Contacts of the helix formed by residues 82 - 97 (chain B) in PDB entry 4OL0
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 SER 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B LEU* 4.7 5.4 - - - +
79B PRO* 2.7 38.7 + - - +
80B THR 2.8 1.8 + - - -
81B ASP* 1.3 80.2 + - - +
83B HIS* 1.3 65.5 + - - +
84B ALA 3.1 3.4 - - - -
85B SER* 2.6 35.0 + - - -
86B LEU* 3.9 1.0 + - - +
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Residues in contact with HIS 83 (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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75B PHE* 3.3 39.8 - + - -
78B LEU* 3.3 41.5 + - + +
79B PRO 2.7 23.8 + - - -
80B THR* 2.6 29.4 + - + +
82B SER* 1.3 76.7 - - - +
84B ALA* 1.3 55.0 + - - +
86B LEU* 2.8 36.2 + - - +
87B ARG* 3.5 6.5 + - - +
115B LEU* 5.1 3.6 - - + +
119B MET* 4.3 25.5 - - + +
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Residues in contact with ALA 84 (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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81B ASP 4.1 12.9 + - - +
83B HIS* 1.3 77.4 - - - +
85B SER* 1.3 58.9 - - - +
86B LEU 3.5 0.2 + - - -
87B ARG* 3.6 24.7 + - - +
88B ASP* 2.8 32.7 + - - +
119B MET* 6.0 0.9 - - - -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 2.6 27.4 + - - -
84B ALA* 1.3 76.9 - - - +
86B LEU* 1.3 57.5 + - - +
88B ASP* 3.6 9.2 + - - +
89B SER* 2.7 33.3 + - - -
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TRP* 4.1 11.2 - - + -
67B MET* 3.5 26.9 - - + -
71B ILE* 3.7 24.5 - - + -
78B LEU* 4.5 13.9 - - + -
82B SER 5.0 0.4 - - - +
83B HIS* 2.8 15.8 + - - +
85B SER* 1.3 79.6 + - - +
87B ARG* 1.3 57.3 + - - +
89B SER* 2.7 29.5 + - - -
90B LEU* 2.9 25.1 + - + +
115B LEU* 3.7 28.5 - - + -
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Residues in contact with ARG 87 (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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83B HIS 3.5 3.6 + - - +
84B ALA* 3.6 32.8 + - - +
86B LEU* 1.3 78.6 - - - +
88B ASP* 1.3 82.8 + - - +
90B LEU* 3.6 3.6 + - - +
91B LEU* 3.0 56.3 + - + +
112B ILE* 5.7 5.4 - - + -
115B LEU* 3.9 17.7 - - + +
119B MET* 3.7 25.9 - - + +
121B SER* 5.1 6.0 + - - -
125B CYS* 4.7 13.0 - - - +
128B THR* 5.9 2.9 - - - -
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Residues in contact with ASP 88 (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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84B ALA* 2.8 20.7 + - - +
85B SER* 3.8 9.8 - - - +
86B LEU 3.1 0.6 - - - -
87B ARG* 1.3 102.8 + - - +
89B SER* 1.3 52.6 + - - +
91B LEU* 3.7 10.9 + - - +
92B THR* 2.6 37.1 + - - +
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Residues in contact with SER 89 (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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48B ASP* 5.1 4.6 + - - -
85B SER* 2.7 20.1 + - - -
86B LEU* 2.7 21.6 + - - +
88B ASP* 1.3 69.6 - - - +
90B LEU* 1.3 57.8 + - - -
92B THR* 2.7 26.4 + - - -
93B HIS* 2.7 37.7 + - - -
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Residues in contact with LEU 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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67B MET* 4.0 22.0 - - + -
71B ILE* 5.0 2.5 - - + -
86B LEU* 2.9 33.5 + - + +
87B ARG* 4.0 3.6 - - - +
89B SER* 1.3 77.5 - - - +
91B LEU* 1.3 58.1 + - - +
93B HIS* 4.0 15.2 - - + +
94B ILE* 2.9 33.9 + - - +
