Contacts of the helix formed by residues 147 - 161 (chain E) in PDB entry 3IT8
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 LEU 147 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E PHE* 4.3 22.4 - - + -
71E SER* 6.2 0.2 - - - +
72E LEU* 4.3 25.1 - - + -
75E GLU* 5.3 4.7 - - - +
145E ASN* 2.6 18.6 + - - +
146E THR* 1.3 85.1 - - + +
148E TRP* 1.3 63.7 + - - +
149E LYS* 3.1 3.1 - - - -
150E ASP* 2.8 36.8 + - - +
151E VAL* 3.1 12.5 + - - +
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Residues in contact with TRP 148 (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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120E TYR* 4.1 10.5 - + - -
125E LYS 3.6 20.6 + - - -
126E ARG* 4.0 7.4 - - - -
127E PHE* 3.7 28.7 - + - -
140E MET* 3.3 25.6 - - - -
141E LEU 4.5 2.2 - - - -
142E THR 3.6 17.5 - - - +
143E VAL* 3.5 45.9 - - + +
145E ASN* 3.1 20.7 + - + +
146E THR 3.4 0.8 - - - -
147E LEU* 1.3 76.5 - - - +
149E LYS* 1.3 75.4 + - + +
151E VAL* 2.9 19.7 + - + +
152E LYS* 2.8 60.4 + - + +
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Residues in contact with LYS 149 (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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143E VAL* 4.8 7.4 - - - +
146E THR 5.2 6.5 - - - +
147E LEU 3.1 1.5 - - - -
148E TRP* 1.3 88.3 - - + +
150E ASP* 1.3 63.5 + - - +
152E LYS* 3.4 35.5 + - + +
153E ALA* 3.2 22.5 + - - +
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Residues in contact with ASP 150 (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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68E PHE* 3.5 24.0 - - + -
147E LEU* 2.8 33.8 + - - +
149E LYS* 1.3 76.4 - - - +
151E VAL* 1.3 61.0 + - - +
153E ALA* 3.2 5.3 + - - +
154E TYR* 2.8 54.5 + - + +
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Residues in contact with VAL 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E PHE* 4.4 2.9 - - + -
69E TRP* 4.2 21.1 - - + -
72E LEU* 3.7 30.3 - - + -
120E TYR* 5.2 2.0 - - + -
127E PHE* 4.3 11.0 - - + -
140E MET* 4.3 13.7 - - + +
145E ASN* 6.4 0.2 - - - -
147E LEU 3.1 10.2 + - - +
148E TRP* 2.9 40.1 + - + +
150E ASP* 1.3 77.6 - - - +
152E LYS* 1.3 64.2 + - - +
155E LEU* 2.8 34.9 + - + +
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Residues in contact with LYS 152 (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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86C SER 5.2 0.5 - - - +
120E TYR* 3.8 20.8 + - - +
125E LYS* 3.9 29.9 - - + +
143E VAL* 5.3 2.2 - - - +
148E TRP* 2.8 45.8 + - + +
149E LYS* 3.4 36.9 - - + +
151E VAL* 1.3 76.2 - - - +
153E ALA* 1.3 57.3 - - - +
156E GLY* 2.9 28.3 + - - +
157E GLY 3.1 3.6 + - - -
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Residues in contact with ALA 153 (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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86C SER 5.9 0.9 - - - -
87C TYR* 5.5 1.2 - - - -
149E LYS 3.2 14.7 + - - +
150E ASP* 3.7 7.2 - - - +
151E VAL 3.2 0.6 - - - -
152E LYS* 1.3 80.6 - - - +
154E TYR* 1.3 72.0 + - + +
157E GLY* 3.2 19.6 + - - +
158E PHE 4.2 0.2 + - - -
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Residues in contact with TYR 154 (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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60E PRO* 6.0 1.0 - - - +
62E ASN* 5.0 3.8 + - - -
65E ASN* 3.5 37.6 + - - +
68E PHE* 3.7 43.5 - + + -
69E TRP* 3.7 16.6 - - + +
150E ASP* 2.8 40.3 + - + +
153E ALA* 1.3 82.4 - - + +
155E LEU* 1.3 60.3 + - - +
158E PHE* 3.3 21.8 + - - +
