 0.4 - - - -
92B GLN* 1.3 77.0 - - + +
94B TYR* 1.3 58.9 + - - +
96B LYS* 3.3 8.1 + - - +
97B ALA 2.9 23.6 + - - -
161B PHE* 3.4 11.5 - - + -
268B LEU* 3.3 53.3 - - + +
271B ASP* 3.6 14.4 - - + +
272B PHE* 3.5 37.9 - - + +
275B LEU* 4.0 16.4 - - + -
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Residues in contact with TYR 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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82B ILE* 5.7 0.4 - - + -
90B ILE 3.3 7.7 + - - +
91B TRP* 3.1 49.0 + + - +
93B MET* 1.3 76.3 - - - +
95B LYS* 1.3 64.7 + - + +
97B ALA* 3.2 2.5 + - + +
98B GLU* 2.9 46.4 + - + +
157B GLU 4.3 5.6 - - - +
160B CYS* 3.7 35.2 - - + -
161B PHE* 3.5 25.2 - - + +
164B PHE* 4.0 24.1 - + + -
167C ALA 4.7 1.2 + - - -
170C ASN* 4.3 11.8 - - + +
171C ILE* 3.7 27.5 + - - +
174C GLU* 4.5 4.6 + - - -
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Residues in contact with LYS 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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91B TRP* 2.9 53.5 + - + +
92B GLN* 3.7 15.5 - - - +
93B MET 3.3 0.2 - - - -
94B TYR* 1.3 79.3 - - + +
96B LYS* 1.3 57.3 + - - +
98B GLU* 2.7 28.0 + - - +
99B ALA* 3.0 29.5 + - - +
105C GLU* 2.5 32.7 + - - -
174C GLU* 2.7 25.9 + - - -
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Residues in contact with LYS 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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92B GLN 2.9 17.0 + - - +
93B MET* 3.4 9.2 - - - +
94B TYR 3.2 0.2 - - - -
95B LYS* 1.3 74.7 - - - +
97B ALA* 1.3 64.0 + - - +
99B ALA* 3.3 8.7 + - + +
100B SER* 2.9 32.6 + - - -
264B ARG* 5.7 8.6 - - - +
268B LEU* 3.8 24.5 - - + -
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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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93B MET 2.9 14.0 + - - +
94B TYR* 3.4 8.3 - - - +
96B LYS* 1.3 75.9 - - - +
98B GLU* 1.3 62.6 + - - +
100B SER* 3.0 18.2 + - - -
101B PHE 3.5 6.9 + - - -
161B PHE* 4.0 13.5 - - + +
164B PHE* 3.5 26.8 - - + -
165B GLN 6.1 0.2 - - - +
168B MET* 5.6 1.2 - - + +
268B LEU* 3.7 20.1 - - + +
269B HIS* 5.9 2.9 - - - +
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Residues in contact with GLU 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 TYR* 2.9 37.2 + - + +
95B LYS* 2.7 40.5 + - - +
97B ALA* 1.3 72.4 - - - +
99B ALA* 1.3 61.1 + - - +
100B SER 3.4 0.5 + - - -
101B PHE* 3.4 18.4 + - - +
164B PHE* 3.6 24.3 - - + -
101C PHE* 4.1 6.8 - - + -
103C THR* 3.5 29.5 - - + +
104C ALA 4.6 0.2 + - - -
105C GLU* 4.2 1.6 - - - +
171C ILE* 3.4 24.0 - - + +
174C GLU* 3.9 6.2 - - - +
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Residues in contact with ALA 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 LYS 3.0 19.3 + - - +
96B LYS* 3.7 10.8 - - + +
97B ALA 3.2 0.4 - - - -
98B GLU* 1.3 75.7 - - - +
100B SER* 1.3 59.2 + - - +
101B PHE 3.4 2.7 + - - +
103C THR* 6.0 1.1 - - - -
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Residues in contact with SER 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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96B LYS* 2.9 25.8 + - - -
97B ALA* 3.0 11.2 + - - -
99B ALA* 1.3 78.3 - - - +
101B PHE* 1.3 65.3 + - - +
102B TRP* 3.2 18.5 - - - +
168B MET* 5.0 0.8 - - - +
264B ARG* 3.3 35.5 + - - +
265B ASP* 4.6 3.6 + - - +
268B LEU* 5.1 3.3 - - - +
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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