Contacts of the helix formed by residues 77 - 93 (chain B) in PDB entry 3BIL
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 ASN 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B SER* 3.1 21.5 + - - +
75B LEU 3.1 7.1 - - - +
76B ILE* 1.3 75.2 - - - +
78B HIS* 1.3 67.9 + - - +
79B TYR* 3.0 25.9 + - - +
80B PHE* 3.1 32.6 + - + -
81B ALA 3.0 18.7 + - - -
248B ASP* 6.1 2.8 - - - +
249B SER* 3.4 14.3 + - - +
250B MET* 4.0 28.2 - - + +
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Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 4.6 33.6 - - + +
75B LEU 5.0 0.2 - - - -
76B ILE 3.3 7.3 + - - +
77B ASN* 1.3 73.8 + - - +
79B TYR* 1.3 60.6 + - - +
81B ALA* 3.2 6.0 + - - +
82B ALA* 2.8 38.2 + - + +
249B SER* 5.1 2.9 + - - +
250B MET* 4.6 6.0 - - + +
276B ASP* 6.3 0.8 - - - +
277B THR* 4.2 9.4 + - - -
278B HIS* 4.1 38.9 + + + +
279B PRO* 3.6 33.1 - - + +
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Residues in contact with TYR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 3.0 12.9 + - - +
78B HIS* 1.3 84.7 + - - +
80B PHE* 1.3 79.4 + + - +
82B ALA* 3.5 5.2 + - - +
83B MET* 2.9 56.9 + - + +
151B ASP* 2.5 30.0 + - - -
249B SER* 3.8 13.3 + - - +
276B ASP* 3.3 24.9 - - + +
293B GLN* 3.2 29.9 + - + -
295B VAL* 3.6 30.7 - - + +
298B LEU* 3.6 12.3 - - - +
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 3.6 20.7 - - + +
73B PRO* 3.5 26.5 - - + -
74B SER* 3.2 24.5 - - - +
75B LEU* 5.1 0.2 - - - -
77B ASN* 3.1 38.7 + - + +
79B TYR* 1.3 97.6 - + - +
81B ALA* 1.3 60.8 + - - +
83B MET* 3.7 9.3 - - + +
84B VAL* 3.1 33.3 + - - +
105B GLU* 5.4 1.3 - - - -
128B VAL* 3.8 21.3 - - + -
151B ASP* 3.5 21.5 - - - -
152B ARG* 4.3 14.1 - - - -
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.3 33.6 - - + +
76A ILE* 4.0 6.7 - - - +
74B SER 4.8 0.4 + - - -
75B LEU* 3.6 21.7 + - - +
77B ASN 3.0 10.5 + - - +
78B HIS* 3.6 7.6 - - - +
80B PHE* 1.3 75.0 - - - +
82B ALA* 1.3 58.4 + - - +
84B VAL* 3.4 9.9 - - - +
85B THR* 2.7 34.6 + - - -
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 3.9 13.3 - - + +
78B HIS* 2.8 31.8 + - + +
79B TYR* 3.7 6.3 - - - +
81B ALA* 1.3 74.7 - - - +
83B MET* 1.3 65.8 + - - +
85B THR* 3.3 0.6 + - - -
86B GLU* 2.7 35.6 + - - +
295B VAL* 4.5 15.7 - - + -
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Residues in contact with MET 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 6.5 0.2 - - - -
72B VAL* 4.9 4.5 - - - -
79B TYR* 2.9 58.3 + - + +
80B PHE* 3.8 21.3 - - + +
81B ALA 3.4 0.4 - - - -
82B ALA* 1.3 76.5 - - - +
84B VAL* 1.3 58.2 + - + +
86B GLU* 3.3 4.2 + - - +
87B ILE* 2.9 45.4 + - + +
128B VAL* 4.5 4.0 - - - -
150B VAL* 3.9 29.8 - - + -
151B ASP* 4.2 9.4 - - + +
295B VAL* 3.6 17.2 - - + +
298B LEU* 5.1 7.2 - - + -
299B ALA* 3.9 9.5 - - + +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.8 28.5 - - + -
102A ASN* 5.5 0.6 + - - -
70B VAL* 3.6 29.3 - - + +
72B VAL* 3.8 22.2 - - + -
75B LEU* 4.3 5.6 - - + -
80B PHE 3.1 17.5 + - - +
81B ALA* 3.4 13.9 - - - +
83B MET* 1.3 74.2 - - + +
85B THR* 1.3 68.2 + - - +
87B ILE* 3.8 9.2 - - + +
88B GLN* 3.1 23.4 + - - +
98B THR* 5.2 2.6 - - - +
100B ILE* 4.4 15.5 - - + +
