Contacts of the helix formed by residues 70 - 85 (chain A) in PDB entry 4IBR
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 THR 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A MET* 2.7 27.2 + - - +
68A MET 3.1 0.4 + - - -
69A SER* 1.3 77.2 - - - +
71A PHE* 1.3 61.7 + - - +
72A LYS 3.0 1.5 + - - -
73A VAL* 3.3 18.4 + - - +
74A LEU* 4.1 5.0 + - - +
185A MET* 4.2 4.1 - - - +
233A LYS* 3.5 31.4 - - - +
234A SER* 4.0 10.8 - - - -
235A GLY* 4.1 3.1 - - - +
243A GLY 4.5 4.7 - - - +
245A ILE* 4.0 23.2 - - + +
261A TYR* 2.8 30.4 + - + +
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Residues in contact with PHE 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 MET* 3.6 34.5 - - + -
68A MET 3.0 24.1 + - - +
69A SER* 3.0 1.2 - - - -
70A THR* 1.3 80.8 + - - +
72A LYS* 1.3 76.3 + - + +
74A LEU* 3.0 12.2 + - + +
75A LEU* 2.8 45.6 + - + -
134A ALA* 4.3 10.3 - - + -
138A LEU* 4.4 7.4 - - + -
147A LEU* 4.1 9.2 - - + -
161A LEU* 3.7 30.1 - - + -
165A GLU* 3.5 18.4 - - + -
168A LEU* 3.4 31.9 - - + -
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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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69A SER* 2.7 45.4 + - - +
71A PHE* 1.3 94.8 - - + +
73A VAL* 1.3 59.7 + - - +
75A LEU* 3.6 6.3 - - + +
76A CYS* 3.1 28.8 + - - +
125A ALA* 3.3 34.1 - - + +
126A ILE* 4.1 3.2 - - + +
129A SER* 2.7 28.6 + - - +
130A ASP 4.0 2.0 + - - -
131A ASN* 3.1 15.3 + - - -
134A ALA* 3.8 25.8 - - + -
165A GLU* 3.4 15.0 - - - -
233A LYS* 4.0 4.3 - - - -
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Residues in contact with VAL 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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70A THR 3.3 7.9 + - - +
71A PHE 3.2 0.6 - - - -
72A LYS* 1.3 76.4 - - - +
74A LEU* 1.3 69.0 + - + +
76A CYS 3.4 1.4 + - - -
77A GLY* 3.0 19.2 + - - -
126A ILE* 4.0 15.3 - - + -
189A LEU* 3.9 28.5 - - + -
192A LEU* 4.6 1.0 - - + +
206A LEU* 3.8 20.1 - - + +
210A MET* 3.7 28.0 - - + -
233A LYS* 3.6 32.3 - - + -
245A ILE* 4.0 6.7 - - + -
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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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67A MET* 4.0 8.1 - - + -
70A THR 4.4 0.9 - - - +
71A PHE* 3.0 12.2 + - + +
73A VAL* 1.3 82.9 - - + +
75A LEU* 1.3 61.9 + - - +
77A GLY* 3.1 3.6 + - - -
78A ALA* 3.1 17.0 + - - +
147A LEU* 3.7 19.6 - - + +
150A PHE* 4.5 4.0 - - - -
151A LEU* 3.9 16.4 - - + -
159A THR* 3.9 22.0 - - + -
185A MET* 3.4 39.9 - - + -
188A THR* 3.5 29.6 - - + -
189A LEU* 4.9 2.5 - - + +
192A LEU* 3.7 16.2 - - + -
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Residues in contact with LEU 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 PHE* 2.8 22.4 + - + +
72A LYS* 3.6 11.4 - - + +
73A VAL 3.3 0.2 - - - -
74A LEU* 1.3 75.0 - - - +
76A CYS* 1.3 59.9 + - - +
78A ALA* 2.9 21.1 + - - +
79A VAL* 3.0 13.6 + - + +
125A ALA* 5.7 0.2 - - + -
134A ALA* 3.4 36.3 - - + +
137A LEU* 3.8 22.9 - - + +
138A LEU* 3.7 25.8 - - + +
141A ILE* 3.6 27.4 - - + -
147A LEU* 3.8 16.5 - - + +
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Residues in contact with CYS 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 3.1 17.1 + - - +
73A VAL 3.9 3.1 - - - +
74A LEU 3.3 0.2 - - - -
75A LEU* 1.3 75.5 - - - +
77A GLY* 1.3 59.2 + - - +
79A VAL* 3.3 4.0 + - - +
80A LEU* 2.8 36.3 + - - +
122A CYS* 2.0 61.0 - - - -
125A ALA* 5.0 1.8 - - - -
126A ILE* 4.0 14.8 - - + -
137A LEU* 3.9 12.1 - - - -
206A LEU* 4.2 2.2 - - + -
209A TRP* 4.1 7.2 - - + -
