Contacts of the helix formed by residues 226 - 231 (chain C) in PDB entry 5UWS
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 TYR 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224C ILE 3.6 2.3 + - - -
225C PRO* 1.3 74.9 - - + +
227C ARG* 1.3 79.1 + - + +
228C TYR 3.2 0.2 - - - -
229C ILE* 3.0 15.5 + - - +
230C TYR* 3.1 19.6 + + + -
231C GLU* 4.7 9.0 + - + -
262C LEU* 4.5 18.6 - - + -
263C LYS 3.2 26.5 - - - +
264C ILE* 4.0 14.6 - - + -
265C PRO* 3.5 39.1 - - + +
268C ASN* 5.9 0.3 + - - -
271C ILE* 3.8 15.4 - - + +
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Residues in contact with ARG 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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191C GLU* 4.5 6.7 + - - +
225C PRO* 3.4 35.4 - - + +
226C TYR* 1.3 92.8 - - + +
228C TYR* 1.3 90.1 + - + +
229C ILE 3.0 0.2 - - - -
231C GLU* 2.9 68.6 + - - +
232C THR* 4.5 0.5 - - - +
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Residues in contact with TYR 228 (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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187C SER 5.4 1.7 + - - -
190C PHE* 3.6 28.9 - + - +
191C GLU* 2.7 56.7 + - - +
194C PHE* 3.1 53.7 - + + -
224C ILE* 4.1 10.3 - - + -
225C PRO* 3.3 36.9 + - + +
226C TYR 3.2 0.8 - - - -
227C ARG* 1.3 102.4 + - + +
229C ILE* 1.3 59.0 + - - +
232C THR* 2.9 23.0 + - + +
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Residues in contact with ILE 229 (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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194C PHE* 4.8 1.1 - - + -
217C LEU* 4.6 11.7 - - + -
221C LEU* 3.4 32.3 - - + -
224C ILE* 4.1 16.4 - - + -
225C PRO 4.9 2.2 - - - +
226C TYR 3.0 7.3 + - - +
227C ARG 3.0 0.8 - - - -
228C TYR* 1.3 86.8 - - + +
230C TYR* 1.3 63.5 + - + +
231C GLU 3.6 0.7 - - - -
232C THR* 3.7 7.8 + - - +
234C ILE* 3.5 28.3 - - + +
235C LEU* 3.6 40.5 - - + +
238C LEU* 5.9 1.6 - - + -
259C VAL* 4.3 7.6 - - + -
262C LEU* 3.8 23.1 - - + -
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Residues in contact with TYR 230 (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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226C TYR* 3.1 23.9 + + + +
229C ILE* 1.3 85.3 - - + +
231C GLU* 1.3 61.4 + - + +
232C THR 3.3 11.1 + - - +
235C LEU* 3.9 13.3 - - + +
259C VAL* 4.4 13.6 + - + +
262C LEU* 4.3 15.3 - - + -
264C ILE* 3.5 38.5 - - + +
271C ILE* 3.5 42.8 + - + +
274C GLN* 3.6 38.3 - - + +
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Residues in contact with GLU 231 (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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226C TYR* 4.7 10.5 + - + -
227C ARG* 2.9 45.4 + - + +
230C TYR* 1.3 80.1 - - + +
232C THR* 1.3 65.3 + - + +
271C ILE* 6.5 0.2 - - + -
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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