Contacts of the helix formed by residues 209 - 220 (chain T) in PDB entry 5IYB
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 PRO 209 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173T GLY 4.5 7.0 - - - +
175T ARG 3.7 14.4 - - - +
177T ARG* 2.1 46.2 + - + +
208T GLN* 1.3 93.2 - - + +
210T VAL* 1.3 58.1 + - - +
211T VAL* 4.9 8.3 - - + +
212T TYR* 5.1 0.7 - - + -
213T LEU* 4.2 2.4 + - - +
19X G 3.0 57.4 - - + +
20X G 4.3 10.7 - - - +
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Residues in contact with VAL 210 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199T LEU* 5.0 17.7 - - + -
203T VAL* 4.0 28.3 - - + -
208T GLN 3.6 1.2 + - - -
209T PRO* 1.3 72.5 - - - +
211T VAL* 1.3 66.8 + - + +
212T TYR 3.3 0.3 + - - -
213T LEU* 3.3 3.9 + - + +
214T LYS* 2.8 40.0 + - + +
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Residues in contact with VAL 211 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209T PRO* 5.0 6.1 - - + -
210T VAL* 1.3 84.8 - - + +
212T TYR* 1.3 87.2 + - + +
214T LYS* 3.7 9.3 - - + +
215T GLU* 3.1 29.2 + - + +
19X G 5.0 9.4 - - - +
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Residues in contact with TYR 212 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177T ARG* 2.9 49.2 - - + +
209T PRO* 5.1 0.9 - - + -
210T VAL 3.4 0.8 - - - -
211T VAL* 1.3 96.4 - - + +
213T LEU* 1.3 58.2 + - - +
215T GLU* 3.3 8.2 + - + +
216T ILE* 2.9 31.8 + - + +
18X G 4.9 11.4 + - - -
19X G 3.8 26.0 + - - -
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Residues in contact with LEU 213 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177T ARG* 3.4 6.9 - - - +
183T VAL* 6.4 0.2 - - + -
187T LEU* 4.1 30.7 - - + -
199T LEU* 5.0 4.9 - - + -
202T LEU* 4.0 30.7 - - + +
203T VAL* 4.0 25.8 - - + -
206T THR* 4.1 7.6 - - + +
208T GLN* 4.0 20.6 - - + +
209T PRO 4.2 2.0 - - - +
210T VAL* 3.3 7.6 + - + +
212T TYR* 1.3 76.0 - - - +
214T LYS* 1.3 54.1 + - - +
216T ILE* 3.0 18.0 + - + +
217T LEU* 2.7 46.1 + - + +
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Residues in contact with LYS 214 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199T LEU* 5.7 7.2 - - + -
210T VAL* 2.8 33.9 + - + +
211T VAL* 3.7 10.3 - - + +
213T LEU* 1.3 72.9 - - - +
215T GLU* 1.3 52.2 + - - +
217T LEU* 3.2 13.9 + - + +
218T LYS* 2.7 38.6 + - - +
233T TRP* 5.1 16.8 - - + -
69Y C 3.4 44.6 + - - +
70Y C 3.8 18.9 + - - -
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Residues in contact with GLU 215 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211T VAL* 3.1 15.6 + - - +
212T TYR* 3.5 12.3 - - + +
214T LYS* 1.3 74.9 - - - +
216T ILE* 1.3 61.3 + - + +
218T LYS* 3.3 29.9 + - - +
219T GLU* 2.8 28.4 + - - +
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Residues in contact with ILE 216 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177T ARG* 4.8 8.3 - - - +
180T LYS* 5.4 20.2 - - + +
183T VAL* 6.2 2.9 - - + -
184T LEU* 4.3 31.0 - - + +
187T LEU* 4.6 11.7 - - + -
208T GLN* 5.3 3.1 - - - +
212T TYR* 2.9 22.1 + - + +
213T LEU* 3.0 22.9 + - + +
215T GLU* 1.3 75.4 - - + +
217T LEU* 1.3 61.7 + - + +
219T GLU* 2.9 28.3 + - + +
220T ILE* 3.0 25.5 + - + +
235T LEU* 5.0 1.6 - - + -
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Residues in contact with LEU 217 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187T LEU* 5.7 0.7 - - + -
191T PHE* 5.0 3.1 - - + -
199T LEU* 3.7 26.0 - - + -
202T LEU* 4.0 22.2 - - + -
213T LEU* 2.7 30.5 + - + +
214T LYS* 3.4 13.5 - - - +
216T ILE* 1.3 73.2 - - + +
218T LYS* 1.3 57.0 + - - +
221T GLY 3.1 34.6 + - - +
233T TRP* 3.5 55.4 - - + -
234T GLU 5.0 2.7 - - - +
235T LEU* 4.3 19.3 - - + -
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Residues in contact with LYS 218 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214T LYS* 2.7 18.8 + - - +
215T GLU* 3.4 36.8 - - - +
216T ILE 3.1 0.2 - - - -
217T LEU* 1.3 77.5 - - - +
219T GLU* 1.3 61.8 + - - +
221T GLY 4.9 2.1 - - - +
233T TRP* 4.9 2.4 - - - -
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Residues in contact with GLU 219 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83R ASN* 3.6 26.1 + - - +
86R LYS* 4.6 13.4 + - - +
180T LYS* 5.3 11.1 + - - -
215T GLU* 2.8 15.1 + - - +
216T ILE* 2.9 18.8 + - - +
218T LYS* 1.3 80.0 - - - +
220T ILE* 1.3 71.5 + - + +
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Residues in contact with ILE 220 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79R ALA* 5.8 4.0 - - + +
83R ASN* 4.8 16.8 - - + +
86R LYS* 5.9 0.7 - - - +
184T LEU* 4.3 14.1 - - + -
188T PHE* 4.0 18.8 - - + -
216T ILE* 3.0 16.8 + - + +
219T GLU* 1.3 98.4 - - + +
221T GLY* 1.3 68.8 + - - +
222T VAL* 5.0 1.6 - - - +
235T LEU* 3.5 41.5 - - + +
236T LYS 4.1 13.3 - - - +
237T PRO* 4.8 8.4 - - + +
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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