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.6 1.7 + - - +
76A ILE* 3.7 25.2 + - + +
102A ASN* 4.1 16.5 + - - +
104A ASN* 4.3 21.4 + - - +
81B ALA 2.7 22.7 + - - -
82B ALA* 3.7 2.0 - - - -
83B MET 3.3 0.2 - - - -
84B VAL* 1.3 77.8 - - - +
86B GLU* 1.3 74.0 + - - +
88B GLN* 3.4 4.2 + - - +
89B SER* 3.0 30.4 + - - -
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 5.7 0.7 - - - +
82B ALA* 2.7 36.2 + - - +
83B MET* 4.9 0.4 - - - -
85B THR* 1.3 87.9 - - - +
87B ILE* 1.3 62.4 + - - +
89B SER* 3.7 7.6 - - - -
90B THR* 2.8 33.5 + - - +
295B VAL* 5.0 1.1 - - + +
296B GLU* 3.9 45.0 - - + +
299B ALA* 3.7 20.6 - - + +
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 4.2 8.7 - - + -
70B VAL* 4.1 31.4 - - + -
83B MET* 2.9 40.0 + - + +
84B VAL* 3.8 5.4 - - + +
86B GLU* 1.3 74.4 - - - +
88B GLN* 1.3 65.4 + - - +
90B THR* 3.9 1.6 - - - -
91B ALA* 3.1 23.0 + - - +
98B THR* 5.3 0.2 - - - +
126B ILE* 3.8 34.5 - - + -
150B VAL* 4.9 1.1 - - + -
299B ALA* 3.6 24.0 - - + +
302B ALA* 5.2 2.2 - - + -
303B VAL* 3.9 18.9 - - + +
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Residues in contact with GLN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASN* 2.9 40.4 + - - +
104A ASN* 2.8 29.1 + - - +
109A THR* 4.1 14.5 - - - +
84B VAL 3.1 18.1 + - - +
85B THR* 3.6 5.8 - - - +
86B GLU 3.4 0.2 - - - -
87B ILE* 1.3 76.7 - - - +
89B SER* 1.3 65.1 + - - +
91B ALA* 3.4 1.9 + - - +
92B SER* 3.1 25.5 + - - -
96B LEU 4.3 1.8 - - - +
97B ALA* 5.8 0.7 - - - -
98B THR* 3.7 41.2 + - + +
100B ILE* 4.1 5.0 - - + +
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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
----------------------------------------------------------
104A ASN* 6.0 1.1 - - - -
85B THR* 3.0 19.9 + - - -
86B GLU* 3.7 10.8 - - - -
87B ILE 3.3 0.2 - - - -
88B GLN* 1.3 76.8 - - - +
90B THR* 1.3 62.4 + - - +
92B SER* 2.8 25.2 + - - -
93B LYS* 3.1 28.0 + - - +
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLU* 2.8 22.4 + - - +
87B ILE* 3.9 3.1 - - - -
89B SER* 1.3 79.0 + - - +
91B ALA* 1.3 59.4 + - - +
93B LYS* 3.4 14.4 + - - +
94B ALA* 3.3 18.7 + - - +
300B GLN* 3.7 37.3 + - + +
303B VAL* 3.5 28.2 - - + +
304B SER 5.6 0.4 - - - +
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 4.1 20.0 - - + -
87B ILE 3.1 18.0 + - - +
88B GLN 3.9 2.7 - - - +
89B SER 3.3 0.2 - - - -
90B THR* 1.3 74.8 - - - +
92B SER* 1.3 55.1 + - - +
93B LYS 3.2 0.4 - - - -
94B ALA* 3.2 6.9 + - - +
95B GLY 3.1 8.8 + - - -
96B LEU* 2.6 53.1 + - + +
98B THR* 4.5 2.0 - - - +
303B VAL* 4.0 14.8 - - + +
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLN* 3.1 16.8 + - - -
89B SER* 2.8 20.6 + - - -
91B ALA* 1.3 75.1 - - - +
93B LYS* 1.3 59.9 + - - +
94B ALA 3.1 2.0 - - - -
95B GLY* 3.1 14.0 + - - -
96B LEU 3.5 15.2 + - - +
97B ALA* 5.9 0.4 - - - -
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Residues in contact with LYS 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 SER* 3.1 26.5 + - - +
90B THR* 3.5 14.4 - - - +
91B ALA 3.2 0.2 - - - -
92B SER* 1.3 83.9 + - - +
94B ALA* 1.3 54.8 + - - +
95B GLY 3.5 1.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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