Contacts of the helix formed by residues 73 - 90 (chain A) in PDB entry 5H4G
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 LEU 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A VAL* 4.7 6.5 - - + -
71A PRO* 2.8 38.0 + - + +
72A LEU* 1.3 75.6 - - - +
74A ASP* 1.3 72.8 + - - +
75A ASP* 4.1 8.5 - - + +
76A ILE* 3.0 17.8 + - + +
77A ALA* 2.9 20.0 + - - +
107A TYR* 3.6 37.2 - - + +
39B ILE* 5.0 0.2 - - - -
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Residues in contact with ASP 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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72A LEU 3.7 0.8 + - - -
73A LEU* 1.3 76.9 - - - +
75A ASP* 1.3 86.5 + - - +
77A ALA* 3.1 6.2 + - - +
78A ILE* 2.9 36.8 + - + +
39B ILE* 4.9 3.4 - - - +
60B PHE* 3.3 46.1 - - + -
61B GLU* 5.1 1.6 - - - +
64B LYS* 4.7 8.7 + - - +
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.2 2.9 - - + +
74A ASP* 1.3 95.0 + - - +
76A ILE* 1.3 58.0 + - - +
78A ILE* 3.9 13.4 - - - +
79A LYS* 3.0 30.1 + - - +
107A TYR* 4.1 29.8 + - + -
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 4.0 15.5 - - + -
71A PRO 3.7 18.8 - - - +
72A LEU* 4.2 17.5 - - + -
73A LEU* 3.0 19.2 + - + +
75A ASP* 1.3 76.1 - - - +
77A ALA* 1.3 60.1 + - - +
79A LYS* 4.7 0.2 - - - -
80A ALA* 2.8 33.6 + - - +
100A ILE* 4.5 8.3 - - + -
103A THR* 3.5 19.3 - - + +
104A THR* 3.7 32.1 - - + +
107A TYR* 3.9 35.2 - - + -
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Residues in contact with ALA 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* 3.7 19.2 - - + +
73A LEU 2.9 12.8 + - - +
74A ASP* 3.4 9.0 - - - +
76A ILE* 1.3 76.7 - - - +
78A ILE* 1.3 57.8 + - - +
80A ALA* 3.7 3.7 - - - +
81A ALA* 2.9 30.7 + - - +
39B ILE* 4.4 12.3 - - + -
42B VAL* 5.3 0.2 - - + -
43B TYR* 3.9 25.0 - - + +
46B LEU* 4.5 10.4 - - + +
60B PHE* 5.3 1.8 - - + -
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Residues in contact with ILE 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 ASP* 2.9 27.5 + - + +
75A ASP* 3.9 14.1 - - - +
77A ALA* 1.3 76.8 - - - +
79A LYS* 1.3 63.9 + - - +
81A ALA* 3.3 4.3 + - - +
82A GLN* 3.1 21.9 + - + +
46B LEU* 3.9 19.5 - - + -
56B ILE* 3.6 26.9 - - + +
57B GLU* 4.4 27.1 - - + +
60B PHE* 4.0 25.4 - - + -
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Residues in contact with LYS 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 3.0 18.8 + - - +
76A ILE* 4.7 0.2 - - - -
78A ILE* 1.3 77.8 - - - +
80A ALA* 1.3 57.7 + - - +
82A GLN* 3.2 11.3 + - + +
83A ILE* 3.0 55.6 + - + +
103A THR* 3.9 13.5 - - + -
106A ILE* 5.3 10.1 - - + -
126A PHE* 4.6 23.6 - - - +
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Residues in contact with ALA 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 ILE 2.8 22.5 + - - +
77A ALA 3.7 2.0 - - - +
79A LYS* 1.3 70.3 - - - +
81A ALA* 1.3 55.3 + - - +
83A ILE* 3.7 2.5 - - - +
84A GLU* 2.7 38.1 + - - +
99A ILE* 3.8 5.6 - - + +
100A ILE* 3.7 26.7 - - + -
103A THR* 3.5 23.0 - - + +
43B TYR* 3.7 11.7 - - + -
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Residues in contact with ALA 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 ALA 2.9 19.3 + - - +
78A ILE* 3.3 5.8 + - - +
80A ALA* 1.3 74.5 - - - +
82A GLN* 1.3 57.0 + - - +
84A GLU* 4.1 0.5 - - - +
85A ALA* 2.9 31.4 + - - +
43B TYR* 4.0 2.8 - - - +
46B LEU* 3.5 18.8 - - + +
47B THR* 3.4 40.7 - - - +
50B ALA* 3.7 6.6 - - + +
