Contacts of the helix formed by residues 161 - 175 (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 MET 161 (chain E).
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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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Residues in contact with GLY 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C TYR* 3.3 35.4 - - - -
58E HIS* 3.8 4.5 - - - +
157E GLY 3.1 9.4 + - - -
158E PHE* 3.7 12.6 - - - -
161E MET* 1.3 78.0 - - - +
163E CYS* 1.3 62.8 + - - +
165E LEU* 3.2 4.4 + - - +
166E ALA* 2.9 22.3 + - - +
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Residues in contact with CYS 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E LEU* 3.9 11.9 - - - -
96E GLY* 3.6 8.5 - - - +
97E CYS* 3.2 46.4 - - + -
106E SER* 5.2 2.2 - - - -
158E PHE* 2.7 59.1 + - + +
159E GLU* 5.1 1.8 - - - -
162E GLY* 1.3 71.1 - - - +
164E SER* 1.3 57.8 + - - +
166E ALA* 2.9 3.0 + - - +
167E ILE* 2.8 30.3 + - - +
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Residues in contact with SER 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG* 5.7 2.3 - - - -
33B ALA* 4.5 15.9 + - - -
97E CYS* 3.9 15.9 - - - +
99E GLU* 5.3 1.6 - - - +
106E SER* 6.1 2.7 - - - -
158E PHE 4.6 0.2 + - - -
161E MET* 2.8 32.1 + - - +
163E CYS* 1.3 78.2 - - - +
165E LEU* 1.3 60.4 + - - +
167E ILE* 3.2 18.6 - - - +
168E LEU* 3.8 11.1 - - - +
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Residues in contact with LEU 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 3.5 29.8 - - + -
147B SER* 6.1 0.7 - - - +
87C TYR* 4.0 6.3 - - + -
91C VAL* 3.5 34.5 - - + -
58E HIS* 3.7 30.8 - - + +
161E MET* 3.1 25.1 + - + +
162E GLY 3.5 5.4 - - - +
163E CYS 3.1 0.8 - - - -
164E SER* 1.3 79.0 + - - +
166E ALA* 1.3 67.8 + - - +
168E LEU* 3.3 25.5 + - + +
169E ASP* 3.9 7.3 + - - +
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Residues in contact with ALA 166 (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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3E LEU* 4.2 11.7 - - + -
5E TYR* 5.2 0.2 - - - +
56E SER* 4.5 0.9 - - - +
58E HIS* 3.7 30.7 - - + +
59E THR* 4.3 2.2 - - - +
158E PHE* 4.7 2.7 - - + -
162E GLY 2.9 15.7 + - - +
163E CYS* 3.5 6.1 - - - +
165E LEU* 1.3 75.5 - - - +
167E ILE* 1.3 56.9 + - - +
169E ASP* 2.7 33.1 + - - +
170E TYR* 3.2 22.6 + - + -
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Residues in contact with ILE 167 (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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1E ILE* 3.8 32.9 - - + +
2E THR* 3.9 6.5 - - - -
3E LEU* 3.8 36.4 - - + +
25E TYR* 4.1 9.5 - - + -
97E CYS* 3.7 25.4 - - - +
98E TYR* 4.5 4.3 - - - -
99E GLU* 4.7 7.9 - - + +
163E CYS 2.8 16.2 + - - +
164E SER* 3.2 21.5 - - - +
166E ALA* 1.3 72.3 - - - +
168E LEU* 1.3 75.6 + - + +
170E TYR* 3.4 5.5 + - - +
171E GLN* 3.1 21.3 + - - +
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Residues in contact with LEU 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG* 3.7 53.4 - - + +
33B ALA* 6.0 1.6 - - + +
1E ILE* 5.0 2.5 - - + -
99E GLU* 4.0 10.3 - - - +
164E SER 3.8 16.4 - - - +
165E LEU* 3.5 17.0 - - + +
166E ALA 2.8 1.0 + - - -
167E ILE* 1.3 82.4 - - + +
169E ASP* 1.3 67.5 + - - +
171E GLN* 3.5 18.8 + - - +
172E LYS* 3.2 28.5 + - - +