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Residues in contact with GLY 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 VAL 3.0 14.6 + - - -
74A LEU 3.1 6.2 + - - -
76A CYS* 1.3 75.9 - - - +
78A ALA* 1.3 56.1 + - - +
80A LEU* 3.5 0.8 + - - -
81A SER* 3.1 26.9 + - - -
150A PHE* 4.0 7.1 - - - -
192A LEU* 4.4 16.4 - - - -
198A LEU* 3.6 14.4 - - - +
206A LEU* 4.3 11.6 - - - +
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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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74A LEU 3.1 4.0 + - - -
75A LEU 2.9 10.6 + - - +
77A GLY* 1.3 73.4 - - - +
79A VAL* 1.3 65.3 + - - +
81A SER* 3.4 3.3 + - - -
82A ARG* 3.2 27.1 + - - +
141A ILE* 4.4 15.5 - - + -
147A LEU* 3.8 14.8 - - + -
150A PHE* 3.8 38.9 - - + -
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Residues in contact with VAL 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 LEU* 3.0 22.7 + - + +
76A CYS* 3.3 13.7 + - - +
78A ALA* 1.3 76.7 - - - +
80A LEU* 1.3 64.5 + - + +
82A ARG* 3.1 10.5 + - - +
83A VAL* 3.0 19.6 + - - +
88A GLU* 4.4 8.7 - - + +
90A LEU* 4.6 8.3 - - + -
118A VAL* 3.6 29.4 - - + -
122A CYS* 4.4 8.5 - - - -
137A LEU* 4.1 20.0 - - + -
140A THR* 4.3 4.7 - - - +
141A ILE* 3.9 22.7 - - + -
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Residues in contact with LEU 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 CYS 2.8 20.7 + - - +
77A GLY 3.9 4.0 - - - +
79A VAL* 1.3 73.4 - - + +
81A SER* 1.3 60.6 + - - +
83A VAL* 3.2 9.1 + - + +
84A ASP* 2.9 31.9 + - - +
90A LEU* 4.0 32.8 - - + -
198A LEU* 4.1 10.3 - - + -
202A SER* 3.5 43.0 + - - +
205A GLN* 4.3 5.8 - - + -
206A LEU* 3.9 18.6 - - + +
209A TRP* 3.6 27.6 - - + -
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Residues in contact with SER 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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77A GLY 3.1 14.5 + - - -
78A ALA 3.5 8.5 - - - -
79A VAL 3.2 0.2 - - - -
80A LEU* 1.3 73.6 - - - +
82A ARG* 1.3 67.1 + - - +
84A ASP* 3.2 7.9 + - - +
85A ALA* 3.1 22.4 + - - +
150A PHE* 3.8 22.8 - - - -
197A LEU* 4.4 9.5 + - - +
198A LEU* 3.7 13.1 - - - +
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Residues in contact with ARG 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 3.2 10.5 + - - +
79A VAL* 3.1 9.5 + - - +
81A SER* 1.3 78.1 - - - +
83A VAL* 1.3 60.8 + - - +
85A ALA* 3.1 6.7 + - - -
87A GLN* 2.8 69.9 + - + +
88A GLU* 3.2 43.6 + - + +
92A ARG* 4.9 1.0 - - - +
140A THR* 3.5 24.1 + - - -
141A ILE* 3.7 30.4 + - - +
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Residues in contact with VAL 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 VAL 3.0 18.7 + - - +
80A LEU* 3.4 14.4 - - + +
81A SER 3.2 0.2 - - - -
82A ARG* 1.3 76.6 - - - +
84A ASP* 1.3 67.4 + - - +
86A GLY* 3.0 13.7 + - - -
88A GLU* 3.5 36.6 - - + +
89A GLN* 5.0 0.7 - - - -
90A LEU* 3.9 38.4 - - + +
202A SER* 5.0 3.4 - - - +
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Residues in contact with ASP 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 LEU 2.9 13.4 + - - +
81A SER* 3.2 8.7 + - - +
83A VAL* 1.3 78.7 - - - +
85A ALA* 1.3 58.3 + - - +
86A GLY 3.2 0.9 + - - -
197A LEU 4.6 2.1 - - - +
198A LEU* 3.6 11.6 - - - +
199A THR* 2.9 46.3 + - + +
202A SER* 2.5 30.0 + - - -
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Residues in contact with ALA 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 SER 3.1 14.0 + - - +
82A ARG* 3.7 4.3 - - - +
83A VAL 3.1 0.8 - - - -
84A ASP* 1.3 76.4 - - - +
86A GLY* 1.3 62.1 + - - +
87A GLN* 3.2 27.0 + - - +
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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