Contacts of the helix formed by residues 213 - 223 (chain E) in PDB entry 3IFS
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 THR 213 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51E LEU* 3.7 23.8 - - + -
202E PRO* 3.8 27.7 - - + +
205E VAL* 3.9 17.9 - - + -
210E SER* 2.6 24.7 + - - +
212E LEU* 1.3 79.5 - - - +
214E PRO* 1.3 78.6 - - - +
215E VAL* 2.9 21.5 + - - +
216E GLY 3.1 9.4 + - - -
217E LEU* 3.1 13.6 + - - +
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Residues in contact with PRO 214 (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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59E GLU* 3.5 34.1 - - - +
63E ILE* 4.0 25.4 - - + -
141E ASN* 5.1 0.5 - - - +
179E THR* 4.1 9.0 + - + +
199E PHE* 3.8 23.6 - - + -
200E VAL 3.4 17.9 - - - +
202E PRO* 5.0 1.8 - - + -
213E THR* 1.3 89.5 - - - +
215E VAL* 1.3 63.6 + - - +
216E GLY 3.1 0.9 + - - -
217E LEU* 3.8 2.7 - - + -
218E LEU* 3.1 25.8 + - + +
219E PRO* 4.0 0.5 - - - +
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Residues in contact with VAL 215 (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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84E GLY 3.5 25.8 - - - +
85E SER* 3.5 19.6 - - - +
89E ALA* 4.5 3.4 - - + +
143E ILE* 3.6 24.3 - - + +
179E THR* 4.0 7.1 - - + +
201E ILE* 3.7 33.2 - - + -
210E SER* 3.5 19.5 - - - +
211E VAL* 5.2 0.9 - - - -
213E THR* 2.9 18.1 + - - +
214E PRO* 1.3 78.9 - - - +
216E GLY* 1.3 59.1 + - - +
219E PRO* 3.5 16.8 - - - +
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Residues in contact with GLY 216 (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 ALA* 4.4 9.2 - - - -
210E SER 4.1 0.2 + - - -
211E VAL* 3.1 28.9 + - - -
213E THR 3.1 4.4 + - - -
215E VAL* 1.3 80.9 - - - +
217E LEU* 1.3 66.7 + - - +
218E LEU 3.3 1.4 + - - -
219E PRO* 3.3 4.2 - - - +
220E ILE* 3.1 32.7 + - - +
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Residues in contact with LEU 217 (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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55E TYR* 6.2 1.8 - - + -
60E PHE* 3.8 30.5 - - + -
63E ILE* 4.0 19.7 - - + -
211E VAL 4.4 5.2 - - - +
212E LEU* 3.3 28.5 - - + +
213E THR 3.1 16.4 + - - +
214E PRO* 4.2 0.4 - - + -
216E GLY* 1.3 77.2 - - - +
218E LEU* 1.3 62.8 + - - +
220E ILE* 4.4 0.7 - - - -
221E ALA* 2.9 27.0 + - - +
227E ILE* 3.7 30.7 - - + +
230E MSE 4.2 20.2 - - + -
231E MSE 4.5 10.3 - - - -
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Residues in contact with LEU 218 (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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63E ILE* 3.6 36.4 - - + +
66E CYS* 4.2 8.1 - - + -
67E ALA* 3.9 17.3 - - + +
70E ILE* 4.4 5.8 - - + -
77E LEU* 5.5 0.7 - - + -
141E ASN* 3.6 32.1 - - + +
177E TYR* 4.2 12.8 - - + -
179E THR* 4.7 1.3 - - - +
199E PHE* 4.0 24.9 - - + -
214E PRO* 3.1 16.0 + - + +
217E LEU* 1.3 75.7 - - - +
219E PRO* 1.4 64.8 - - + +
221E ALA* 3.1 2.9 + - - +
222E VAL* 2.9 38.0 + - + +
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Residues in contact with PRO 219 (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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77E LEU* 4.0 13.5 - - + -
79E VAL* 3.9 27.4 - - + -
89E ALA* 3.8 17.9 - - + -
93E ILE* 3.8 12.5 - - + +
114E VAL* 4.3 2.6 - - + +
141E ASN* 3.7 13.5 - - - +
143E ILE* 4.8 3.4 - - + -
214E PRO 4.0 0.2 - - - +
215E VAL 3.5 19.7 - - - +
216E GLY 3.3 11.9 - - - +
218E LEU* 1.4 94.8 - - + +
220E ILE* 1.3 59.9 + - - +
222E VAL* 3.3 2.8 + - - +
223E SER* 3.1 22.9 + - - -
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Residues in contact with ILE 220 (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 ALA* 4.2 13.9 - - - +
92E ALA* 3.4 29.2 - - + -
93E ILE* 4.3 3.4 - - + -
211E VAL* 4.3 16.8 - - + +
216E GLY* 3.1 30.3 + - - +
217E LEU* 3.8 3.8 - - - +
219E PRO* 1.3 77.0 - - - +
221E ALA* 1.3 62.3 + - - +
223E SER* 2.8 24.4 + - - -
225E LEU* 3.4 34.9 + - + -
227E ILE* 3.9 10.3 - - + -
230E MSE 3.8 30.1 - - + -
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Residues in contact with ALA 221 (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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63E ILE* 4.8 1.8 - - + +
64E GLN* 5.5 2.5 - - + -
67E ALA* 3.7 19.2 - - + +
71E LYS* 3.2 14.4 + - - -
217E LEU 2.9 18.8 + - - +
218E LEU* 3.6 3.8 - - - +
220E ILE* 1.3 74.1 - - - +
222E VAL* 1.3 67.2 + - - +
224E GLY* 3.0 13.0 + - - -
225E LEU 3.7 13.1 + - - +
227E ILE* 3.9 22.0 - - + -
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Residues in contact with VAL 222 (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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67E ALA* 3.9 22.2 - - - +
70E ILE* 3.8 35.7 - - + -
71E LYS* 3.6 21.7 - - + +
77E LEU* 3.9 29.8 - - + -
111E THR* 3.8 0.7 - - - -
112E PRO* 3.6 27.3 - - + +
114E VAL* 4.5 3.8 - - + -
218E LEU* 2.9 23.0 + - + +
219E PRO 3.3 5.4 + - - +
221E ALA* 1.3 77.8 - - - +
223E SER* 1.3 58.2 + - - +
224E GLY 3.0 6.2 + - - -
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Residues in contact with SER 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ILE* 3.7 14.9 - - - +
97E ASN* 3.3 36.3 + - - -
101E TYR* 3.5 20.1 + - - -
111E THR* 3.4 14.8 + - - +
114E VAL* 4.1 10.0 - - - +
219E PRO 3.1 12.7 + - - -
220E ILE 2.8 19.0 + - - -
221E ALA 3.2 0.2 - - - -
222E VAL* 1.3 74.4 - - - +
224E GLY* 1.3 54.6 + - - +
225E LEU* 3.5 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