Contacts of the helix formed by residues 286 - 300 (chain C) in PDB entry 4HH3
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 286 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C TYR* 3.7 0.2 - - - +
280C GLY* 3.6 24.0 - - - -
281C VAL 4.7 0.7 - - - +
284C HIS* 3.5 11.0 - - + +
285C LYS* 1.3 83.1 - - - +
287C ILE* 1.3 58.3 + - - +
289C GLU* 3.3 17.5 - - + +
290C ALA* 2.9 28.6 + - - +
308C HIS* 3.8 8.3 - - + +
330C ALA* 3.5 22.9 - - + +
331C PRO 3.5 24.5 - - - +
332C SER* 3.5 14.3 - - - +
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Residues in contact with ILE 287 (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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131A VAL* 3.9 12.8 - - + +
134A GLN* 3.8 17.0 - - + +
135A LEU* 3.7 34.1 - - + +
138A GLU* 3.7 28.9 - - + +
253C TYR* 3.0 8.6 + - + +
257C GLN* 3.6 20.6 - - - +
285C LYS* 2.8 33.2 + - + +
286C PRO* 1.3 73.0 - - - +
288C LEU* 1.3 64.2 + - - +
290C ALA* 4.1 1.6 - - - +
291C ALA* 3.1 22.7 + - - +
308C HIS* 3.8 17.7 + - + +
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Residues in contact with LEU 288 (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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224C PHE* 4.7 3.6 - - + -
228C PHE* 3.6 42.8 - - + -
253C TYR* 2.9 28.5 + - + +
256C LEU* 3.8 22.7 - - + +
257C GLN* 4.0 28.2 + - + +
260C LEU* 3.8 25.1 - - + -
287C ILE* 1.3 79.8 - - - +
289C GLU* 1.3 58.3 + - - +
291C ALA* 3.3 5.2 + - + +
292C LEU* 2.9 39.6 + - + +
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Residues in contact with GLU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C PHE* 3.8 26.0 - - + -
253C TYR* 2.6 32.2 + - - -
286C PRO* 3.3 11.4 - - + +
288C LEU* 1.3 72.6 - - - +
290C ALA* 1.3 58.1 + - - +
292C LEU* 3.4 2.3 + - - +
293C ALA* 2.9 29.1 + - - +
330C ALA* 4.3 5.8 - - + -
331C PRO* 3.2 27.4 - - + +
332C SER* 3.7 3.7 - - - -
333C LEU* 2.8 39.4 + - + +
334C LEU 4.1 2.9 + - - -
387C LEU* 4.0 22.3 - - + +
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C VAL* 3.8 27.9 - - + +
280C GLY 5.5 1.3 - - - +
286C PRO 2.9 18.6 + - - +
287C ILE 4.1 0.9 - - - +
289C GLU* 1.3 73.5 - - - +
291C ALA* 1.3 60.6 + - - +
293C ALA* 3.3 2.6 + - - +
294C ALA* 2.9 29.3 + - - +
306C VAL* 4.0 15.3 - - + +
308C HIS* 4.0 18.8 - - + +
330C ALA* 3.9 8.9 - - + +
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLU* 3.9 12.3 - - - +
257C GLN* 6.3 1.1 - - + -
260C LEU* 3.9 13.2 - - + -
261C ARG* 3.5 25.6 + - - +
287C ILE 3.1 19.8 + - - +
288C LEU* 3.5 6.5 - - + +
290C ALA* 1.3 77.6 - - - +
292C LEU* 1.3 56.1 + - - +
294C ALA* 3.3 7.1 + - - +
295C GLU* 3.0 33.5 + - - +
306C VAL* 5.3 3.5 - - - +
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ALA* 3.9 23.6 - - + +
224C PHE* 3.6 31.4 - - + -
225C ALA* 4.2 5.8 - - + +
228C PHE* 4.0 20.2 - - + -
260C LEU* 3.8 22.7 - - + -
288C LEU* 2.9 27.4 + - + +
289C GLU 3.7 4.5 - - - +
291C ALA* 1.3 75.2 - - - +
293C ALA* 1.3 65.6 + - - +
295C GLU* 3.2 4.6 + - + +
296C MET* 3.0 33.5 + - + +
387C LEU* 3.9 26.0 - - + -
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Residues in contact with ALA 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C VAL* 4.0 20.4 - - + -
289C GLU 2.9 18.7 + - - +
290C ALA* 3.5 5.8 - - - +
292C LEU* 1.3 74.8 - - - +
294C ALA* 1.3 58.2 + - - +
