Contacts of the helix formed by residues 220 - 227 (chain C) in PDB entry 5TIN
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 220 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C PRO* 4.2 14.6 - - + +
147C MET* 3.6 28.0 - - + -
218C ARG 3.7 3.0 + - - +
219C GLN* 1.3 73.3 - - - +
221C GLY* 1.3 66.4 + - - +
222C TYR 3.3 0.9 - - - -
223C TYR* 2.9 18.3 + - - +
224C LEU* 3.3 26.9 + - + +
228C TYR* 3.4 35.2 - - + -
342C TRP* 3.5 30.1 - - + -
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Residues in contact with GLY 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B SER* 3.5 27.8 + - - -
220C MET* 1.3 76.7 - - - +
222C TYR* 1.3 62.3 + - - +
224C LEU* 3.2 24.5 + - - +
225C ILE* 3.2 20.1 + - - +
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Residues in contact with TYR 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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271B ARG* 4.7 19.3 - - + -
276B LYS* 3.6 69.2 + - + +
277B VAL 3.5 19.3 - - - +
278B SER* 3.2 11.7 + - - +
281B LYS* 6.1 0.2 - - - -
219C GLN 5.1 0.4 - - - +
220C MET 3.2 0.6 + - - -
221C GLY* 1.3 74.8 - - - +
223C TYR* 1.3 93.6 + + + +
225C ILE* 3.4 7.6 + - + +
226C GLN* 3.0 64.7 + - + +
227C MET* 4.6 4.9 - - + +
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Residues in contact with TYR 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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276B LYS* 4.8 3.9 + - + +
145C PHE* 3.5 28.0 - + - -
146C PRO* 3.7 28.7 - - + -
186C GLN* 3.9 12.0 + - + -
218C ARG* 3.6 37.6 + - + -
219C GLN 3.8 19.1 - - - -
220C MET* 2.9 11.3 + - - +
222C TYR* 1.3 103.6 - + + +
224C LEU* 1.3 63.7 + - - +
226C GLN* 4.7 0.2 - - - -
227C MET* 3.1 35.7 + - + +
228C TYR* 2.9 35.9 + - + -
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Residues in contact with LEU 224 (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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220C MET* 3.3 37.1 + - + +
221C GLY* 3.2 18.8 + - - +
223C TYR* 1.3 77.4 - - - +
225C ILE* 1.3 62.8 + - + +
228C TYR* 4.1 15.0 - - + -
229C ILE* 2.9 49.4 + - + +
230C PRO* 3.7 0.2 - - - +
342C TRP* 4.5 10.1 - - + -
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Residues in contact with ILE 225 (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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267B SER* 5.3 2.0 + - - +
271B ARG* 3.4 40.7 + - - +
277B VAL 5.2 1.8 - - - +
278B SER 5.0 2.5 - - - +
279B TYR 4.2 21.1 - - - +
280B VAL* 4.5 17.0 - - + -
281B LYS* 5.4 1.8 - - - +
284B ASP* 4.5 15.5 - - + +
221C GLY* 3.2 19.8 + - - +
222C TYR* 3.8 9.0 - - - +
224C LEU* 1.3 80.2 - - + +
226C GLN* 1.3 57.9 + - - +
229C ILE* 4.9 6.7 - - + +
230C PRO* 3.2 20.1 - - - +
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Residues in contact with GLN 226 (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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268B SER* 3.4 29.2 + - - +
271B ARG* 2.9 36.1 + - - +
222C TYR* 3.0 51.9 + - + +
225C ILE* 1.3 77.8 - - - +
227C MET* 1.3 77.9 + - + +
230C PRO* 3.4 12.7 - - - +
266C GLN* 3.9 8.7 + - - +
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Residues in contact with MET 227 (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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145C PHE* 5.2 2.0 - - + -
222C TYR* 4.6 4.3 - - + +
223C TYR* 3.1 43.8 + - + +
225C ILE 3.5 1.2 - - - -
226C GLN* 1.3 99.5 - - + +
228C TYR* 1.3 64.1 + - + +
229C ILE 3.6 0.4 - - - -
230C PRO* 3.6 2.7 - - - +
231C SER* 2.9 28.2 + - - -
266C GLN* 4.1 6.5 + - - +
269C GLY 4.6 5.4 - - - +
270C SER* 3.9 36.3 - - - +
283C ILE* 4.0 18.6 - - + -
287C MET* 3.7 24.3 - - + +
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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