Contacts of the helix formed by residues 78 - 91 (chain A) 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 GLU 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLN 6.1 0.2 - - - -
73A VAL* 4.0 7.2 - - + +
74A THR 2.8 23.9 + - - +
75A ASP* 4.3 11.7 - - - +
76A TYR 3.6 1.0 - - - -
77A ASP* 1.3 78.6 + - - +
79A PHE* 1.3 69.2 + - - +
80A VAL 3.2 1.2 + - - -
81A TYR* 3.7 5.3 + - - +
82A HIS* 2.8 60.8 + - + -
111A ARG* 3.1 23.7 + - - -
141A GLN* 5.9 2.3 - - - +
142A ILE* 3.5 31.7 - - + +
280A LYS* 6.1 0.5 - - - -
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Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ASP 5.2 2.9 - - - -
76A TYR* 3.0 28.7 - + - -
77A ASP* 4.2 1.6 - - - -
78A GLU* 1.3 93.0 + - - +
80A VAL* 1.3 90.8 + - + +
81A TYR 3.5 0.2 - - - -
82A HIS* 4.0 1.6 - - - -
83A GLU* 3.0 41.1 + - + +
111A ARG* 4.9 4.5 - - - +
280A LYS* 3.5 44.6 - - + -
281A TYR* 3.8 16.4 - - + -
214B TRP* 3.6 23.8 - + - -
296B PHE* 3.8 21.1 - + - -
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP* 3.1 13.2 + - + +
79A PHE* 1.3 101.9 - - + +
81A TYR* 1.3 64.0 + - - +
83A GLU* 4.0 0.7 - - - +
84A VAL* 3.0 29.8 + - - +
240A MSE 4.3 6.5 - - + -
241A HIS 3.3 23.1 - - - +
242A VAL* 3.8 14.4 - - + -
281A TYR* 3.5 34.3 - - + +
214B TRP* 3.5 21.5 - - + -
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLN 6.1 0.9 - - - -
77A ASP 4.4 1.7 + - - +
78A GLU 3.7 6.5 + - - +
80A VAL* 1.3 80.0 - - - +
82A HIS* 1.3 79.5 + + + +
84A VAL* 4.2 0.2 - - - -
85A LEU* 3.2 51.0 + - + +
176A ASP* 2.6 34.9 + - - -
209A GLN* 2.7 32.9 + - + +
240A MSE 3.9 24.2 - - + -
242A VAL* 4.6 10.1 - - + +
250A ILE* 4.1 29.8 - - + -
251A GLY 5.0 1.1 - - - -
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Residues in contact with HIS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 4.9 8.9 - - + +
78A GLU* 2.8 52.4 + - + +
79A PHE 3.6 3.1 + - - +
80A VAL 3.3 0.4 - - - -
81A TYR* 1.3 94.2 - + - +
83A GLU* 1.3 59.3 + - - +
85A LEU* 4.3 0.5 - - - +
86A GLY* 3.1 22.3 + - - -
106A ASP* 3.5 21.3 + - - -
108A GLY* 3.5 40.3 - - - +
109A VAL* 3.8 14.7 - - + -
112A GLU* 3.4 18.6 - - + +
142A ILE* 4.1 5.8 - - + -
176A ASP* 5.5 1.5 + - - -
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE* 3.0 35.0 + - - +
80A VAL 4.0 1.6 - - - +
82A HIS* 1.3 74.1 - - - +
84A VAL* 1.3 61.5 + - - +
87A HIS* 2.8 49.3 + - + +
112A GLU* 3.6 26.1 - - - +
115A ARG* 6.0 0.2 + - - -
279A LEU* 3.8 10.8 - - + +
280A LYS* 3.0 28.3 + - - +
281A TYR* 2.8 27.1 + - + +
282A TYR* 2.9 19.9 + - + +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL 3.0 21.0 + - - +
81A TYR 4.2 0.4 - - - +
83A GLU* 1.3 76.8 - - - +
85A LEU* 1.3 60.4 + - - +
88A THR* 2.7 44.8 + - - +
238A ALA* 5.0 6.1 - - + -
239A LEU 5.4 1.8 - - - +
240A MSE 3.4 43.5 - - + -
252A THR* 4.0 11.1 - - + +
281A TYR* 3.6 31.9 - - + -
