Contacts of the helix formed by residues 82 - 99 (chain F) 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 PHE 82 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E LEU* 4.2 6.5 - - + -
158E LEU* 3.3 32.7 + - + +
159E GLY* 4.3 1.0 + - - -
187E TRP* 4.3 4.9 - - + -
191E CYS* 3.4 63.9 - - + -
194E ILE* 3.9 21.1 - - + -
195E HIS* 4.1 11.4 - - + -
79F MET* 3.0 10.4 + - + +
81F GLY* 1.3 78.2 - - - +
83F LEU* 1.3 65.4 + - - +
84F PRO 3.4 0.7 - - - -
85F PHE* 3.0 50.6 + + - +
86F SER* 3.1 25.5 + - - -
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Residues in contact with LEU 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E ILE* 3.9 31.0 - - + -
198E MET* 5.2 1.1 - - + -
64F PHE 3.2 9.9 - - - +
65F TYR* 3.4 23.8 - - + +
66F MET 3.7 18.8 - - - +
67F MET* 4.2 33.9 - - + -
68F PRO* 4.9 0.2 - - + -
76F PRO 5.7 0.4 - - - +
79F MET 3.3 10.8 + - - +
80F GLU* 4.0 22.7 - - + +
82F PHE* 1.3 78.0 - - + +
84F PRO* 1.3 70.7 - - + +
86F SER* 3.1 4.9 + - - -
87F ASN* 3.0 26.6 + - - +
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Residues in contact with PRO 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F HIS* 3.8 17.9 + - + +
50F MET* 4.8 5.2 - - + -
64F PHE* 3.0 29.2 - - + +
65F TYR* 3.9 20.6 - - + +
80F GLU 3.1 22.0 - - - +
81F GLY* 3.5 12.8 - - - +
82F PHE 3.6 0.7 - - - -
83F LEU* 1.3 88.4 - - + +
85F PHE* 1.3 57.0 + - - +
87F ASN* 4.1 0.5 - - - +
88F LEU* 2.8 34.1 + - - +
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Residues in contact with PHE 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E LEU* 4.9 8.1 - - + -
157E ASP 5.2 7.0 - - - +
158E LEU* 4.6 5.2 - - + +
195E HIS* 4.7 6.3 - + - -
46F HIS* 4.0 15.6 - + + -
81F GLY 5.1 2.0 - - - +
82F PHE* 3.0 48.4 + + + +
84F PRO* 1.3 80.5 - - - +
86F SER* 1.3 69.7 + - - +
88F LEU* 3.2 2.8 + - - +
89F VAL* 2.9 39.0 + - + +
106F THR* 3.7 29.4 - - + -
109F ILE* 4.0 16.4 - - + -
110F LEU* 3.4 45.3 - - + -
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Residues in contact with SER 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E ILE* 4.1 2.2 - - - +
195E HIS* 3.0 35.7 + - - -
198E MET* 3.1 24.2 - - - +
82F PHE* 3.1 29.6 + - - -
83F LEU 3.1 5.1 + - - -
85F PHE* 1.3 84.0 - - - +
87F ASN* 1.3 52.6 + - - +
89F VAL* 3.4 4.5 + - - +
90F THR* 2.8 34.2 + - - -
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Residues in contact with ASN 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E MET* 3.5 24.5 - - - +
202E SER* 4.2 8.9 + - - -
63F HIS 3.8 12.0 + - - -
64F PHE* 3.2 30.2 - - + +
66F MET* 3.4 22.8 + - - +
83F LEU 3.0 21.3 + - - +
84F PRO 4.1 1.6 - - - +
86F SER* 1.3 73.1 - - - +
88F LEU* 1.3 66.8 + - - +
90F THR* 3.0 7.3 + - - +
91F HIS* 2.9 41.4 + - + -
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Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F HIS* 4.1 34.8 - - + +
49F TYR* 4.1 20.2 - - + -
50F MET* 4.2 1.8 - - + +
53F LEU* 3.5 24.9 - - + -
64F PHE* 3.9 16.3 - - + -
84F PRO 2.8 26.2 + - - +
85F PHE* 3.2 4.9 + - - +
87F ASN* 1.3 72.7 - - - +
89F VAL* 1.3 57.3 + - + +
91F HIS* 3.5 1.1 + - - +
92F LEU* 2.9 44.9 + - + +
109F ILE* 3.8 31.9 - - + -
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Residues in contact with VAL 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E HIS* 3.8 18.4 - - + +
199E LYS* 5.1 3.1 - - - +
85F PHE* 2.9 37.3 + - + +
86F SER 3.5 4.3 - - - +
88F LEU* 1.3 74.2 - - - +
90F THR* 1.3 67.7 + - - +
92F LEU* 3.4 5.9 + - - +
93F ASP* 2.9 40.0 + - - +
104F PHE* 4.9 6.1 - - + -
106F THR* 3.6 37.0 - - + +
109F ILE* 4.2 15.7 - - + -
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Residues in contact with THR 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E HIS* 4.9 4.5 - - - -
198E MET* 3.1 37.3 - - + +
199E LYS* 5.9 1.4 - - - +
