Contacts of the helix formed by residues 77 - 99 (chain A) in PDB entry 4ZCU
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 PHE 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TYR 4.1 7.0 - - - -
25A GLU* 3.6 48.7 - - + -
28A PHE* 3.7 40.1 - + + -
37A GLY 4.1 2.5 + - - +
76A ASP* 1.3 76.0 - - - +
78A GLU* 1.3 60.9 + - + +
80A PHE* 3.4 1.3 + + - +
81A MET* 2.9 60.0 + - + +
1006A SO4 4.5 1.8 - - - -
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Residues in contact with GLU 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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76A ASP* 3.1 25.1 - - - +
77A PHE* 1.3 84.4 - - + +
79A GLU* 1.3 62.4 + - + +
81A MET* 3.9 6.7 - - - +
82A LYS* 2.9 34.2 + - - +
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Residues in contact with GLU 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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67A GLY* 3.2 28.5 - - - +
68A ASP* 4.0 0.4 - - - -
69A VAL* 3.3 19.5 + - + +
70A ASN* 2.6 18.4 + - - +
74A LYS 2.8 10.2 - - - +
75A LEU* 3.3 5.1 - - + -
76A ASP* 3.0 38.4 + - - +
78A GLU* 1.3 79.5 - - + +
80A PHE* 1.3 59.2 + - - +
82A LYS* 3.4 11.0 + - - +
83A TYR* 2.9 30.8 + - - +
1002A CA 2.3 30.6 - - - -
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Residues in contact with PHE 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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24A TYR* 3.6 18.4 - - + -
27A LEU* 3.6 32.8 - - + -
28A PHE* 3.6 26.7 - + + -
31A LEU* 3.6 27.8 - - + -
39A VAL* 5.7 2.0 - - + -
44A LEU* 5.2 5.8 - - + -
63A ILE* 6.1 4.0 - - + -
75A LEU* 4.6 24.3 - - + +
76A ASP 3.1 14.0 + - - +
77A PHE* 3.6 4.9 - + - +
79A GLU* 1.3 78.6 - - - +
81A MET* 1.3 64.5 + - - +
83A TYR* 3.2 9.9 + + - +
84A LEU* 3.0 51.4 + - + +
153A PHE* 5.3 4.3 - + - -
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Residues in contact with MET 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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23A ARG* 4.7 3.8 - - - +
24A TYR* 3.6 33.2 - - + -
77A PHE* 2.9 45.8 + - + +
78A GLU* 3.9 5.8 - - - +
80A PHE* 1.3 76.5 - - - +
82A LYS* 1.3 60.3 + - - +
84A LEU 3.5 0.5 + - - -
85A LYS* 2.9 36.0 + - + +
1006A SO4 3.7 24.2 - - - +
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Residues in contact with LYS 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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69A VAL* 3.2 39.9 - - - +
78A GLU* 2.9 20.3 + - - +
79A GLU* 3.8 10.4 - - - +
81A MET* 1.3 76.4 - - - +
83A TYR* 1.3 64.7 + - - +
85A LYS* 3.3 26.2 + - - +
86A ASP* 2.9 45.3 + - - +
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Residues in contact with TYR 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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63A ILE* 3.5 51.1 - - + +
66A THR* 3.7 38.4 - - + +
67A GLY* 4.3 11.4 - - - -
79A GLU 2.9 17.8 + - - +
80A PHE* 3.2 8.9 + + - +
82A LYS* 1.3 79.0 - - - +
84A LEU* 1.3 80.4 + - + +
86A ASP* 3.9 5.0 - - + +
87A HIS* 2.9 49.4 + + + +
152A LEU 5.4 1.3 - - - -
153A PHE 5.7 0.5 - - - -
154A ASN 5.0 0.3 - - - -
155A PRO* 3.6 21.3 - - - +
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Residues in contact with LEU 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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24A TYR* 3.5 38.4 - - + -
