Contacts of the helix formed by residues 77 - 99 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.8 8.1 - - + -
25B GLU* 3.4 49.6 - - + -
28B PHE* 3.4 35.0 - + + -
76B ASP* 1.3 72.5 - - - +
78B GLU* 1.3 62.5 + - + +
80B PHE* 3.4 0.7 + - - +
81B MET* 2.9 59.9 + - + +
1006B SO4 4.2 2.2 - - - -
1008B GOL 2.8 26.6 + - - +
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 5.5 3.1 - - - +
76B ASP* 3.3 14.4 + - - +
77B PHE* 1.3 84.1 - - + +
79B GLU* 1.3 71.4 + - - +
81B MET* 3.8 7.2 - - - +
82B LYS* 2.9 47.7 + - + +
1008B GOL 5.6 0.4 - - - -
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY* 3.3 26.7 - - - +
68B ASP* 4.1 0.7 - - - -
69B VAL* 3.2 21.6 + - + +
70B ASN* 2.8 16.5 + - - +
74B LYS 2.9 9.9 - - - +
75B LEU* 3.3 7.8 - - + +
76B ASP* 2.9 35.0 + - - +
78B GLU* 1.3 89.3 - - - +
80B PHE* 1.3 60.2 + - - +
82B LYS* 3.3 4.0 + - - +
83B TYR* 2.9 30.0 + - - +
1002B CA 2.4 31.1 - - - -
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.9 7.0 - - + -
27B LEU* 3.6 14.4 - - + -
28B PHE* 3.5 55.6 - + + -
31B LEU* 3.6 33.0 - - + -
39B VAL* 5.6 2.5 - - + -
44B LEU* 5.2 5.4 - - + -
63B ILE* 6.0 5.4 - - + -
75B LEU* 4.6 23.3 - - + +
76B ASP 3.2 7.4 + - - +
77B PHE* 3.6 1.6 - + - +
79B GLU* 1.3 79.6 - - - +
81B MET* 1.3 65.9 + - - +
83B TYR* 3.2 10.2 + + - +
84B LEU* 3.0 55.3 + - + +
153B PHE* 5.1 5.2 - + - -
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Residues in contact with MET 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.8 30.7 - - + -
77B PHE* 2.9 39.1 + - + +
78B GLU* 3.8 6.1 - - - +
80B PHE* 1.3 77.9 - - - +
82B LYS* 1.3 59.1 + - - +
84B LEU 3.5 0.2 + - - -
85B LYS* 2.9 43.5 + - + +
1006B SO4 3.4 34.1 - - - +
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 4.4 26.3 - - + +
78B GLU* 2.9 35.6 + - + +
79B GLU* 3.6 5.2 - - - +
80B PHE 3.2 0.2 - - - -
81B MET* 1.3 74.9 - - - +
83B TYR* 1.3 65.9 + - - +
85B LYS* 3.6 7.6 - - + +
86B ASP* 2.9 50.6 + - - +
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 3.4 51.3 - - + +
66B THR* 3.7 37.0 - - + -
67B GLY* 4.3 11.4 - - - -
79B GLU 2.9 17.5 + - - +
80B PHE* 3.6 8.3 - + - +
82B LYS* 1.3 77.2 - - - +
84B LEU* 1.3 82.0 + - + +
86B ASP* 3.9 5.0 - - + +
87B HIS* 2.9 48.4 + + + +
152B LEU 5.3 1.3 - - - -
153B PHE* 5.7 0.7 - - - -
154B ASN 4.9 0.2 - - - -
155B PRO* 3.5 22.5 + - - +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.5 28.0 - - + -
27B LEU* 3.7 22.4 - - + -
80B PHE* 3.0 52.0 + - + +
83B TYR* 1.3 98.3 - - + +
85B LYS* 1.3 58.7 + - - +
87B HIS* 3.7 3.9 - - + +
88B GLU* 2.9 34.5 + - - +
152B LEU* 4.0 27.8 - - + +
153B PHE* 4.8 11.0 - - + -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.7 13.8 - - + -
81B MET* 2.9 32.7 + - + +
82B LYS* 3.6 8.7 - - + +
84B LEU* 1.3 74.2 - - - +
86B ASP* 1.3 83.6 + - - +
88B GLU* 3.1 6.3 + - - +
89B LYS* 3.0 60.4 + - + +
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Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS* 2.9 42.6 + - - +
83B TYR* 3.9 4.1 - - + +
85B LYS* 1.3 92.7 + - - +
87B HIS* 1.3 64.6 + - - +
89B LYS* 3.1 13.2 + - - +
90B LYS* 3.0 38.2 + - - +
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Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 2.9 39.8 + + + +
84B LEU* 3.7 7.9 - - + +
86B ASP* 1.3 78.4 - - - +
88B GLU* 1.3 63.1 + - - +
90B LYS* 3.2 11.7 + - - +
91B MET* 2.9 45.6 + - + +
151B PHE 2.6 24.3 + - - -
152B LEU 3.2 21.5 + - - -
153B PHE 5.6 0.2 - - - -
154B ASN 2.8 22.6 + - - -
155B PRO* 4.3 3.1 - - + +
156B VAL 3.0 24.8 + - - -
157B THR* 5.3 1.0 - - - +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.2 26.5 - - - +
84B LEU 2.9 14.9 + - - +
85B LYS* 3.5 5.4 - - - +
87B HIS* 1.3 78.9 - - - +
89B LYS* 1.3 60.1 + - - +
91B MET* 3.4 8.5 + - - +
92B LYS* 2.9 36.8 + - - +
144B TRP* 4.0 13.7 - - + -