86F SER 2.8 16.5 + - - -
87F ASN* 3.0 10.7 + - - +
89F VAL* 1.3 76.7 - - - +
91F HIS* 1.3 65.0 + - + +
93F ASP* 3.2 24.5 - - - +
94F SER* 3.8 5.2 + - - -
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Residues in contact with HIS 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F LEU* 3.7 25.3 - - + +
57F TYR* 5.2 5.0 - + + -
59F ILE* 4.2 25.9 - - + +
63F HIS* 4.8 9.6 - - + -
64F PHE* 3.9 16.3 - + - -
87F ASN* 2.9 44.3 + - + +
90F THR* 1.3 79.2 - - + +
92F LEU* 1.3 57.4 + - - +
93F ASP 2.9 4.9 - - - -
94F SER* 2.8 25.2 + - - +
95F PHE* 2.9 12.8 + - - +
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Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F TYR* 3.8 35.0 - - + +
53F LEU* 3.9 20.4 - - + -
88F LEU* 2.9 29.0 + - + +
89F VAL 4.0 0.7 - - - +
91F HIS* 1.3 75.8 - - - +
93F ASP* 1.3 62.3 + - - +
95F PHE* 3.8 12.3 - - + +
96F LEU* 3.1 44.3 + - + +
97F PRO* 3.9 0.2 - - - +
104F PHE* 3.5 40.6 - - + +
109F ILE* 3.6 18.8 - - + -
124F ILE* 5.3 0.2 - - + -
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Residues in contact with ASP 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E LYS* 5.3 5.9 + - - -
89F VAL* 2.9 33.0 + - - +
90F THR* 3.2 16.2 - - + +
91F HIS 2.9 0.2 - - - -
92F LEU* 1.3 78.7 - - - +
94F SER* 1.3 56.7 + - - +
97F PRO* 3.0 24.8 - - - +
104F PHE* 4.3 15.3 - - - +
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Residues in contact with SER 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F TYR* 3.2 18.4 + - - -
90F THR 4.5 5.8 - - - -
91F HIS* 2.8 10.0 + - - -
93F ASP* 1.3 82.2 - - - +
95F PHE* 1.3 62.7 + - - +
97F PRO* 3.4 9.7 - - - +
98F ILE* 3.8 15.4 - - - +
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Residues in contact with PHE 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ALA* 4.5 11.0 - - + -
53F LEU* 3.7 24.2 - - + -
56F VAL* 3.8 26.2 - - + -
57F TYR* 3.6 24.0 - + - +
91F HIS 2.9 14.1 + - - +
92F LEU* 4.3 9.4 - - + +
94F SER* 1.3 76.5 + - - +
96F LEU* 1.3 70.5 + - + +
97F PRO 3.3 0.2 - - - -
98F ILE* 2.8 34.1 + - + +
99F CYS* 3.1 31.7 + - - -
124F ILE* 3.7 25.8 - - + -
127F PHE* 3.8 26.7 - + - -
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Residues in contact with LEU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F TYR* 5.2 2.2 - - + -
92F LEU* 3.1 27.1 + - + +
95F PHE* 1.3 80.9 - - + +
97F PRO* 1.4 69.1 - - + +
99F CYS* 3.0 13.9 + - + +
100F ARG 3.1 0.2 + - - -
101F VAL* 2.8 44.2 + - + +
104F PHE* 3.0 49.6 - - + -
120F PHE* 4.8 10.8 - - + -
124F ILE* 3.8 35.2 - - + -
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Residues in contact with PRO 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F LEU 3.9 0.2 - - - +
93F ASP* 3.0 28.7 - - - +
94F SER* 3.4 11.0 - - - +
96F LEU* 1.4 91.8 - - + +
98F ILE* 1.3 55.3 + - + +
100F ARG* 2.9 25.1 + - - -
101F VAL 3.0 13.2 - - - +
102F ASN* 3.8 20.3 - - - +
104F PHE* 6.3 0.2 - - + -
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Residues in contact with ILE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E LEU* 5.5 2.5 - - + -
230E ILE* 3.7 42.2 - - + -
233E TYR* 3.5 22.2 - - + -
57F TYR* 3.3 27.8 - - + +
94F SER* 3.8 13.2 - - - +
95F PHE* 2.8 16.9 + - + +
97F PRO* 1.3 74.4 - - + +
99F CYS* 1.3 54.7 + - - +
100F ARG* 3.0 13.7 + - - +
127F PHE* 3.6 35.9 - - + -
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Residues in contact with CYS 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E TYR* 4.7 1.6 - - - -
95F PHE* 3.4 49.8 - - - -
96F LEU* 3.0 13.4 + - + +
98F ILE* 1.3 72.5 - - - +
100F ARG* 1.3 70.9 + - - +
101F VAL* 3.3 5.1 + - + +
123F GLY* 3.3 36.5 - - - +
124F ILE* 3.7 19.5 - - + +
127F PHE* 4.0 13.7 - - - -
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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