Contacts of the helix formed by residues 88 - 106 (chain E) in PDB entry 3IZ0
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 ASP 88 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85E PRO* 2.8 27.4 + - + +
87E ASN* 1.3 80.5 + - - +
89E LYS* 1.3 68.0 + - - +
90E ALA* 3.0 20.5 + - - +
91E PHE* 3.1 18.1 + - + +
92E ILE* 3.1 14.7 + - - +
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Residues in contact with LYS 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A ASP* 5.4 5.6 + - - -
87E ASN 3.8 4.2 + - - +
88E ASP* 1.3 72.5 + - - +
90E ALA* 1.3 52.1 + - - +
92E ILE* 3.2 8.1 + - - +
93E GLN* 2.7 44.2 + - + +
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Residues in contact with ALA 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E ASP* 3.0 15.1 + - - +
89E LYS* 1.3 77.5 - - - +
91E PHE* 1.3 57.5 + - - +
93E GLN* 3.3 8.4 + - - +
94E GLN* 2.7 30.0 + - - +
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Residues in contact with PHE 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E ARG* 3.8 36.6 - - + -
85E PRO* 3.6 45.8 - - + +
86E LEU* 4.2 11.0 - - + -
88E ASP* 3.1 8.4 + - + +
90E ALA* 1.3 75.3 - - - +
92E ILE* 1.3 68.0 + - + +
94E GLN* 3.2 25.3 + - - +
95E CYS* 2.9 57.3 + - - -
183E ALA* 5.1 0.4 - - + -
74F MET* 6.3 0.9 - - - -
75F TYR* 3.5 25.1 - + - -
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Residues in contact with ILE 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E LEU* 3.3 31.4 - - + +
88E ASP 3.1 10.3 + - - +
89E LYS* 3.8 8.3 - - - +
91E PHE* 1.3 90.8 - - + +
93E GLN* 1.3 60.0 + - - +
95E CYS* 3.3 6.5 + - - +
96E ILE* 3.0 43.3 + - + +
178E TRP* 5.0 4.5 - - + -
179E PRO* 3.6 42.8 - - + +
182E VAL* 4.1 14.6 - - + -
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Residues in contact with GLN 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E LYS* 2.7 25.2 + - + +
90E ALA* 3.6 8.3 - - - +
92E ILE* 1.3 76.5 - - + +
94E GLN* 1.3 63.9 + - - +
96E ILE* 3.4 9.0 + - - +
97E ARG* 3.0 29.4 + - - +
114E MET* 3.4 33.3 - - + +
118E GLN* 3.1 33.7 + - - +
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Residues in contact with GLN 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E ALA 2.7 20.6 + - - +
91E PHE* 3.4 29.2 - - - +
93E GLN* 1.3 73.1 - - - +
95E CYS* 1.3 62.0 + - - +
97E ARG* 3.3 10.0 + - + +
98E GLN* 3.0 46.3 + - + +
74F MET* 4.4 19.8 - - - +
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Residues in contact with CYS 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E PHE* 2.9 53.8 + - - -
92E ILE* 3.4 12.3 - - - +
94E GLN* 1.3 77.3 - - - +
96E ILE* 1.3 62.9 + - - +
98E GLN* 3.1 8.0 + - - +
99E LEU* 3.0 19.6 + - - +
182E VAL* 3.9 20.9 - - + +
183E ALA* 4.5 15.7 - - - -
186E VAL* 3.5 25.8 - - + +
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Residues in contact with ILE 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E ILE* 3.0 27.2 + - + +
93E GLN* 3.5 27.4 - - - +
95E CYS* 1.3 73.4 - - - +
97E ARG* 1.3 52.7 + - - +
99E LEU* 3.1 5.2 + - - +
100E CYS* 2.7 33.4 + - - +
114E MET* 3.8 26.5 - - + +
117E LEU* 3.7 30.6 - - + +
118E GLN* 3.7 13.2 - - - +
178E TRP* 3.6 30.5 - - + +
182E VAL* 4.0 13.2 - - + -
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Residues in contact with ARG 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLN* 3.0 18.5 + - - +
94E GLN* 3.3 14.4 - - + +
96E ILE* 1.3 76.5 - - - +
98E GLN* 1.3 58.5 + - + +
100E CYS* 3.7 0.7 - - - +
101E GLU* 2.8 60.2 + - - +
