Contacts of the helix formed by residues 77 - 91 (chain B) in PDB entry 3BWB
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 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TRP* 4.6 6.7 - - + -
73B VAL* 5.4 0.3 - - - -
74B THR* 2.6 31.5 + - - +
76B TYR* 1.3 80.1 - - + +
78B GLU* 1.3 68.8 + - - +
79B PHE* 3.1 9.2 + - - -
80B VAL* 3.1 19.7 + - - +
81B TYR* 4.4 1.6 + - - +
242B VAL* 3.4 17.8 - - - +
243B PRO* 3.7 24.5 - - + -
244B THR* 2.5 38.0 + - - +
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLN 6.1 0.4 - - - -
73B VAL* 4.2 10.8 - - + +
74B THR 3.0 21.3 + - - +
75B ASP* 4.1 13.6 + - - +
76B TYR 3.6 1.4 - - - -
77B ASP* 1.3 82.3 + - - +
79B PHE* 1.3 79.8 + - - +
80B VAL 3.3 1.0 + - - -
81B TYR* 3.7 6.1 + - - +
82B HIS* 3.1 47.8 + - + +
111B ARG* 3.2 28.5 + - - -
141B GLN* 5.5 3.1 - - - +
142B ILE* 3.5 30.3 - - + +
280B LYS* 5.3 2.3 + - - -
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A TRP* 3.9 16.4 - + - -
296A PHE* 3.8 29.6 - + + -
75B ASP 5.2 2.5 - - - -
76B TYR* 3.0 26.9 - + - -
77B ASP* 4.4 0.9 - - - -
78B GLU* 1.3 92.1 + - - +
80B VAL* 1.3 82.4 + - + +
82B HIS* 4.1 1.1 - - - -
83B GLU* 3.0 41.5 + - + +
111B ARG* 4.7 6.3 - - - +
280B LYS* 3.8 39.7 - - + +
281B TYR* 3.7 21.8 - - + -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A TRP* 3.7 12.8 - - + -
77B ASP* 3.1 15.8 + - + +
79B PHE* 1.3 93.4 - - + +
81B TYR* 1.3 64.7 + - - +
83B GLU* 4.0 0.5 - - - +
84B VAL* 3.0 31.5 + - - +
240B MSE 4.3 7.2 - - + -
241B HIS 3.3 26.5 - - - +
242B VAL* 3.7 15.7 - - + -
281B TYR* 3.5 44.2 - - + -
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Residues in contact with TYR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLN* 5.9 8.1 - - - +
77B ASP 4.4 1.3 + - - +
78B GLU* 3.7 7.9 + - - +
79B PHE 3.5 0.2 - - - -
80B VAL* 1.3 79.3 - - - +
82B HIS* 1.3 77.6 + + + +
84B VAL* 4.1 0.9 - - - +
85B LEU* 3.2 47.3 + - + +
109B VAL* 4.9 0.2 - - + -
176B ASP* 2.7 35.1 + - - -
209B GLN* 3.0 35.0 + - + +
240B MSE 3.9 24.0 - - + -
242B VAL* 4.6 9.4 - - + +
250B ILE* 4.1 28.5 - - + -
251B GLY 5.3 0.9 - - - -
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Residues in contact with HIS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 4.6 9.1 - - + +
78B GLU* 3.1 45.7 + - + +
79B PHE 4.3 1.1 - - - +
80B VAL 3.3 0.6 - - - -
81B TYR* 1.3 90.2 - + + +
83B GLU* 1.3 60.2 + - - +
85B LEU* 4.3 0.3 - - - +
86B GLY* 3.1 22.2 + - - -
106B ASP* 3.8 18.3 + - - -
108B GLY* 3.5 42.6 - - - +
109B VAL* 3.7 21.7 - - + -
111B ARG* 4.1 6.8 + - - +
112B GLU* 3.5 17.3 - - + +
142B ILE* 4.0 9.2 - - + +
176B ASP* 5.2 1.1 + - - -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.0 37.2 + - - +
80B VAL 4.0 1.6 - - - +
82B HIS* 1.3 73.3 - - - +
84B VAL* 1.3 60.8 + - - +
87B HIS* 2.9 44.1 + - + +
112B GLU* 3.7 26.5 - - - +
115B ARG* 5.5 1.2 + - - -
278B ASP 4.8 0.3 - - - +
279B LEU* 3.7 13.9 - - - +
280B LYS* 3.0 26.2 + - - +
281B TYR* 2.8 27.5 + - + +
282B TYR* 3.0 21.7 + - + +
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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
----------------------------------------------------------
80B VAL 3.0 24.7 + - - +
81B TYR 4.1 0.4 - - - +
83B GLU* 1.3 75.7 - - - +
85B LEU* 1.3 62.6 + - - +
88B THR* 2.6 43.3 + - - +
238B ALA* 5.0 5.8 - - + +
239B LEU 5.5 1.6 - - - +
240B MSE 3.3 42.6 - - + -
252B THR* 4.0 12.2 - - + +
