Contacts of the helix formed by residues 64 - 79 (chain A) in PDB entry 4BZ5
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 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 4.2 0.2 - - - -
63A HIS* 1.3 74.9 - - - +
65A THR* 1.3 65.8 + - - +
66A GLU* 3.2 17.5 - - - +
67A TYR* 3.0 20.6 + - - +
68A VAL* 3.0 21.7 + - - +
145A ARG* 3.1 37.0 + - - +
146A SER* 2.7 27.6 + - - -
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Residues in contact with THR 65 (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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56A TYR* 2.8 39.1 + - + +
60A THR* 3.8 15.5 - - + +
63A HIS 3.8 0.6 + - - -
64A SER* 1.3 72.0 - - - +
66A GLU* 1.3 69.0 + - - +
68A VAL 3.3 1.0 + - - -
69A ASP* 2.9 36.7 + - - -
145A ARG* 5.3 0.2 - - - +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 3.2 25.2 - - - +
65A THR* 1.3 88.3 + - - +
67A TYR* 1.3 54.2 + - - +
69A ASP* 3.4 10.1 + - - +
70A ALA* 3.0 28.8 + - - +
95A PHE* 3.8 25.0 - - + -
145A ARG* 4.3 8.7 + - - -
146A SER* 4.5 2.3 + - - +
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Residues in contact with TYR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A HIS* 3.7 20.0 - + + -
64A SER* 3.0 22.0 + - - +
66A GLU* 1.3 75.3 - - - +
68A VAL* 1.3 68.3 + - + +
70A ALA* 3.1 2.3 + - - +
71A LEU* 2.9 27.0 + - + +
95A PHE* 3.6 38.4 - + + -
97A LEU* 4.1 15.6 - - + +
144A LYS 4.5 2.0 - - - -
145A ARG 3.7 13.5 - - - +
146A SER* 3.7 16.4 - - - -
147A GLU 4.0 1.1 - - - -
148A ALA* 3.3 40.2 + - - +
153A TYR* 2.6 32.1 + - - +
154A LEU* 4.3 7.2 - - + -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A MET* 5.5 1.8 - - + -
56A TYR* 3.8 26.9 - - + -
59A VAL* 3.7 23.1 - - + -
60A THR* 3.9 9.2 - - + -
63A HIS* 3.7 22.9 - - + -
64A SER 3.0 16.7 + - - +
65A THR 3.9 2.9 - - - +
67A TYR* 1.3 78.0 - - + +
69A ASP* 1.3 64.5 + - - +
71A LEU* 3.3 7.1 + - - +
72A LYS* 3.0 23.1 + - + +
108A PHE* 3.9 25.0 - - + -
154A LEU* 4.8 2.0 - - + -
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Residues in contact with ASP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 2.9 30.1 + - - -
65A THR* 2.9 23.9 + - - +
66A GLU* 3.5 9.0 - - - +
68A VAL* 1.3 76.8 - - - +
70A ALA* 1.3 56.0 + - - +
72A LYS* 3.3 7.6 + - - +
73A LYS* 2.9 28.3 + - - +
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Residues in contact with ALA 70 (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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66A GLU 3.0 18.1 + - - +
67A TYR 3.1 3.8 + - - +
69A ASP* 1.3 75.2 - - - +
71A LEU* 1.3 59.6 + - - +
73A LYS* 3.2 6.0 + - - -
74A LEU* 2.8 26.5 + - - +
91A LEU* 4.7 11.0 - - + -
92A MET* 3.4 15.7 - - - +
95A PHE* 3.5 31.0 - - + -
97A LEU* 4.1 8.5 - - + -
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Residues in contact with LEU 71 (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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67A TYR* 2.9 20.1 + - + +
68A VAL* 3.7 5.8 - - - +
70A ALA* 1.3 75.0 - - - +
72A LYS* 1.3 63.5 + - - +
74A LEU* 3.3 7.2 + - + +
75A GLN* 3.3 19.6 + - - +
97A LEU* 3.7 33.3 - - + +
107A VAL* 4.0 14.6 - - + +
108A PHE* 3.7 25.5 - - + +
111A SER* 4.4 4.3 - - - -
153A TYR* 3.7 27.4 - - + +
154A LEU* 3.8 36.1 - - + -
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Residues in contact with LYS 72 (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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55A MET* 6.0 2.4 - - - +
68A VAL* 3.0 15.3 + - + +