27A LEU* 3.7 15.7 - - + -
80A PHE* 3.0 49.7 + - + +
81A MET 4.0 0.9 - - - +
83A TYR* 1.3 99.3 - - + +
85A LYS* 1.3 57.4 + - - +
87A HIS* 3.8 4.0 - - + +
88A GLU* 2.9 36.1 + - + +
152A LEU* 4.1 27.4 - - + +
153A PHE* 5.0 10.1 - - + -
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Residues in contact with LYS 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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24A TYR* 3.6 17.6 + - + +
81A MET* 2.9 25.3 + - + +
82A LYS* 3.6 24.2 - - - +
84A LEU* 1.3 76.8 - - - +
86A ASP* 1.3 82.1 + - - +
88A GLU* 3.2 4.6 + - - +
89A LYS* 3.0 37.2 + - + +
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Residues in contact with ASP 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 LYS* 2.9 31.6 + - - +
83A TYR* 3.9 5.4 - - + +
85A LYS* 1.3 97.7 - - - +
87A HIS* 1.3 62.3 + - - +
89A LYS* 3.2 22.8 + - - +
90A LYS* 2.9 45.1 + - - +
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Residues in contact with HIS 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 TYR* 2.9 40.7 + + + +
84A LEU* 3.8 7.6 - - + +
86A ASP* 1.3 77.6 - - - +
88A GLU* 1.3 65.7 + - - +
90A LYS* 3.1 14.8 + - - +
91A MET* 2.9 42.6 + - + +
151A PHE 2.7 23.4 + - - -
152A LEU 3.3 22.6 + - - -
154A ASN 2.8 23.4 + - - -
155A PRO* 4.2 3.1 + - + +
156A VAL 2.9 25.1 + - - -
157A THR* 5.2 1.2 - - - +
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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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24A TYR* 3.3 17.0 - - + +
84A LEU 2.9 25.4 + - - +
85A LYS* 3.2 5.1 + - - +
87A HIS* 1.3 78.6 - - - +
89A LYS* 1.3 66.2 + - - +
91A MET* 3.3 7.2 + - - +
92A LYS* 2.9 30.0 + - - +
144A TRP* 4.2 12.2 - - + -
148A ARG* 3.1 36.3 + - - +
151A PHE 4.8 0.2 - - - +
152A LEU* 3.0 42.4 - - + +
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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 LYS* 3.0 26.6 + - + +
86A ASP* 3.2 27.3 + - - +
88A GLU* 1.3 75.9 - - - +
90A LYS* 1.3 62.9 + - + +
92A LYS* 3.2 12.3 + - + +
93A LEU* 2.9 23.6 + - - +
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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 ASP* 2.9 39.6 + - - +
87A HIS* 3.1 13.6 + - - +
89A LYS* 1.3 76.8 - - + +
91A MET* 1.3 63.9 + - + +
93A LEU* 3.2 12.8 + - + +
94A ALA* 2.9 27.2 + - - +
157A THR* 3.3 46.8 - - + +
158A ASP* 5.8 0.9 - - - -
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Residues in contact with MET 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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87A HIS* 2.9 35.4 + - + +
88A GLU* 3.8 9.9 - - - +
90A LYS* 1.3 85.1 - - + +
92A LYS* 1.3 60.7 + - - +
94A ALA* 3.4 2.9 + - + +
95A PHE* 2.9 23.0 + - - +
144A TRP* 4.1 5.8 - - + -
147A TRP* 3.0 24.8 + - + +
148A ARG* 5.6 2.2 - - - +
151A PHE* 3.6 34.1 - - + +
156A VAL* 3.2 40.4 - - + +
157A THR 4.1 7.4 - - - -
158A ASP* 4.4 1.3 - - - +
162A ILE* 4.2 15.9 - - + -
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Residues in contact with LYS 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 GLU* 2.9 20.0 + - - +
89A LYS* 3.2 9.8 + - + +
91A MET* 1.3 73.6 - - - +
93A LEU* 1.3 59.7 + - - +
95A PHE* 3.3 2.0 + - + +
96A LYS* 2.9 53.6 + - + +
144A TRP* 3.6 40.7 - - + +
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Residues in contact with LEU 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 LYS 2.9 12.9 + - - +
