Contacts of the helix formed by residues 72 - 94 (chain A) in PDB entry 5HI7
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 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A MET* 3.8 12.3 - - - +
70A TYR* 3.4 7.6 - - - +
71A CYS* 1.3 92.7 - - - +
73A ALA* 1.3 64.5 + - - +
74A LYS* 3.4 12.3 + - - +
75A CYS* 3.1 21.2 + - - +
76A GLN* 3.2 18.4 + - - +
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Residues in contact with ALA 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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60A MET* 4.5 4.6 - - - +
72A SER* 1.3 73.6 - - - +
74A LYS* 1.3 63.2 + - - +
76A GLN* 3.3 16.8 + - + +
77A LYS* 3.0 25.5 + - - +
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 3.1 11.5 + - - +
73A ALA* 1.3 79.4 - - - +
75A CYS* 1.3 60.3 + - - +
77A LYS* 3.5 5.1 + - - +
78A LYS* 3.0 30.1 + - + +
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Residues in contact with CYS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A CYS* 3.6 13.0 - - - -
51A ARG* 3.5 22.3 - - + +
52A CYS* 3.9 7.2 - - - -
70A TYR* 3.9 3.1 - - + -
71A CYS* 3.5 7.0 - - - -
72A SER* 3.1 16.4 + - - +
74A LYS* 1.3 78.9 - - - +
76A GLN* 1.3 60.7 + - - +
78A LYS* 4.6 0.4 - - - -
79A ALA* 2.9 31.0 + - - +
503A ZN 2.2 37.7 - - - -
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Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.5 38.4 + - + -
72A SER 3.2 8.2 + - - +
73A ALA* 3.3 21.9 + - + +
75A CYS* 1.3 76.3 - - - +
77A LYS* 1.3 75.8 + - - +
79A ALA* 3.6 0.7 - - - +
80A TRP* 2.9 39.1 + - - +
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Residues in contact with LYS 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 ALA 3.0 18.8 + - - +
74A LYS* 3.8 5.2 - - - +
76A GLN* 1.3 86.8 - - - +
78A LYS* 1.3 65.4 + - - +
80A TRP* 3.3 15.7 + - - +
81A PRO* 3.6 9.4 - - - +
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Residues in contact with LYS 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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51A ARG* 3.8 35.5 + - + +
74A LYS* 3.0 20.5 + - + +
75A CYS* 4.0 2.7 - - - +
77A LYS* 1.3 77.1 - - - +
79A ALA* 1.3 59.4 + - - +
81A PRO* 3.5 11.8 - - - +
82A ASP* 5.2 2.1 + - - +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 5.4 1.1 - - + -
51A ARG* 3.9 21.7 - - + +
70A TYR* 3.4 28.9 - - + +
75A CYS 2.9 20.2 + - - +
76A GLN 3.6 0.4 - - - +
77A LYS 3.2 0.2 - - - -
78A LYS* 1.3 75.0 - - - +
80A TRP* 1.3 59.6 + - - +
81A PRO 3.4 1.3 - - - -
82A ASP* 3.2 10.3 + - + +
83A HIS* 2.9 27.9 + - + +
107A ARG* 5.6 4.9 - - - +
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Residues in contact with TRP 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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70A TYR* 5.4 0.4 - - - -
76A GLN* 2.9 26.7 + - - +
77A LYS* 3.3 8.9 + - - +
79A ALA* 1.3 77.6 - - - +
81A PRO* 1.3 75.8 - - + +
83A HIS* 4.4 10.8 - + - +
84A LYS* 2.8 73.2 + - + +
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Residues in contact with PRO 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 LYS 3.6 6.5 - - - +
78A LYS* 3.5 13.9 - - - +
79A ALA 3.5 4.0 - - - -
80A TRP* 1.3 108.3 - - + +
82A ASP* 1.3 65.7 + - - +
84A LYS* 3.8 12.3 + - + +
85A ARG 5.1 0.5 + - - -
110A PHE* 6.0 1.7 - - - +
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Residues in contact with ASP 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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36A LEU 6.1 1.3 - - - -
37A ALA* 6.0 2.0 - - - -
38A TYR* 4.4 7.6 - - - -
51A ARG* 3.8 20.9 + - - -
78A LYS 5.5 1.6 - - - -
79A ALA* 3.2 10.3 + - - +
81A PRO* 1.3 83.3 - - - +
83A HIS* 1.3 60.6 + - - +
84A LYS 3.7 0.3 + - - -
85A ARG 4.9 0.9 + - - -
86A GLU* 3.9 12.0 + - - +
107A ARG* 3.9 40.2 + - + +
110A PHE* 5.1 8.4 - - - +
111A LYS* 4.9 15.1 + - - +
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Residues in contact with HIS 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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62A CYS* 3.8 7.6 - - + -
65A CYS* 3.4 12.4 - - - -
68A ALA* 3.6 17.7 - - + +
70A TYR* 3.6 21.3 - + - +
79A ALA 2.9 17.9 + - - +
80A TRP* 4.0 10.3 - + - +
82A ASP* 1.3 76.4 - - - +
84A LYS* 1.3 65.5 + - - +
85A ARG 3.4 1.6 - - - -
86A GLU* 2.9 30.1 + - - +
87A CYS* 2.9 32.8 + - + +
90A LEU* 4.0 7.6 - - + -
107A ARG* 4.1 5.1 + - - +
502A ZN 2.0 36.2 - - - -
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TRP* 2.8 65.0 + - + +
81A PRO* 4.1 9.4 - - + +
82A ASP 3.4 2.6 - - - -
83A HIS* 1.3 79.8 - - - +
85A ARG* 1.3 71.1 + - + +
87A CYS* 3.5 12.9 - - - +
88A LYS* 4.2 3.5 + - - +
