Contacts of the helix formed by residues 213 - 223 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51F LEU* 3.8 24.7 - - + -
200F VAL 4.9 0.2 + - - -
202F PRO* 3.8 29.2 - - + +
205F VAL* 3.9 17.9 - - + -
210F SER* 2.7 23.4 + - - +
212F LEU* 1.3 81.3 - - - +
214F PRO* 1.3 77.7 - - - +
215F VAL* 2.9 21.5 + - - +
216F GLY 3.1 9.7 + - - -
217F LEU* 3.2 11.8 + - - +
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Residues in contact with PRO 214 (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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59F GLU* 3.4 34.3 - - - +
63F ILE* 4.0 23.6 - - + -
141F ASN* 5.1 0.3 - - - +
179F THR* 4.2 9.6 + - + +
199F PHE* 3.7 22.4 - - + -
200F VAL 3.4 20.4 - - - +
202F PRO* 5.0 1.3 - - + -
213F THR* 1.3 89.4 - - - +
215F VAL* 1.3 62.7 + - - +
217F LEU* 3.8 2.7 - - + -
218F LEU* 3.2 25.7 + - + +
219F PRO* 4.1 0.3 - - - +
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Residues in contact with VAL 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F GLY 3.6 23.6 - - - +
85F SER* 3.6 19.9 - - - +
89F ALA* 4.5 4.6 - - + +
143F ILE* 3.6 25.9 - - + +
179F THR* 3.9 7.6 - - + +
201F ILE* 3.8 34.8 - - + -
210F SER* 3.6 17.7 - - - +
211F VAL* 5.2 0.7 - - - -
213F THR* 2.9 17.5 + - - +
214F PRO* 1.3 80.2 - - - +
216F GLY* 1.3 59.7 + - - +
219F PRO* 3.5 14.0 - - - +
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Residues in contact with GLY 216 (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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89F ALA* 4.3 10.1 - - - -
211F VAL* 3.2 23.3 + - - -
213F THR 3.1 4.2 + - - -
215F VAL* 1.3 79.6 - - - +
217F LEU* 1.3 66.1 + - - +
218F LEU 3.2 1.1 + - - -
219F PRO* 3.3 4.2 - - - +
220F ILE* 3.0 38.0 + - - +
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Residues in contact with LEU 217 (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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55F TYR* 6.1 2.0 - - + -
60F PHE* 3.9 30.1 - - + -
63F ILE* 3.8 23.1 - - + +
211F VAL 4.4 5.6 - - - +
212F LEU* 3.5 26.5 - - + +
213F THR 3.2 16.0 + - - +
214F PRO* 3.5 0.9 + - + -
216F GLY* 1.3 76.2 - - - +
218F LEU* 1.3 57.7 + - - +
220F ILE* 4.2 3.6 - - - -
221F ALA* 3.0 30.1 + - - +
227F ILE* 3.7 28.2 - - + +
230F MSE 4.3 18.6 - - + -
231F MSE 4.8 10.1 - - + -
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Residues in contact with LEU 218 (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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63F ILE* 3.6 37.7 - - + +
66F CYS* 4.2 9.2 - - + -
67F ALA* 4.1 11.7 - - - +
70F ILE* 4.7 4.3 - - + -
77F LEU* 5.5 0.9 - - + -
141F ASN* 3.7 30.1 - - + +
177F TYR* 4.1 13.2 - - + -
179F THR* 4.7 1.3 - - - +
199F PHE* 3.9 27.1 - - + -
214F PRO* 3.2 13.0 + - + +
217F LEU* 1.3 77.7 - - - +
219F PRO* 1.3 72.7 - - + +
221F ALA* 3.1 3.3 + - - +
222F VAL* 3.0 34.8 + - + +
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Residues in contact with PRO 219 (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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77F LEU* 4.1 13.7 - - + -
79F VAL* 4.0 25.4 - - + -
89F ALA* 4.0 12.6 - - + -
93F ILE* 3.7 23.3 - - + +
114F VAL* 4.4 2.6 - - + +
141F ASN* 3.7 15.5 - - - +
143F ILE* 4.6 3.6 - - + -
215F VAL 3.5 20.4 - - - +
216F GLY 3.3 8.5 - - - +
218F LEU* 1.3 95.9 - - + +
220F ILE* 1.3 60.3 - - - +
222F VAL* 3.2 2.9 + - - +
223F SER* 3.1 18.5 + - - -
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Residues in contact with ILE 220 (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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89F ALA* 4.3 12.3 - - - +
92F ALA* 3.4 29.8 - - + -
93F ILE* 4.2 3.4 - - + -
211F VAL* 4.3 11.7 - - + +
216F GLY* 3.0 34.1 + - - +
217F LEU* 3.9 4.5 - - - +
219F PRO* 1.3 75.9 - - - +
221F ALA* 1.3 61.8 + - - +
223F SER* 2.8 23.5 + - - -
225F LEU* 3.3 30.9 + - + -
227F ILE* 3.8 11.7 - - + -
230F MSE 3.7 32.5 - - + -
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Residues in contact with ALA 221 (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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63F ILE* 4.6 3.4 - - + +
64F GLN* 5.4 2.9 - - + -
67F ALA* 3.7 18.8 - - + -
71F LYS* 3.0 21.7 + - - -
217F LEU 3.0 19.4 + - - +
218F LEU 3.1 3.6 + - - +
220F ILE* 1.3 74.3 - - - +
222F VAL* 1.3 65.0 + - - +
224F GLY* 3.0 7.1 + - - -
225F LEU 3.8 13.2 + - - +
227F ILE* 4.1 22.4 - - + -
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Residues in contact with VAL 222 (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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67F ALA* 3.8 22.0 - - - -
70F ILE* 4.0 27.1 - - + -
71F LYS* 3.5 18.6 - - + +
77F LEU* 3.9 31.0 - - + -
111F THR* 3.7 0.5 - - - -
112F PRO* 3.5 38.1 - - + +
114F VAL* 4.6 4.7 - - + -
218F LEU* 3.0 20.7 + - + +
219F PRO 3.2 7.4 + - - +
221F ALA* 1.3 74.6 - - - +
223F SER* 1.3 57.4 + - - +
224F GLY 3.0 4.7 + - - -
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Residues in contact with SER 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F ILE* 3.7 18.0 - - - +
97F ASN* 3.1 38.9 + - - -
101F TYR* 3.4 17.8 + - - -
111F THR* 3.3 14.2 + - - +
114F VAL* 4.2 7.4 - - - +
219F PRO 3.1 11.5 + - - -
220F ILE 2.8 18.7 + - - -
221F ALA 3.2 0.2 - - - -
222F VAL* 1.3 75.0 - - - +
224F GLY* 1.3 56.0 + - - +
225F 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