282A TYR* 4.6 6.7 - - + -
290A SER* 6.0 2.5 - - - -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A TYR* 3.2 66.0 + - + +
84A VAL* 1.3 81.7 - - - +
86A GLY* 1.3 54.6 + - - +
89A SER* 2.6 31.7 + - - -
109A VAL* 3.9 21.8 - - + -
174A ILE* 3.8 11.8 - - + +
175A ILE 5.3 0.4 - - - +
176A ASP* 4.1 13.0 - - + +
207A CYS* 3.8 20.5 - - - -
209A GLN* 4.9 4.5 - - + -
240A MSE 4.1 7.0 - - + -
252A THR* 3.8 28.3 - - - +
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Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A HIS 3.1 16.8 + - - -
85A LEU* 1.3 80.2 - - - +
87A HIS* 1.3 62.1 + - - +
89A SER* 3.3 2.4 + - - -
90A LEU* 3.1 31.7 + - - +
109A VAL* 4.3 3.0 - - - +
112A GLU* 4.3 9.2 - - - -
113A VAL* 4.3 12.8 - - - -
116A HIS* 4.9 0.2 - - - -
174A ILE* 4.2 10.8 - - - -
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Residues in contact with HIS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU* 2.8 45.3 + - + +
86A GLY* 1.3 70.7 - - - +
88A THR* 1.3 60.7 + - - +
89A SER 3.2 2.2 - - - -
91A CYS* 2.8 39.0 + - - +
112A GLU* 2.7 52.2 + - + +
115A ARG* 4.1 1.3 - - - -
116A HIS* 3.0 26.6 + - - -
270A VAL* 5.2 0.4 - - + +
275A PHE* 3.7 22.1 - + - -
279A LEU* 3.6 16.6 - - + +
282A TYR* 3.6 26.5 - + + -
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL* 2.7 36.9 + - - +
87A HIS* 1.3 76.3 - - - +
89A SER* 1.3 54.9 + - - +
92A SER* 2.7 30.0 + - - +
238A ALA* 4.8 5.4 - - + -
252A THR* 5.7 0.7 - - - -
254A VAL* 3.9 15.3 - - + +
282A TYR* 3.4 14.1 - - - -
287A HIS* 3.4 31.2 - - + +
290A SER* 5.1 2.9 + - - +
291A PHE* 3.9 26.9 - - + -
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU 2.6 25.0 + - - -
86A GLY 3.3 4.3 + - - -
88A THR* 1.3 78.9 - - - +
90A LEU* 1.3 73.8 + - - +
92A SER* 3.2 12.9 + - - -
93A HIS* 3.5 10.2 + - - +
172A VAL* 4.1 8.2 - - - +
174A ILE* 3.6 6.8 - - - +
205A ILE* 3.8 26.1 - - - +
207A CYS* 3.8 23.6 - - - -
254A VAL* 4.8 5.6 - - - +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLY 3.1 21.7 + - - +
89A SER* 1.3 88.3 + - - +
91A CYS* 1.3 62.6 + - - +
93A HIS* 3.2 16.6 + - - +
96A PRO* 3.9 15.9 - - + +
99A VAL* 4.7 4.9 - - + -
113A VAL* 3.8 33.7 - - + +
116A HIS* 3.4 43.5 - - + +
119A VAL* 3.8 15.7 - - + -
172A VAL* 4.0 22.9 - - + -
174A ILE* 4.3 1.6 - - + -
268A ARG* 3.3 16.2 + - - -
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Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A HIS* 2.8 27.8 + - - +
88A THR 4.6 1.1 - - - +
90A LEU* 1.3 72.2 - - - +
92A SER* 1.3 56.7 + - - +
93A HIS 3.4 1.1 - - - -
116A HIS* 3.9 20.2 - - - -
266A PRO* 4.8 4.3 - - + -
267A LEU* 3.0 8.9 + - - +
268A ARG* 2.8 53.3 + - - +
270A VAL* 4.1 21.5 - - - -
273A MSE 5.1 1.8 - - - -
282A TYR* 3.4 22.2 - - - +
287A HIS* 4.7 3.4 - - + +
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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