69A ASP* 3.5 10.1 - - - +
71A LEU* 1.3 77.2 - - - +
73A LYS* 1.3 61.9 + - - +
75A GLN* 3.3 14.1 + - - +
76A MET* 3.2 22.4 + - + +
108A PHE* 3.8 35.5 - - + -
212B SER* 5.6 1.0 - - - -
213B PRO* 3.8 30.4 - - - +
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Residues in contact with LYS 73 (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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69A ASP 2.9 16.1 + - - +
70A ALA* 3.2 7.2 + - - +
72A LYS* 1.3 73.4 - - - +
74A LEU* 1.3 60.4 + - - +
76A MET* 3.2 23.1 + - + +
77A LEU* 2.9 45.9 + - + +
88A ASP* 2.7 35.9 + - - +
91A LEU* 4.2 22.3 - - + +
92A MET* 3.9 4.0 - - + -
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Residues in contact with LEU 74 (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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70A ALA 2.8 13.5 + - - +
71A LEU* 3.5 12.8 - - + +
72A LYS 3.2 0.4 - - - -
73A LYS* 1.3 77.0 - - - +
75A GLN* 1.3 61.7 + - - +
77A LEU* 3.4 2.3 + - - +
78A HIS* 3.0 53.7 + - + +
84A LEU* 5.0 4.7 - - + -
92A MET* 3.5 32.7 - - + +
97A LEU* 3.9 37.5 - - + +
102A PRO 4.3 3.4 - - - +
103A GLY* 3.5 27.6 - - - +
107A VAL* 4.0 12.6 - - + -
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Residues in contact with GLN 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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71A LEU 3.3 3.6 + - - -
72A LYS* 3.5 17.0 - - + +
73A LYS 3.3 0.2 - - - -
74A LEU* 1.3 79.6 - - - +
76A MET* 1.3 63.9 + - - +
78A HIS* 3.1 3.6 + - - +
79A CYS* 3.0 27.2 + - - -
104A PHE 4.2 3.4 - - - -
105A PRO 3.2 20.8 - - - +
106A SER* 3.1 9.8 - - - -
107A VAL* 3.8 16.9 - - + +
108A PHE* 2.8 35.2 + - + +
109A ASP* 3.0 36.7 + - - +
213B PRO* 4.7 6.1 - - - +
224B MET* 4.6 3.8 - - - -
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Residues in contact with MET 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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72A LYS* 3.2 12.9 + - + +
73A LYS* 3.2 25.0 + - + +
75A GLN* 1.3 79.3 - - - +
77A LEU* 1.3 93.6 + - + +
79A CYS* 3.1 18.3 + - + +
80A GLU* 3.4 31.6 + - + +
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Residues in contact with LEU 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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73A LYS* 2.9 25.8 + - + +
74A LEU* 3.8 4.9 - - - +
76A MET* 1.3 96.4 - - + +
78A HIS* 1.3 58.6 + - + +
79A CYS 3.1 0.4 - - - -
80A GLU* 3.3 37.3 + - - +
82A LYS* 4.4 9.9 - - + +
84A LEU* 3.8 39.1 - - + +
88A ASP* 3.7 29.6 - - + +
92A MET* 3.9 22.4 - - + -
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Residues in contact with HIS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 3.0 46.8 + - + +
75A GLN 3.1 2.9 + - - +
77A LEU* 1.3 77.3 - - - +
79A CYS* 1.3 58.7 + - - +
80A GLU 3.3 6.1 + - - +
84A LEU* 4.3 19.0 - - + +
103A GLY* 3.5 33.9 + - - -
104A PHE* 3.7 26.2 + - - +
105A PRO* 3.7 18.1 - - + +
228B ASP 4.7 5.2 - - - +
229B LYS 5.0 0.7 - - - +
230B LEU* 5.1 2.6 - - - +
231B PRO* 4.9 0.7 - - - +
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Residues in contact with CYS 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 GLN* 3.0 15.8 + - - +
76A MET* 3.1 13.8 + - - +
78A HIS* 1.3 78.3 - - - +
80A GLU* 1.3 58.6 + - + +
105A PRO* 3.1 30.5 - - - -
224B MET* 4.7 2.9 - - - -
230B LEU* 3.9 13.9 - - - +
231B PRO* 3.4 37.4 - - + +
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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