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Residues in contact with ASP 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ARG 3.6 22.3 - - - +
56E SER* 3.7 18.4 + - - +
57E PRO* 3.6 18.9 - - - +
58E HIS* 4.3 9.7 - - - -
165E LEU 4.0 11.9 - - - +
166E ALA* 2.7 17.9 + - - +
168E LEU* 1.3 72.1 - - - +
170E TYR* 1.3 64.0 + - - +
172E LYS* 3.3 18.3 + - - +
173E MET* 3.2 29.1 + - + +
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Residues in contact with TYR 170 (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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3E LEU* 3.7 28.9 - - + -
5E TYR* 2.7 15.7 + - - -
23E ASP* 2.7 38.1 + - - -
25E TYR* 3.6 31.6 - + + -
30E VAL* 4.0 10.8 - - + -
50E TRP* 3.7 5.8 - + + -
51E PHE* 3.5 34.5 - + - -
56E SER* 3.8 4.9 - - - -
59E THR* 3.3 25.2 + - - +
166E ALA* 3.2 25.4 + - + -
167E ILE 3.6 4.0 - - - +
168E LEU 3.3 0.2 - - - -
169E ASP* 1.3 79.3 - - - +
171E GLN* 1.3 57.8 + - - +
173E MET* 3.2 3.7 + - - -
174E ALA* 2.8 32.3 + - - +
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Residues in contact with GLN 171 (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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21B GLN* 4.0 34.1 + - - +
32B ARG* 4.8 5.9 + - - -
1E ILE* 3.8 29.2 - - + +
25E TYR* 3.3 22.1 + - - +
167E ILE 3.1 10.4 + - - +
168E LEU* 3.6 27.7 - - - +
169E ASP 3.3 0.2 - - - -
170E TYR* 1.3 79.3 - - - +
172E LYS* 1.3 63.9 + - + +
174E ALA* 3.1 1.1 + - - +
175E LYS* 2.9 24.0 + - - +
286E ASP* 5.4 0.8 + - - -
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Residues in contact with LYS 172 (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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20B PRO* 6.0 5.8 - - - -
21B GLN* 5.8 4.9 - - - +
145B ALA* 4.1 19.4 + - - +
55E ARG* 5.5 8.5 - - - +
168E LEU* 3.2 16.2 + - - +
169E ASP* 3.5 19.5 + - - +
171E GLN* 1.3 82.8 - - + +
173E MET* 1.3 63.7 + - + +
174E ALA 3.3 0.3 + - - -
175E LYS* 3.5 17.0 + - - +
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Residues in contact with MET 173 (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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50E TRP* 3.4 36.3 - - + +
51E PHE* 3.8 21.5 - - + -
52E ASN* 3.4 42.8 - - - +
55E ARG* 3.4 61.9 - - + +
56E SER* 4.0 1.6 - - - -
169E ASP 3.2 22.6 + - - +
170E TYR 3.2 3.8 + - - +
172E LYS* 1.3 77.9 - - + +
174E ALA* 1.3 60.2 + - - +
176E GLY 5.1 0.7 + - - -
177E LYS* 4.9 3.5 - - - +
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Residues in contact with ALA 174 (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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25E TYR* 3.7 24.9 - - + -
50E TRP* 3.5 24.5 - - + -
170E TYR 2.8 16.4 + - - +
171E GLN 3.8 2.5 - - - +
172E LYS 3.1 0.2 - - - -
173E MET* 1.3 79.6 - - - +
175E LYS* 1.3 68.8 - - - +
176E GLY 3.3 1.3 - - - -
177E LYS* 2.8 16.4 + - - +
178E ILE* 3.6 21.5 + - + +
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Residues in contact with LYS 175 (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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21B GLN* 4.1 24.5 - - - +
23B GLU* 4.5 13.5 + - - -
171E GLN 2.9 13.0 + - - +
172E LYS* 3.5 15.9 + - - +
173E MET 3.5 0.2 - - - -
174E ALA* 1.3 75.4 - - - +
176E GLY* 1.3 61.9 + - - +
178E ILE* 4.5 10.2 + - - +
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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