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Residues in contact with LEU 155 (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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69E TRP* 3.9 16.4 - - + -
93E LEU* 4.3 20.6 - - + -
95E THR* 3.7 31.9 - - + +
108E GLY* 4.1 13.0 - - - +
120E TYR* 3.9 21.8 - - + -
127E PHE* 3.6 32.3 - - + -
151E VAL* 2.8 23.7 + - + +
154E TYR* 1.3 73.3 - - - +
156E GLY* 1.3 66.4 + - - +
158E PHE* 3.4 3.0 + - - +
159E GLU* 3.0 24.8 + - - +
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Residues in contact with GLY 156 (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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86C SER* 4.2 3.8 - - - -
120E TYR* 3.4 31.5 - - - -
122E THR* 4.1 2.5 + - - -
151E VAL 3.4 2.0 + - - -
152E LYS 2.9 14.7 + - - -
155E LEU* 1.3 78.7 - - - +
157E GLY* 1.3 53.2 + - - +
159E GLU* 3.3 2.0 + - - +
160E TYR* 2.7 37.6 + - - +
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Residues in contact with GLY 157 (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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86C SER 2.9 23.0 + - - -
87C TYR* 3.4 16.9 - - - -
152E LYS 3.1 9.9 + - - -
153E ALA* 3.2 14.0 + - - -
156E GLY* 1.3 76.8 - - - +
158E PHE* 1.3 62.4 + - - +
160E TYR* 3.1 1.4 + - - +
161E MET 3.0 20.1 + - - -
162E GLY 3.1 5.9 + - - -
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Residues in contact with PHE 158 (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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87C TYR* 4.5 3.1 - + - -
3E LEU* 4.6 1.8 - - + -
5E TYR* 3.1 49.8 - + - -
58E HIS 4.1 15.9 - - - -
60E PRO* 4.1 15.9 - - + -
95E THR* 3.8 28.0 - - + -
96E GLY* 4.3 4.3 - - - -
153E ALA 4.2 0.4 + - - -
154E TYR 3.3 20.6 + - - +
155E LEU* 3.4 4.7 + - - +
156E GLY 3.4 0.4 - - - -
157E GLY* 1.3 74.8 - - - +
159E GLU* 1.3 61.4 + - - +
161E MET 3.6 0.9 + - - -
162E GLY* 3.3 9.8 + - - +
163E CYS* 2.7 77.1 + - + +
166E ALA* 4.7 2.0 - - + -
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Residues in contact with GLU 159 (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 THR* 4.7 4.0 - - - +
96E GLY 5.7 0.4 - - - -
106E SER* 2.7 43.4 + - - +
107E TYR* 3.5 19.9 - - - +
108E GLY* 3.4 29.4 + - - -
120E TYR* 3.2 40.7 - - - +
122E THR* 4.2 13.4 + - - +
155E LEU* 3.0 17.8 + - - +
156E GLY* 3.7 3.6 - - - +
158E PHE* 1.3 74.8 - - - +
160E TYR* 1.3 65.6 + - - +
161E MET 3.5 0.2 + - - -
163E CYS* 5.1 0.7 - - - -
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Residues in contact with TYR 160 (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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82C ARG* 3.3 28.7 + - - -
84C ALA* 4.1 4.7 - - + -
86C SER* 3.6 29.4 - - - +
87C TYR* 4.3 1.8 - - + -
125C GLN 5.4 0.5 + - - -
127C GLU* 3.2 44.8 - - + +
122E THR* 3.3 34.9 + - + +
156E GLY 2.7 21.5 + - - +
157E GLY 3.1 4.2 + - - +
159E GLU* 1.3 75.4 - - - +
161E MET* 1.3 74.9 + - + +
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Residues in contact with MET 161 (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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33B ALA* 4.9 9.0 - - + +
34B ASN* 3.6 17.7 - - - +
82C ARG* 3.1 35.7 - - - +
84C ALA* 4.8 4.0 - - + -
87C TYR* 4.1 12.1 - - + -
91C VAL* 4.1 22.2 - - - -
157E GLY 3.0 3.4 + - - -
158E PHE 3.8 0.2 - - - -
159E GLU 3.4 1.8 - - - -
160E TYR* 1.3 95.0 - - + +
162E GLY* 1.3 72.0 + - - +
163E CYS 3.3 2.5 - - - -
164E SER* 2.8 31.3 + - - +
165E LEU* 3.1 30.7 + - + +
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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
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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