Contacts of the helix formed by residues 213 - 223 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C LEU* 3.7 24.0 - - + -
200C VAL 4.6 0.4 - - - -
201C ILE* 4.9 1.0 - - - +
202C PRO* 3.8 29.0 - - + +
205C VAL* 4.0 17.5 - - + -
210C SER* 2.6 24.9 + - - +
212C LEU* 1.3 82.8 - - - +
214C PRO* 1.3 78.2 - - - +
215C VAL* 2.9 21.0 + - - +
216C GLY 3.1 9.4 + - - -
217C LEU* 3.2 11.6 + - - +
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Residues in contact with PRO 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C GLU* 3.4 36.1 - - - +
63C ILE* 3.9 25.6 - - + -
141C ASN* 5.0 0.7 - - - +
179C THR* 4.2 10.3 + - + +
199C PHE* 3.7 23.3 - - + -
200C VAL 3.5 16.2 - - - +
202C PRO* 5.2 1.1 - - + -
213C THR* 1.3 89.8 - - - +
215C VAL* 1.3 64.5 + - - +
216C GLY 3.2 0.2 - - - -
217C LEU* 3.8 2.9 - - + -
218C LEU* 3.2 25.6 + - + +
219C PRO* 3.9 0.2 - - - +
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Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLY 3.4 25.6 - - - +
85C SER* 3.6 18.8 - - - +
89C ALA* 4.4 5.5 - - + +
143C ILE* 3.6 23.9 - - + +
179C THR* 3.9 7.1 - - + +
201C ILE* 3.7 30.7 - - + -
210C SER* 3.6 19.3 - - - +
211C VAL* 5.1 1.3 - - - -
213C THR* 3.0 16.6 - - - +
214C PRO* 1.3 79.3 - - - +
216C GLY* 1.3 61.4 + - - +
219C PRO* 3.4 16.8 - - - +
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Residues in contact with GLY 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA* 4.2 12.1 - - - -
211C VAL* 3.2 21.6 + - - -
213C THR 3.1 4.2 + - - -
215C VAL* 1.3 82.0 - - - +
217C LEU* 1.3 63.8 + - - +
218C LEU 3.4 0.4 - - - -
219C PRO* 3.2 5.2 - - - +
220C ILE* 3.0 37.8 + - - +
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Residues in contact with LEU 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C TYR* 6.0 1.8 - - + -
60C PHE* 3.8 30.7 - - + -
63C ILE* 3.9 21.3 - - + +
211C VAL 4.4 5.4 - - - +
212C LEU* 3.5 24.9 - - + +
213C THR 3.2 16.2 + - - +
214C PRO* 4.1 1.1 - - + -
216C GLY* 1.3 75.3 - - - +
218C LEU* 1.3 57.5 + - - +
220C ILE* 4.3 1.3 - - - -
221C ALA* 2.9 31.2 + - - +
227C ILE* 3.7 28.4 - - + +
230C MSE 4.3 18.6 - - + -
231C MSE 4.4 13.0 - - + -
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ILE* 3.6 35.8 - - + +
66C CYS* 4.3 8.3 - - + -
67C ALA* 4.2 7.6 - - - +
70C ILE* 4.3 5.4 - - + -
77C LEU* 5.7 0.9 - - + -
141C ASN* 3.6 31.6 - - + +
177C TYR* 4.0 12.8 - - + -
179C THR* 4.6 1.3 - - - +
199C PHE* 3.9 26.2 - - + -
214C PRO* 3.2 13.8 + - + +
217C LEU* 1.3 75.5 - - - +
219C PRO* 1.3 65.8 - - + +
221C ALA* 3.2 2.8 + - - +
222C VAL* 2.9 47.3 + - + +
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Residues in contact with PRO 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LEU* 4.0 14.1 - - + -
79C VAL* 4.1 23.6 - - + -
89C ALA* 4.1 11.4 - - + -
93C ILE* 3.7 24.6 - - + +
114C VAL* 4.6 2.5 - - + +
141C ASN* 3.7 16.4 - - - +
143C ILE* 4.4 3.6 - - + -
215C VAL 3.4 20.9 - - - +
216C GLY 3.2 9.4 - - - +
218C LEU* 1.3 96.1 - - + +
220C ILE* 1.3 60.0 + - - +
222C VAL* 3.3 2.8 + - - +
223C SER* 3.1 18.0 + - - -
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Residues in contact with ILE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA* 4.3 15.3 - - - +
92C ALA* 3.4 29.8 - - + -
93C ILE* 4.1 4.9 - - + -
211C VAL* 4.5 9.0 - - + +
216C GLY* 3.0 35.4 + - - +
217C LEU* 3.8 4.3 - - - +
219C PRO* 1.3 74.4 - - - +
221C ALA* 1.3 62.8 + - - +
223C SER* 2.8 24.5 + - - -
225C LEU* 3.4 27.3 + - + -
227C ILE* 4.0 11.4 - - + -
230C MSE 3.7 36.8 - - + -
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Residues in contact with ALA 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ILE* 4.5 3.4 - - + -
64C GLN* 5.4 2.7 - - + -
67C ALA* 3.7 19.8 - - + +
71C LYS* 3.3 15.1 + - - -
217C LEU 2.9 20.0 + - - +
218C LEU 3.6 3.8 - - - +
220C ILE* 1.3 73.8 - - - +
222C VAL* 1.3 65.7 + - - +
224C GLY* 3.0 12.8 + - - -
225C LEU 3.8 13.7 + - - +
227C ILE* 4.1 21.5 - - + -
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Residues in contact with VAL 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ALA* 3.8 25.4 - - - +
70C ILE* 3.8 29.2 - - + -
71C LYS* 3.7 11.5 - - + +
77C LEU* 3.8 27.4 - - + -
111C THR* 3.7 0.3 - - - -
112C PRO* 3.5 39.9 - - + +
114C VAL* 4.7 4.0 - - + -
218C LEU* 2.9 22.8 + - + +
219C PRO 3.3 5.1 + - - +
221C ALA* 1.3 75.6 - - - +
223C SER* 1.3 59.3 + - - +
224C GLY 3.0 5.1 + - - -
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Residues in contact with SER 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ILE* 3.8 17.9 - - - +
97C ASN* 3.1 39.2 + - - -
101C TYR* 3.4 18.1 + - - -
111C THR* 3.4 15.4 + - - +
114C VAL* 4.3 7.1 - - - +
219C PRO 3.1 11.9 + - - -
220C ILE 2.8 18.6 + - - -
221C ALA 3.2 0.4 - - - -
222C VAL* 1.3 74.7 - - - +
224C GLY* 1.3 55.2 + - - +
225C LEU* 3.5 9.5 - - - +
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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