56B ILE* 4.6 2.0 - - + -
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Residues in contact with GLN 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 ILE* 3.1 14.0 + - + +
79A LYS* 3.2 19.9 + - + +
81A ALA* 1.3 75.8 - - - +
83A ILE* 1.3 60.8 + - + +
85A ALA* 3.4 3.8 + - - +
86A ASN* 3.2 18.9 + - - +
126A PHE* 4.8 5.2 - - + -
50B ALA* 4.3 11.1 - - + +
56B ILE* 5.9 3.8 - - + -
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Residues in contact with ILE 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 LYS* 3.0 35.4 + - + +
80A ALA* 3.7 4.9 - - - +
82A GLN* 1.3 75.1 - - - +
84A GLU* 1.3 59.7 + - - +
86A ASN* 2.9 7.6 + - - +
87A LEU* 2.9 33.0 + - + +
99A ILE* 4.5 8.3 - - + -
103A THR* 3.6 21.5 - - - +
106A ILE* 4.1 13.7 - - + -
123A ILE* 4.1 24.0 - - + -
126A PHE* 3.7 53.2 - - + -
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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 ALA 2.7 21.8 + - - +
83A ILE* 1.3 75.5 - - - +
85A ALA* 1.3 55.8 + - - +
87A LEU* 3.1 8.0 + - + +
88A ILE* 2.9 54.1 + - + +
94A LEU 5.0 6.4 - - - +
96A MET* 5.9 0.9 - - - -
99A ILE* 4.0 22.3 - - + +
43B TYR* 2.0 38.3 + - - -
44B ARG* 3.8 13.6 + - - -
47B THR* 4.1 15.6 - - + +
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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 ALA 2.9 19.0 + - - +
82A GLN* 3.8 5.4 - - - +
83A ILE 3.2 0.2 - - - -
84A GLU* 1.3 77.2 - - - +
86A ASN* 1.3 60.9 + - - +
88A ILE* 3.6 1.5 + - - -
89A LYS* 3.1 22.3 + - - +
47B THR* 4.2 7.3 - - - +
50B ALA* 3.9 8.3 - - + +
51B TYR* 3.5 47.0 - - + +
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Residues in contact with ASN 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 GLN 3.2 9.4 + - - +
83A ILE 2.9 10.1 + - - +
85A ALA* 1.3 76.0 - - - +
87A LEU* 1.3 64.3 + - - +
89A LYS* 3.1 23.1 + - - +
90A LYS* 2.9 40.2 + - - +
125A ARG* 4.7 4.9 - - - -
126A PHE* 3.4 33.3 - - + -
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Residues in contact with LEU 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 ILE* 2.9 18.7 + - + +
84A GLU* 3.1 8.9 + - + +
86A ASN* 1.3 81.3 - - - +
88A ILE* 1.3 62.4 + - + +
90A LYS* 3.1 11.0 + - + +
92A ILE* 2.9 48.9 + - + +
94A LEU* 3.7 21.8 - - + +
99A ILE* 3.3 33.9 - - + -
122A PRO* 3.8 37.7 - - + +
123A ILE* 4.0 8.3 - - + -
126A PHE* 4.9 3.6 - - + -
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Residues in contact with ILE 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* 2.9 37.1 + - + +
85A ALA* 3.9 5.2 - - - +
87A LEU* 1.3 73.5 - - - +
89A LYS* 1.3 59.5 + - - +
91A GLU* 3.0 20.4 + - - +
92A ILE 4.5 7.0 - - - +
47B THR* 3.9 24.0 - - + -
51B TYR* 3.9 29.2 + - + +
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Residues in contact with LYS 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 ALA 3.1 15.1 + - - +
86A ASN* 3.1 19.0 + - - +
88A ILE* 1.3 78.4 - - - +
90A LYS* 1.3 59.7 + - + +
91A GLU 3.7 0.3 + - - -
51B TYR* 3.7 18.3 - - + +
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Residues in contact with LYS 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 ASN* 2.9 39.4 + - - +
87A LEU* 3.1 12.6 + - + +
89A LYS* 1.3 79.5 - - + +
91A GLU* 1.3 69.2 + - - +
92A ILE* 3.2 29.3 + - + +
122A PRO* 5.8 1.1 - - + -
125A ARG* 4.0 28.1 - - - +
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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