281B TYR* 3.6 30.7 - - + -
282B TYR* 4.8 6.3 - - + -
290B SER* 5.9 2.9 - - - -
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 3.2 54.4 + - + +
84B VAL* 1.3 80.5 - - - +
86B GLY* 1.3 59.7 + - - +
89B SER* 2.8 26.9 + - - -
109B VAL* 4.1 20.2 - - + -
174B ILE* 4.2 19.6 - - + +
175B ILE 5.1 1.1 - - - +
176B ASP* 4.2 9.6 - - + +
207B CYS* 3.4 15.4 - - - -
209B GLN* 4.7 9.0 - - + +
240B MSE 4.7 4.9 - - + -
252B THR* 3.1 38.1 - - + +
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Residues in contact with GLY 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B HIS 3.1 16.3 + - - -
85B LEU* 1.3 79.6 - - - +
87B HIS* 1.3 61.8 + - - +
89B SER* 3.3 3.2 + - - -
90B LEU* 3.2 34.0 - - - +
109B VAL* 4.4 6.5 - - - +
112B GLU* 4.4 7.6 - - - -
113B VAL* 4.3 19.5 - - - -
116B HIS* 5.0 0.2 - - - -
174B ILE* 4.4 0.4 - - - -
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Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLU* 2.9 34.5 + - + +
86B GLY* 1.3 71.1 - - - +
88B THR* 1.3 61.1 + - - +
89B SER 3.2 2.2 - - - -
91B CYS* 2.8 37.6 + - - +
112B GLU* 2.9 45.5 + - + +
115B ARG* 4.1 2.0 - - - -
116B HIS* 2.7 34.4 + + - -
270B VAL* 5.3 0.2 - - + -
275B PHE* 3.4 21.1 - + - -
279B LEU* 3.4 22.8 - - + +
282B TYR* 3.7 24.5 - + + -
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Residues in contact with THR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 2.6 37.2 + - - +
85B LEU 4.9 0.2 - - - -
87B HIS* 1.3 77.9 - - - +
89B SER* 1.3 56.4 + - - +
92B SER* 2.6 31.3 + - - +
238B ALA* 4.7 5.8 - - + -
252B THR* 5.3 0.9 - - - -
254B VAL* 4.0 14.7 - - + +
282B TYR* 3.6 14.0 - - - -
287B HIS* 3.5 29.3 - - + +
290B SER* 5.1 2.6 + - - +
291B PHE* 3.8 25.1 - - + -
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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
----------------------------------------------------------
85B LEU 2.8 23.5 + - - -
86B GLY 3.3 4.3 + - - -
88B THR* 1.3 78.9 - - - +
90B LEU* 1.3 79.4 + - - +
92B SER* 3.3 11.9 + - - -
93B HIS* 3.5 11.4 + - - +
172B VAL* 3.9 14.8 - - - +
174B ILE* 4.0 3.8 - - - +
205B ILE* 4.0 19.9 - - - +
207B CYS* 3.7 24.0 - - - -
254B VAL* 5.0 5.3 - - - +
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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
----------------------------------------------------------
86B GLY 3.2 19.7 + - - +
87B HIS 4.3 0.2 - - - +
89B SER* 1.3 89.3 + - - +
91B CYS* 1.3 58.0 + - - +
93B HIS* 3.1 21.5 + - - +
96B PRO* 3.8 16.7 - - + +
99B VAL* 4.7 3.6 - - + -
113B VAL* 3.7 38.6 - - + +
116B HIS* 3.5 42.4 - - + +
119B VAL* 3.9 10.5 - - + -
172B VAL* 3.9 22.2 - - + -
174B ILE* 4.3 2.0 - - + -
268B ARG* 3.2 16.2 + - - -
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Residues in contact with CYS 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 HIS* 2.8 29.3 + - - +
88B THR 4.6 1.3 - - - +
90B LEU* 1.3 72.4 - - - +
92B SER* 1.3 57.3 + - - +
93B HIS 3.4 1.3 - - - -
116B HIS* 4.0 20.0 - - - -
266B PRO* 4.7 6.5 - - + -
267B LEU* 2.9 8.1 + - - +
268B ARG* 2.8 54.2 + - - +
270B VAL* 4.0 22.2 - - - -
273B MSE 5.9 1.1 - - - -
282B TYR* 3.6 22.0 - - - +
287B HIS* 4.9 0.7 - - + -
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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
------------------------------------------------------------
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