Contacts of the helix formed by residues 255 - 264 (chain C) in PDB entry 5UH6
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 SER 255 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252C PHE 3.2 14.2 + - - +
253C GLY 3.2 11.6 - - - +
254C PHE* 1.3 84.9 - - - +
256C GLU* 1.3 61.4 + - - +
257C ILE* 3.9 5.8 - - - -
258C MET* 3.3 22.3 + - - +
259C ARG* 3.3 17.2 + - - +
346C VAL* 3.4 18.4 - - - +
350C GLU* 3.2 24.5 - - - -
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Residues in contact with GLU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C SER* 1.3 73.8 - - - +
257C ILE* 1.3 64.2 + - + +
258C MET 3.3 1.1 - - - -
259C ARG* 4.0 15.1 + - - +
260C SER* 3.1 28.6 + - - -
350C GLU* 4.6 1.8 + - - -
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Residues in contact with ILE 257 (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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216C VAL* 5.4 4.3 - - + -
220C ASP* 2.9 51.6 - - + +
221C THR* 4.4 0.2 - - - -
222C VAL* 3.7 26.0 - - + -
255C SER* 3.7 13.9 - - - +
256C GLU* 1.3 82.9 - - + +
258C MET* 1.3 57.9 + - + +
260C SER* 3.9 1.8 - - - -
261C THR* 2.4 31.0 + - - -
346C VAL* 3.6 27.8 - - + +
349C HIS* 4.2 28.5 - - + +
350C GLU* 4.9 3.8 - - + +
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Residues in contact with MET 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C VAL* 3.7 26.2 - - - -
234C VAL* 3.9 22.7 - - + -
235C THR* 4.7 9.9 - - + -
238C LEU* 5.0 4.3 - - + -
248C ILE* 5.0 4.7 - - + +
252C PHE* 3.3 50.0 - - + +
255C SER* 3.3 20.1 + - - +
256C GLU 3.3 0.2 - - - -
257C ILE* 1.3 86.3 - - + +
259C ARG* 1.3 61.0 + - - +
260C SER 3.2 1.1 - - - -
261C THR* 3.0 5.4 + - - -
262C LEU* 2.9 29.6 + - - +
342C ILE* 4.6 11.7 - - + -
346C VAL* 4.2 8.3 - - + -
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Residues in contact with ARG 259 (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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249C VAL* 3.4 39.2 + - - +
252C PHE 5.2 0.4 - - - -
253C GLY* 3.2 34.7 + - - +
255C SER 3.3 19.5 + - - +
256C GLU* 3.8 20.1 + - - +
257C ILE 3.5 0.2 - - - -
258C MET* 1.3 77.2 - - - +
260C SER* 1.3 61.2 + - - +
262C LEU* 3.6 6.9 + - - +
263C GLU* 3.2 25.6 + - - +
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Residues in contact with SER 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C ARG 4.5 0.7 + - - -
220C ASP* 3.9 13.2 + - - +
221C THR* 4.9 0.2 - - - -
256C GLU* 3.1 21.5 + - - -
257C ILE* 3.9 7.2 - - - -
258C MET 3.2 0.2 - - - -
259C ARG* 1.3 77.1 - - - +
261C THR* 1.3 57.8 + - - +
263C GLU* 4.0 5.5 - - - +
264C LYS* 3.1 57.8 + - - +
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Residues in contact with THR 261 (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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221C THR* 3.6 8.6 - - - -
222C VAL* 3.4 39.3 + - - +
233C PRO* 4.4 8.3 - - + +
234C VAL* 4.2 12.1 - - + +
235C THR* 3.9 18.8 + - + +
257C ILE 2.4 26.7 + - - -
258C MET* 3.0 13.5 + - - -
260C SER* 1.3 76.5 - - - +
262C LEU* 1.3 60.1 + - - +
263C GLU 3.1 1.3 - - - -
264C LYS* 3.4 4.4 + - - +
265C ASP* 3.0 26.3 + - - +
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Residues in contact with LEU 262 (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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235C THR* 3.7 24.6 - - + +
239C LYS* 3.6 34.7 + - - +
245C SER* 3.7 11.0 - - - +
248C ILE* 3.7 21.1 - - + -
249C VAL* 3.6 31.2 - - + -
258C MET 2.9 14.3 + - - +
259C ARG* 4.2 7.6 - - - +
261C THR* 1.3 77.2 - - - +
263C GLU* 1.3 57.7 + - - +
265C ASP* 3.2 17.6 - - - +
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Residues in contact with GLU 263 (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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259C ARG 3.2 18.9 + - - +
260C SER* 4.1 5.8 - - - +
261C THR 3.1 0.4 - - - -
262C LEU* 1.3 77.6 - - - +
264C LYS* 1.3 71.4 + - - +
265C ASP 3.1 12.5 + - - +
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Residues in contact with LYS 264 (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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219C ARG* 3.4 23.0 + - - +
221C THR* 3.5 17.0 - - + +
233C PRO* 5.1 7.0 - - + +
260C SER* 3.1 37.9 + - - +
261C THR* 3.4 4.2 + - - +
263C GLU* 1.3 86.1 - - - +
265C ASP* 1.3 64.1 + - - +
266C ASN* 3.3 4.0 + - - +
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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