Contacts of the helix formed by residues 338 - 350 (chain C) in PDB entry 2IHU
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 ASP 338 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C LYS* 3.0 33.3 + - - -
194C PRO 4.9 4.5 - - - +
196C GLY* 6.5 0.2 - - - -
197C VAL 4.5 0.2 + - - -
198C VAL* 4.3 9.0 - - + +
230C SER* 2.9 19.1 + - - -
320C PRO* 4.6 9.8 - - - +
337C THR* 1.3 83.0 + - - +
339C VAL* 1.3 57.9 + - - +
340C LEU* 3.5 0.7 - - - +
341C ALA* 3.2 31.8 + - + +
342C PHE 2.9 25.3 + - - -
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Residues in contact with VAL 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ALA 4.2 4.7 - - - +
227C ALA* 3.8 20.9 - - + -
230C SER* 3.5 12.7 + - - +
232C ALA* 3.8 11.7 - - + -
294C VAL* 3.7 27.4 - - + -
295C GLY* 3.9 26.2 - - - +
318C ILE* 4.6 9.9 - - + -
320C PRO* 4.2 19.6 - - + +
337C THR 3.5 0.2 + - - -
338C ASP* 1.3 74.4 + - - +
340C LEU* 1.3 58.3 + - - +
342C PHE* 3.1 8.2 + - + +
343C VAL* 2.9 29.1 + - + +
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Residues in contact with LEU 340 (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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193C LYS* 4.0 6.5 - - - +
230C SER* 3.0 29.3 + - - +
231C GLY* 4.0 18.8 - - - +
232C ALA* 4.0 8.5 - - + -
235C ALA* 3.9 26.9 - - + -
338C ASP* 3.3 9.2 + - - +
339C VAL* 1.3 75.2 - - - +
341C ALA* 1.3 63.3 + - - +
343C VAL* 3.2 1.7 + - - +
344C GLU* 2.9 53.4 + - + +
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Residues in contact with ALA 341 (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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202C TRP* 3.5 20.5 - - + -
337C THR* 4.2 4.5 - - - +
338C ASP* 3.2 26.4 + - + +
340C LEU* 1.3 78.1 - - - +
342C PHE* 1.3 62.9 + - - +
344C GLU* 4.0 8.6 - - - +
345C HIS* 3.1 24.3 + - - +
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Residues in contact with PHE 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C TRP* 3.8 9.1 - - - -
206C ALA* 3.9 26.7 - - + -
209C ALA* 4.8 2.9 - - + -
221C LEU* 6.5 0.4 - - + -
239C LEU* 5.7 2.2 - - + -
292C LEU* 4.6 5.8 - - + -
294C VAL* 4.9 9.4 - - + -
318C ILE* 3.6 50.3 - - + -
335C VAL* 4.0 15.3 - - + -
337C THR* 3.7 6.3 - - + -
338C ASP 2.9 13.7 + - - +
339C VAL 3.4 6.3 - - - +
341C ALA* 1.3 77.2 - - - +
343C VAL* 1.3 68.2 + - + +
345C HIS* 3.2 3.5 + - - +
346C PHE* 2.7 78.8 + + + +
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Residues in contact with VAL 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ALA* 4.6 2.7 - - + -
235C ALA* 3.7 40.8 - - + +
236C ILE* 3.9 22.9 - - + +
239C LEU* 4.4 17.5 - - + -
294C VAL* 4.8 2.5 - - + -
339C VAL* 2.9 28.1 + - + +
340C LEU* 3.2 4.7 + - - +
342C PHE* 1.3 89.7 - - + +
344C GLU* 1.3 57.1 + - - +
346C PHE* 3.2 4.8 + - - +
347C GLU* 2.8 34.9 + - + +
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Residues in contact with GLU 344 (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 ALA* 5.3 4.5 - - + -
340C LEU* 2.9 48.0 + - + +
341C ALA* 4.0 7.9 - - - +
343C VAL* 1.3 75.2 - - - +
345C HIS* 1.3 61.3 + - - +
347C GLU* 3.5 10.2 - - - +
348C THR* 3.4 20.4 + - - -
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Residues in contact with HIS 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C TRP* 3.8 13.9 - + + -
203C GLN* 3.4 34.5 + - + +
206C ALA* 3.5 24.5 - - + -
207C ASP* 2.9 27.1 + - - -
341C ALA 3.1 18.6 + - - +
342C PHE 3.5 3.1 - - - +
344C GLU* 1.3 73.8 - - - +
346C PHE* 1.3 65.7 + - - +
348C THR* 3.2 12.0 + - + -
349C ALA* 3.0 22.5 + - + +
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Residues in contact with PHE 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ALA* 3.9 11.7 - - + -
209C ALA* 3.8 8.5 - - + -
210C ALA* 3.5 33.2 - - + -
213C LEU* 3.6 34.1 - - + -
221C LEU* 5.7 1.8 - - + -
239C LEU* 3.7 32.5 - - + -
245C ILE* 5.8 0.9 - - + -
292C LEU* 4.0 24.5 - - + -
342C PHE* 2.7 45.6 + + + +
343C VAL* 3.2 7.6 + - - +
345C HIS* 1.3 74.4 - - - +
347C GLU* 1.3 53.1 + - - +
349C ALA* 3.3 3.4 + - + -
350C THR* 2.7 46.7 + - + +
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Residues in contact with GLU 347 (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 ALA* 3.9 5.7 - - + +
238C ALA* 4.0 6.9 - - - +
239C LEU* 3.4 35.0 + - + +
242C ARG* 2.6 41.6 + - - -
343C VAL* 2.8 25.7 + - + +
344C GLU* 3.5 13.7 - - - +
346C PHE* 1.3 76.9 - - - +
348C THR* 1.3 61.8 + - - +
350C THR* 3.6 4.0 + - - -
351C ALA* 3.1 25.5 + - - +
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Residues in contact with THR 348 (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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344C GLU 3.4 9.8 + - - -
345C HIS* 3.2 14.9 + - + -
347C GLU* 1.3 77.0 - - - +
349C ALA* 1.3 62.1 + - - +
350C THR 3.1 1.0 + - - -
351C ALA* 3.3 19.7 + - - +
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Residues in contact with ALA 349 (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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207C ASP* 4.0 19.3 - - - +
210C ALA* 3.9 21.4 - - + +
345C HIS* 3.0 18.8 + - + +
346C PHE* 3.3 8.5 + - + +
348C THR* 1.3 77.1 - - - +
350C THR* 1.3 58.2 + - - +
351C ALA 3.5 0.4 - - - -
353C PHE* 3.5 18.5 - - - -
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Residues in contact with THR 350 (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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210C ALA* 4.0 7.4 - - + -
213C LEU* 3.9 15.0 - - + -
239C LEU* 3.9 5.9 - - - +
242C ARG* 2.8 38.4 + - - -
243C LEU* 4.2 6.1 - - - -
346C PHE* 2.7 38.4 + - + +
347C GLU 3.6 0.2 + - - -
348C THR 3.1 0.2 - - - -
349C ALA* 1.3 80.2 - - - +
351C ALA* 1.3 57.5 + - - +
352C SER 3.2 2.9 - - - -
353C PHE* 3.1 47.2 + - + +
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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