114E MET* 3.5 46.2 - - - +
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Residues in contact with GLN 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLN* 3.0 32.2 + - + +
95E CYS* 3.1 10.4 + - - +
97E ARG* 1.3 76.6 - - + +
99E LEU* 1.3 57.9 + - - +
101E GLU* 3.7 12.1 - - - +
102E PHE* 2.9 32.3 + - - +
186E VAL* 3.2 33.6 - - + +
189E ILE* 4.3 5.1 - - + +
190E ASP* 5.9 0.6 + - - -
74F MET* 3.2 34.9 - - - +
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Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E CYS 3.0 11.1 + - - +
96E ILE* 3.4 7.4 - - - +
98E GLN* 1.3 73.8 - - - +
100E CYS* 1.3 69.2 + - - +
102E PHE* 3.3 0.7 + - - +
103E LEU* 3.0 39.7 + - + +
117E LEU* 4.1 20.4 - - + -
128E ILE* 4.1 23.6 - - + -
132E LEU* 4.1 11.4 - - + -
178E TRP* 4.1 20.4 - - + -
182E VAL* 4.3 6.7 - - + -
185E LEU* 4.0 25.6 - - + -
186E VAL* 4.4 5.7 - - + +
189E ILE* 4.0 22.0 - - + -
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Residues in contact with CYS 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ILE 2.7 19.8 + - - +
97E ARG 3.7 4.9 - - - +
99E LEU* 1.3 75.1 - - - +
101E GLU* 1.3 65.2 + - + +
103E LEU* 3.3 2.0 + - - +
104E THR* 3.1 28.7 + - - -
112E VAL* 4.1 12.6 - - - -
113E SER* 3.7 39.7 - - - -
114E MET* 3.9 14.8 - - - -
117E LEU* 3.7 12.5 - - + +
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Residues in contact with GLU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ARG* 2.8 53.4 + - - +
98E GLN* 3.7 10.4 - - - +
100E CYS* 1.3 73.1 - - - +
102E PHE* 1.3 62.4 + - - +
104E THR* 3.4 4.2 + - - -
105E GLU* 3.0 50.8 + - - +
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Residues in contact with PHE 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E GLN 2.9 21.4 + - - +
99E LEU 3.8 1.1 - - - +
101E GLU* 1.3 72.4 - - - +
103E LEU* 1.3 67.6 + - + +
105E GLU* 3.3 3.4 + - - -
106E ASN* 2.8 54.8 + - + +
131E PHE* 4.6 0.9 - + - -
132E LEU* 3.5 34.3 - - + -
135E PHE* 4.1 23.3 - + - -
189E ILE* 3.6 33.9 - - + -
192E ILE* 4.1 28.3 - - + -
193E LYS* 5.2 11.9 - - + -
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E LEU* 3.0 38.6 + - + +
100E CYS 3.7 2.7 - - - +
102E PHE* 1.3 77.5 - - - +
104E THR* 1.3 63.1 + - - +
106E ASN* 3.3 4.5 + - - +
108E TYR* 3.1 44.9 + - + +
112E VAL* 4.1 26.9 - - + -
117E LEU* 4.7 3.1 - - + -
128E ILE* 3.9 31.0 - - + -
131E PHE* 3.5 31.4 - - + -
132E LEU* 4.2 14.6 - - + -
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Residues in contact with THR 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E CYS* 3.1 21.9 + - - -
101E GLU* 3.8 5.4 - - - -
103E LEU* 1.3 74.9 - - - +
105E GLU* 1.3 65.2 + - + +
106E ASN 3.4 0.3 + - - -
107E GLY* 3.7 9.0 + - - -
108E TYR* 5.2 1.3 - - - +
112E VAL* 3.7 18.6 + - - +
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Residues in contact with GLU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E GLU* 3.0 44.3 + - - +
102E PHE* 4.0 3.9 - - - +
104E THR* 1.3 81.7 - - + +
106E ASN* 1.3 67.3 + - - +
107E GLY 3.5 1.3 + - - -
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Residues in contact with ASN 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E PHE* 2.8 52.6 + - + +
103E LEU 3.3 0.2 + - - -
104E THR 3.2 0.2 - - - -
105E GLU* 1.3 87.9 + - - +
107E GLY* 1.3 60.2 + - - +
108E TYR 3.4 2.7 - - - -
131E PHE* 3.4 17.5 - - + -
135E PHE* 3.8 31.6 - - + -
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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