Contacts of the helix formed by residues 74 - 89 (chain A) in PDB entry 3BUC
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 GLY 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A VAL* 5.7 0.9 - - - -
72A LEU 4.3 0.4 + - - -
73A PHE* 1.3 76.6 - - - +
75A LYS* 1.3 66.1 + - - -
76A ALA 3.4 2.4 + - - -
77A GLU* 3.5 7.1 + - - +
78A ALA* 3.0 19.1 + - - +
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Residues in contact with LYS 75 (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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74A GLY* 1.3 69.8 - - - -
76A ALA* 1.3 58.9 + - - +
78A ALA* 3.3 5.1 + - - +
79A ASP* 2.8 63.8 + - - +
220A HIS* 4.8 10.5 - - + -
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Residues in contact with ALA 76 (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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74A GLY 3.4 0.8 - - - -
75A LYS* 1.3 79.7 - - - +
77A GLU* 1.3 61.2 + - - +
79A ASP* 3.6 8.1 + - - +
80A GLU* 3.3 23.5 + - - +
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Residues in contact with GLU 77 (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 LEU 5.3 0.2 - - - +
73A PHE* 3.4 34.8 - - + +
74A GLY* 3.5 9.2 + - - +
75A LYS 3.3 0.6 - - - -
76A ALA* 1.3 74.9 - - - +
78A ALA* 1.3 66.9 + - - +
80A GLU* 3.2 12.4 + - - +
81A ILE* 2.9 32.3 + - + +
140A ARG* 3.0 30.9 + - - +
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Residues in contact with ALA 78 (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 PHE* 4.0 15.8 - - + +
74A GLY 3.0 19.6 + - - +
75A LYS 3.7 0.4 - - - +
77A GLU* 1.3 76.3 - - - +
79A ASP* 1.3 57.2 + - - +
81A ILE* 4.5 0.4 - - - -
82A PHE* 2.9 24.4 + - - +
189A PHE* 3.6 12.2 - - + -
220A HIS* 3.2 36.3 - - + +
221A GLY* 4.1 15.0 - - - -
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Residues in contact with ASP 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 LYS* 2.8 52.7 + - - +
76A ALA* 3.6 8.0 - - - +
78A ALA* 1.3 72.0 - - - +
80A GLU* 1.3 57.3 + - - +
82A PHE* 3.3 7.3 + - - +
83A GLN* 2.9 42.5 + - - +
220A HIS* 2.7 32.8 + - - -
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Residues in contact with GLU 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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76A ALA 3.3 11.1 + - - +
77A GLU* 3.2 11.8 + - - +
79A ASP* 1.3 75.0 - - - +
81A ILE* 1.3 62.8 + - - +
83A GLN* 3.4 14.0 + - - +
84A GLU* 3.0 28.3 + - + +
140A ARG* 3.4 31.4 + - - +
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Residues in contact with ILE 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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73A PHE* 4.1 31.6 - - + -
77A GLU* 2.9 30.0 + - + +
78A ALA 3.8 3.8 - - - +
80A GLU* 1.3 72.7 - - + +
82A PHE* 1.3 61.6 + - - +
84A GLU* 3.2 8.2 + - - +
85A LEU* 2.8 32.9 + - + +
137A VAL* 4.3 6.3 - - + -
140A ARG* 3.7 40.4 - - - +
141A ILE* 3.7 22.4 - - + -
189A PHE* 3.6 24.0 - - + -
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Residues in contact with PHE 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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78A ALA 2.9 18.3 + - - +
79A ASP* 3.4 7.2 - - - +
81A ILE* 1.3 77.1 - - - +
83A GLN* 1.3 65.0 + - + +
85A LEU* 3.1 10.7 + - + +
86A GLU* 2.8 59.7 + - + +
189A PHE* 3.8 25.3 - - + -
190A GLY* 4.0 18.6 - - - -
220A HIS* 4.1 7.2 - + + -
247A PRO* 4.0 28.9 - - + -
249A VAL* 3.8 22.9 - - + -
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Residues in contact with GLN 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 ASP* 2.9 27.6 + - - +
80A GLU* 3.7 13.9 - - - +
81A ILE 3.3 0.2 - - - -
82A PHE* 1.3 82.2 - - + +
84A GLU* 1.3 56.1 + - - +
86A GLU* 3.6 8.0 + - - +
87A LYS* 3.0 29.2 + - - +
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Residues in contact with GLU 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 GLU* 3.0 14.6 + - + +
81A ILE* 3.3 11.2 - - - +
83A GLN* 1.3 74.2 - - - +
85A LEU* 1.3 55.6 + - - +
87A LYS* 2.9 13.2 + - - +
88A GLU* 2.8 56.5 + - + +
136A PRO* 5.8 2.2 - - - +
137A VAL* 3.4 37.8 + - + +
140A ARG* 5.0 8.6 + - - +
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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 ILE* 2.8 26.2 + - + +
82A PHE* 3.4 8.7 - - - +
84A GLU* 1.3 74.4 - - - +
86A GLU* 1.3 58.4 + - - +
89A VAL* 3.0 49.6 + - + +
91A TYR* 5.3 0.9 + - - -
137A VAL* 4.0 16.6 - - + -
138A LEU* 3.7 30.3 - - + -
141A ILE* 4.3 3.6 - - + -
158A ILE* 5.6 0.4 - - + -
189A PHE* 3.6 36.1 - - + -
249A VAL* 4.0 19.5 - - + -
251A LEU* 3.9 15.5 - - + -
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Residues in contact with GLU 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 PHE* 2.8 56.4 + - + +
83A GLN* 3.8 7.6 - - - +
85A LEU* 1.3 75.2 - - - +
87A LYS* 1.3 62.6 + - - +
89A VAL 4.6 4.9 + - - +
91A TYR* 4.8 2.5 + - - -
160A ARG* 2.8 49.8 + - - -
247A PRO* 4.2 2.4 - - - +
249A VAL* 3.7 9.2 - - - +
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Residues in contact with LYS 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 GLN 3.0 18.8 + - - +
84A GLU* 2.9 15.3 + - - +
86A GLU* 1.3 78.5 - - - +
88A GLU* 1.3 78.0 + - - +
89A VAL 5.4 0.4 - - - -
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Residues in contact with GLU 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 GLU* 2.8 42.1 + - + +
85A LEU 5.1 0.2 - - - -
87A LYS* 1.3 106.9 + - + +
89A VAL* 1.3 64.3 + - - +
90A GLU* 3.6 7.6 + - - +
115A TYR* 4.3 3.1 + - - -
135A ILE* 3.8 24.5 - - + +
137A VAL* 4.6 4.3 - - + -
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Residues in contact with VAL 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* 3.0 46.1 + - + +
86A GLU 4.9 4.7 - - - +
87A LYS 3.9 0.2 - - - -
88A GLU* 1.3 77.5 - - - +
90A GLU* 1.3 63.5 + - - +
91A TYR* 3.5 47.7 - - + +
113A ALA* 4.2 7.0 - - + -
115A TYR* 3.8 7.9 - - + +
135A ILE* 4.9 9.9 - - + -
138A LEU* 5.0 1.1 - - + -
158A ILE* 4.1 25.6 - - + -
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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