108B LEU* 4.7 11.4 - - + +
111B ALA* 3.6 33.9 - - + +
112B ILE* 3.7 28.1 - - + +
115B LEU* 4.4 18.6 - - + -
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Residues in contact with LEU 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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87B ARG* 3.0 47.0 + - + +
88B ASP* 3.7 13.5 - - - +
89B SER 3.1 0.2 - - - -
90B LEU* 1.3 76.5 - - - +
92B THR* 1.3 57.0 - - - +
94B ILE* 3.5 7.4 - - + +
95B GLN* 3.1 33.8 + - - +
112B ILE* 3.8 33.7 - - + -
129B LEU* 4.6 12.3 - - + -
132B LYS* 4.9 11.0 - - + -
133B TYR* 3.4 30.2 + - + +
142B PHE* 6.5 0.2 - - + -
146B ILE* 5.7 0.2 - - + -
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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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88B ASP* 2.6 19.7 + - - +
89B SER* 2.7 17.2 + - - -
91B LEU* 1.3 71.1 - - - +
93B HIS* 1.3 62.2 + - + +
95B GLN* 2.7 34.9 + - - +
96B ASN* 3.0 29.7 + - - +
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Residues in contact with HIS 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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48B ASP* 3.1 32.5 + - + -
51B LEU* 3.3 49.5 - - + +
52B GLN* 4.3 9.3 + - + +
54B ARG* 6.1 1.6 - - - -
67B MET* 6.0 1.1 - - + -
89B SER* 2.7 37.0 + - - +
90B LEU* 4.0 9.8 + - + +
92B THR* 1.3 76.7 - - + +
94B ILE* 1.3 58.5 + - - +
96B ASN* 2.8 8.1 + - - -
97B LEU* 2.8 42.2 + - + +
108B LEU* 4.0 17.9 - - + +
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Residues in contact with ILE 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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90B LEU 2.9 25.0 + - - +
91B LEU* 3.5 15.9 - - + +
93B HIS* 1.3 76.7 - - - +
95B GLN* 1.3 58.8 + - - +
97B LEU* 4.2 2.9 - - - +
98B LYS* 3.0 23.7 + - - +
105B VAL* 3.8 29.4 - - + +
108B LEU* 3.6 23.0 - - + +
109B ALA* 4.0 7.2 - - + +
112B ILE* 4.0 20.9 - - + -
133B TYR* 5.6 0.2 - - - +
142B PHE* 3.8 49.4 - - + -
146B ILE* 4.5 2.7 - - + -
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Residues in contact with GLN 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 LEU 3.1 17.5 + - - +
92B THR* 2.7 23.0 + - - +
94B ILE* 1.3 80.8 - - - +
96B ASN* 1.3 64.9 + - - +
98B LYS* 3.0 26.0 - - + +
132B LYS* 3.8 8.0 + - - -
133B TYR* 2.6 40.4 + - + +
139B SER* 5.3 3.1 - - - +
142B PHE* 4.5 9.2 - - + -
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Residues in contact with ASN 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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54B ARG* 3.4 35.3 + - - +
92B THR* 3.5 30.9 + - - +
93B HIS* 2.8 8.0 + - - +
95B GLN* 1.3 88.1 + - - +
97B LEU* 1.3 63.4 + - + +
98B LYS* 3.2 8.4 + - - +
99B ASP 4.9 1.2 + - - -
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Residues in contact with LEU 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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51B LEU* 4.1 28.9 - - + +
54B ARG* 4.3 13.2 - - + +
60B CYS* 3.7 29.6 - - + -
93B HIS* 2.8 31.9 + - + +
94B ILE* 4.4 3.1 - - - -
96B ASN* 1.3 86.1 - - + +
98B LYS* 1.3 65.3 + - - +
99B ASP 3.5 1.8 - - - -
100B LEU* 3.8 26.2 + - + +
101B SER 4.5 1.6 + - - +
104B ILE* 3.7 29.6 - - + +
105B VAL* 3.5 14.1 + - - +
108B LEU* 4.6 4.3 - - + -
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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