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Residues in contact with ARG 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 PRO 5.1 1.2 + - - -
82A ASP 4.9 1.4 + - - -
83A HIS 3.4 0.2 - - - -
84A LYS* 1.3 83.7 - - + +
86A GLU* 1.3 66.3 + - - +
87A CYS 3.1 2.5 + - - -
88A LYS* 3.3 9.2 + - - +
89A CYS* 3.7 1.9 + - - -
110A PHE* 3.3 44.9 - - + -
113A MET* 4.4 12.3 - - - +
114A ASP* 2.9 38.8 + - - -
158A GLU* 2.7 69.2 + - - +
159A ILE* 4.1 7.3 - - - +
164A GLN* 5.1 6.9 + - - +
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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 ASP 3.9 3.5 + - - +
83A HIS* 2.9 29.7 + - - +
85A ARG* 1.3 75.4 - - - +
87A CYS* 1.3 62.3 + - - +
89A CYS* 3.0 8.3 + - - +
90A LEU* 2.8 37.9 + - + +
103A ARG* 3.2 35.9 + - - +
106A GLY* 5.9 0.7 - - - -
107A ARG* 2.8 49.8 + - + +
110A PHE* 3.6 20.4 - - + -
154A PHE* 4.9 8.5 - - + -
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Residues in contact with CYS 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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62A CYS* 3.9 1.8 - - - -
64A GLN* 3.5 29.6 - - - -
65A CYS* 3.5 6.9 - - - +
83A HIS* 2.9 30.6 + - + +
84A LYS* 3.5 9.2 - - - +
85A ARG 3.1 0.4 - - - -
86A GLU* 1.3 75.6 - - - +
88A LYS* 1.3 58.5 + - - +
90A LEU* 4.7 0.4 - - - -
91A LYS* 3.0 29.9 + - - +
502A ZN 2.3 34.5 - - - -
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Residues in contact with LYS 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 LYS 4.2 2.2 + - - +
85A ARG* 3.3 4.5 + - - +
86A GLU 3.2 0.4 - - - -
87A CYS* 1.3 79.7 - - - +
89A CYS* 1.3 60.6 + - - +
91A LYS* 3.7 6.7 + - - +
92A SER* 3.2 24.6 + - - -
157A GLU* 4.5 9.1 - - + +
158A GLU* 3.7 23.6 - - + +
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Residues in contact with CYS 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 ARG 3.8 4.7 - - - -
86A GLU* 3.0 11.5 + - - +
88A LYS* 1.3 75.7 - - - +
90A LEU* 1.3 65.7 + - - +
92A SER* 3.2 8.8 + - - -
93A CYS* 3.1 26.3 + - - -
110A PHE* 4.4 0.9 - - - -
154A PHE* 3.4 37.5 - - + +
155A MET* 4.0 20.2 - - - -
157A GLU* 4.6 2.5 - - - -
158A GLU* 3.5 37.9 - - - -
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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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65A CYS* 4.3 1.8 - - + -
67A VAL* 4.0 32.6 - - + +
83A HIS* 4.0 19.1 - - + -
86A GLU* 2.8 32.1 + - - +
87A CYS 4.0 2.7 - - - +
89A CYS* 1.3 72.3 - - - +
91A LYS* 1.3 63.5 + - - +
93A CYS* 3.5 2.4 + - - +
94A LYS* 3.4 19.4 + - - +
96A ARG 5.1 1.4 - - - +
97A TYR* 4.2 17.9 - - + -
98A PRO* 4.0 18.4 - - + -
103A ARG* 4.0 28.0 - - - +
154A PHE* 3.7 25.6 - - + -
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Residues in contact with LYS 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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64A GLN* 3.8 19.3 - - + +
65A CYS* 4.1 17.4 - - - +
87A CYS* 3.0 19.5 + - - +
88A LYS* 3.7 7.9 - - - +
89A CYS 3.2 0.2 - - - -
90A LEU* 1.3 79.9 - - - +
92A SER* 1.3 63.6 + - - +
93A CYS 3.3 0.3 + - - -
94A LYS* 3.5 14.9 + - - +
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Residues in contact with SER 92 (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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88A LYS 3.2 12.2 + - - -
89A CYS* 3.2 14.7 + - - -
91A LYS* 1.3 81.2 - - - +
93A CYS* 1.3 65.8 + - - +
94A LYS 3.7 5.2 + - - +
154A PHE 4.9 0.3 + - - -
156A ARG* 3.6 25.4 + - - -
157A GLU* 4.2 12.5 - - - +
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Residues in contact with CYS 93 (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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89A CYS 3.1 20.4 + - - +
90A LEU* 4.3 2.9 - - - +
91A LYS 3.2 0.2 - - - -
92A SER* 1.3 74.9 - - - +
94A LYS* 1.3 65.2 + - - +
95A PRO* 4.5 0.3 - - - +
96A ARG* 2.9 39.6 + - + +
98A PRO* 5.7 0.7 - - + -
153A HIS* 4.3 11.3 + - + +
154A PHE* 3.6 36.3 - - + -
156A ARG* 3.2 29.6 - - - +
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Residues in contact with LYS 94 (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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65A CYS 6.0 1.6 - - - +
67A VAL* 5.8 5.2 - - + -
90A LEU 3.4 10.6 + - - +
91A LYS* 3.8 12.9 - - - +
92A SER 3.4 7.3 - - - +
93A CYS* 1.3 80.4 - - - +
95A PRO* 1.3 72.8 - - + +
96A ARG 3.9 1.8 - - - -
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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
------------------------------------------------------------
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