148B ARG* 3.3 32.7 + - - +
152B LEU* 3.2 35.5 + - + +
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LYS* 3.0 49.4 + - + +
86B ASP* 3.1 13.0 + - - +
88B GLU* 1.3 76.1 - - - +
90B LYS* 1.3 58.5 + - + +
92B LYS* 3.3 12.4 + - + +
93B LEU* 2.9 29.7 + - - +
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Residues in contact with LYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASP* 3.0 29.9 + - - +
87B HIS* 3.5 11.7 - - - +
89B LYS* 1.3 76.6 - - + +
91B MET* 1.3 63.4 + - + +
93B LEU* 3.2 11.7 + - + +
94B ALA* 2.9 27.5 + - - +
157B THR* 3.4 49.3 - - + +
158B ASP* 5.7 1.2 - - - -
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Residues in contact with MET 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B HIS* 2.9 37.6 + - + +
88B GLU* 3.9 11.2 - - - +
90B LYS* 1.3 82.0 - - + +
92B LYS* 1.3 60.8 + - - +
94B ALA* 3.4 2.9 + - + +
95B PHE* 2.9 23.4 + - - +
144B TRP* 4.2 4.9 - - + -
147B TRP* 3.2 23.8 + - + +
148B ARG* 5.8 2.0 - - - -
151B PHE* 3.7 29.6 - - + +
156B VAL* 3.2 44.2 - - + +
157B THR 4.0 12.6 - - - -
158B ASP* 4.3 3.1 - - - +
162B ILE* 4.1 14.1 - - + -
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Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU* 2.9 22.2 + - - +
89B LYS* 3.5 10.8 - - + +
91B MET* 1.3 73.9 - - - +
93B LEU* 1.3 60.7 + - - +
95B PHE* 3.3 2.0 + - + +
96B LYS* 2.9 61.7 + - + +
144B TRP* 3.6 39.0 - - + +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LYS 2.9 14.1 + - - +
90B LYS* 3.4 13.9 - - + +
92B LYS* 1.3 76.6 - - - +
94B ALA* 1.3 56.2 + - - +
96B LYS* 3.4 8.2 + - + -
97B SER* 2.9 35.6 + - - +
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LYS 2.9 13.8 + - - +
91B MET* 3.6 10.3 - - + +
93B LEU* 1.3 76.8 - - - +
95B PHE* 1.3 63.6 + - - +
97B SER* 2.9 23.5 + - - -
98B LEU* 3.0 15.6 + - - +
147B TRP* 4.3 4.9 - - + -
158B ASP* 5.2 1.3 - - - -
159B ILE* 4.8 18.2 - - + +
162B ILE* 4.1 25.8 - - + -
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Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B MET 2.9 18.3 + - - +
92B LYS* 3.5 4.7 - - + +
94B ALA* 1.3 75.4 - - - +
96B LYS* 1.3 69.1 + - + +
98B LEU* 3.0 6.2 + - - +
99B ASP* 2.9 31.0 + - + +
104B GLY* 3.5 31.4 - - - -
105B LYS* 4.1 1.6 - - - -
106B ILE* 3.5 30.2 - - + +
142B VAL 4.3 1.1 - - - -
143B ASP 3.6 9.0 - - - -
144B TRP* 3.4 52.3 - + + -
147B TRP* 3.4 33.3 - + + +
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LYS* 2.9 47.0 + - + +
93B LEU* 4.0 8.3 - - + +
95B PHE* 1.3 87.1 - - + +
97B SER* 1.3 59.4 + - - +
99B ASP* 3.4 22.1 - - - +
102B ASN* 4.8 3.6 - - - +
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 2.9 20.6 + - - -
94B ALA* 2.9 16.3 + - - -
96B LYS* 1.3 76.2 - - - +
98B LEU* 1.3 68.1 + - - +
99B ASP 4.7 0.3 - - - -
100B LYS* 2.9 30.4 + - - +
114B SER* 4.1 0.7 + - - -
159B ILE* 5.3 6.9 - - - +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ALA 3.0 14.3 + - - +
95B PHE 3.5 6.7 - - - +
97B SER* 1.3 83.6 + - - +
99B ASP* 1.3 59.2 + - - +
100B LYS* 2.9 14.6 + - - +
106B ILE* 3.8 21.5 - - + -
110B GLU* 3.4 23.5 - - + +
111B ILE* 4.9 7.4 - - + -
114B SER* 3.3 30.9 + - - +
115B LEU* 5.7 2.2 - - + -
147B TRP* 3.4 37.0 - - + -
159B ILE* 3.9 26.9 - - + -
166B TRP* 4.3 9.6 - - + -
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 2.9 23.9 + - + +
96B LYS* 3.4 16.3 + - - +
97B SER 3.4 0.8 - - - -
98B LEU* 1.3 71.8 - - - +
100B LYS* 1.3 62.3 + - - +
101B ASN* 2.8 10.7 - - - +
102B ASN* 3.2 26.9 - - - +
103B ASP* 3.0 3.2 + - - +
104B GLY* 2.7 32.2 + - - -
105B LYS 3.2 14.1 - - - +
106B ILE* 4.7 1.3 - - + +
110B GLU* 3.9 5.2 - - - -
1003B CA 2.4 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
------------------------------------------------------------
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