90A LYS* 3.2 14.3 + - + +
92A LYS* 1.3 77.0 - - - +
94A ALA* 1.3 56.2 + - - +
96A LYS* 3.3 9.4 + - + -
97A SER* 2.9 30.2 + - - -
113C GLN* 5.5 0.9 - - + +
116C GLN* 3.8 41.3 - - + +
117C THR* 3.8 27.4 - - + -
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Residues in contact with ALA 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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90A LYS 2.9 12.9 + - - +
91A MET* 3.6 11.0 - - + +
92A LYS 3.3 0.2 - - - -
93A LEU* 1.3 76.0 - - - +
95A PHE* 1.3 63.4 + - - +
97A SER* 2.8 24.5 + - - -
98A LEU* 2.9 12.8 + - - +
147A TRP* 4.0 7.0 - - + -
158A ASP* 5.3 2.0 - - - -
159A ILE* 5.0 15.0 - - + +
162A ILE* 4.0 27.4 - - + -
117C THR* 6.1 2.0 - - - -
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Residues in contact with PHE 95 (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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91A MET 2.9 14.1 + - - +
92A LYS* 3.5 8.1 - - + +
94A ALA* 1.3 77.1 - - - +
96A LYS* 1.3 66.4 + - + +
98A LEU* 3.0 6.1 + - - +
99A ASP* 2.9 35.3 + - + +
104A GLY* 3.5 28.9 - - - -
105A LYS* 4.1 1.3 - - - -
106A ILE* 3.5 30.7 - - + +
142A VAL 4.0 1.3 - - - -
143A ASP 3.6 22.0 - - - -
144A TRP* 3.5 37.5 - + + -
147A TRP* 3.5 32.6 - + + +
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Residues in contact with LYS 96 (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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92A LYS* 2.9 41.9 + - + +
93A LEU* 3.9 9.2 - - + +
95A PHE* 1.3 85.2 - - + +
97A SER* 1.3 61.2 + - - +
99A ASP* 3.6 20.5 - - - +
102A ASN* 5.0 2.9 - - - +
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Residues in contact with SER 97 (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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93A LEU* 2.9 16.8 + - - +
94A ALA* 2.8 17.0 + - - +
95A PHE 3.1 0.2 - - - -
96A LYS* 1.3 78.3 - - - +
98A LEU* 1.3 66.2 + - - +
99A ASP 4.8 0.3 - - - -
100A LYS* 3.3 24.8 + - - +
114A SER* 4.0 1.2 + - - -
159A ILE* 5.2 7.4 - - - +
100C LYS* 6.6 0.4 - - - -
117C THR* 4.4 22.6 - - - -
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Residues in contact with LEU 98 (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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94A ALA 2.9 15.5 + - - +
95A PHE 3.5 6.5 - - - +
97A SER* 1.3 82.0 + - - +
99A ASP* 1.3 59.4 + - - +
100A LYS* 3.0 14.4 + - - +
106A ILE* 3.7 24.9 - - + -
110A GLU* 3.3 22.3 - - - +
111A ILE* 4.6 8.1 - - + -
114A SER* 3.3 32.5 + - - +
115A LEU* 5.5 2.0 - - + -
147A TRP* 3.4 36.8 - - + -
159A ILE* 4.0 22.0 - - + -
166A TRP* 4.1 15.3 - - + -
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Residues in contact with ASP 99 (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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95A PHE* 2.9 26.1 + - + +
96A LYS* 3.6 14.6 + - - +
97A SER 3.5 1.2 - - - -
98A LEU* 1.3 73.7 - - - +
100A LYS* 1.3 60.4 + - - +
101A ASN* 3.0 6.4 - - - +
102A ASN* 3.3 25.4 - - - +
103A ASP* 2.7 6.9 + - - +
104A GLY* 2.8 31.5 + - - -
105A LYS 2.6 12.2 - - - +
106A ILE* 4.5 2.4 - - + +
110A GLU* 3.8 4.7 - - - -
1003A CA 2.3 29.5 - - - -
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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