296C MET* 3.3 8.5 + - - +
297C LEU* 3.0 35.5 + - - +
328C VAL* 4.7 3.8 - - + -
330C ALA* 5.3 2.2 - - + -
384C PHE* 6.2 0.2 - - + -
387C LEU* 4.6 6.3 - - + -
390C LEU* 3.6 25.6 - - + -
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Residues in contact with ALA 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 5.1 0.7 - - - +
261C ARG* 5.9 1.6 - - - +
278C VAL* 4.4 1.3 - - + +
290C ALA 2.9 16.5 + - - +
291C ALA* 3.7 6.5 - - - +
292C LEU 3.2 0.2 - - - -
293C ALA* 1.3 77.4 - - - +
295C GLU* 1.3 58.1 + - - +
297C LEU* 4.1 0.3 - - - +
298C ARG* 2.9 51.9 + - - +
304C THR* 3.9 20.2 - - + -
306C VAL* 3.7 24.7 - - + -
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Residues in contact with GLU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.5 12.1 + - - -
221C ALA* 3.4 22.2 - - + +
260C LEU* 4.8 4.9 - - + -
261C ARG* 3.0 31.1 + - - +
264C HIS* 3.9 16.4 - - + +
265C HIS 3.7 3.5 + - - -
266C LEU* 3.0 42.7 + - - +
291C ALA 3.0 19.4 + - - +
292C LEU* 3.2 7.4 + - - +
294C ALA* 1.3 77.8 - - - +
296C MET* 1.3 59.2 + - - +
298C ARG* 4.6 8.1 + - - -
299C ALA* 2.9 30.1 + - - +
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Residues in contact with MET 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ALA* 4.0 5.8 - - + -
222C ALA* 3.8 41.3 - - + +
225C ALA* 4.2 5.4 - - + -
292C LEU 3.0 23.7 + - - +
293C ALA* 3.3 15.2 + - - +
295C GLU* 1.3 77.7 - - - +
297C LEU* 1.3 64.9 + - + +
299C ALA* 3.4 14.3 + - - +
300C VAL* 3.5 18.5 + - - +
387C LEU* 3.3 43.3 - - + +
388C ALA* 3.9 10.3 - - - -
390C LEU* 4.5 6.1 - - + -
391C PRO* 4.1 23.0 - - + +
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C VAL* 3.7 33.0 - - + -
278C VAL* 4.2 10.8 - - + -
293C ALA 3.0 20.8 + - - +
294C ALA 4.1 1.1 - - - +
296C MET* 1.3 76.4 - - - +
298C ARG* 1.3 63.5 - - - +
300C VAL* 3.2 14.2 + - + +
301C GLY 3.3 0.5 + - - -
302C TRP* 3.0 31.5 + - + +
304C THR* 3.7 12.1 - - - +
328C VAL* 4.2 7.0 - - + -
390C LEU* 4.0 28.7 - - + -
391C PRO* 4.7 10.8 - - + -
394C LEU* 3.5 28.0 - - + -
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Residues in contact with ARG 298 (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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141A TYR* 4.2 5.7 - - - -
142A GLU* 2.9 42.4 + - - -
145A ARG* 3.8 16.9 - - - +
244B ALA* 3.8 10.5 - - - +
261C ARG* 5.8 0.4 - - - +
266C LEU* 3.8 22.0 + - + +
267C PRO 4.2 6.0 - - - +
268C ASP* 2.9 37.5 + - - +
269C PRO* 3.8 17.9 - - + +
294C ALA* 2.9 33.1 + - - +
295C GLU* 3.9 8.3 + - - +
297C LEU* 1.3 76.0 - - - +
299C ALA* 1.3 63.2 + - - +
301C GLY* 3.1 12.5 + - - -
302C TRP 3.6 7.2 + - - -
304C THR* 2.9 35.5 + - - +
305C SER* 4.6 0.2 - - - +
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Residues in contact with ALA 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ALA* 5.9 3.1 - - + +
266C LEU* 3.5 19.7 - - + +
295C GLU 2.9 19.0 + - - +
296C MET* 3.6 9.6 - - - +
297C LEU 3.2 0.4 - - - -
298C ARG* 1.3 77.8 - - - +
300C VAL* 1.3 64.3 + - + +
301C GLY 3.8 0.3 + - - -
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Residues in contact with VAL 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C VAL* 4.2 13.2 - - - +
296C MET 3.5 13.0 + - - +
297C LEU* 3.5 16.8 - - + +
298C ARG 3.1 0.2 - - - -
299C ALA* 1.3 83.6 - - + +
301C GLY* 1.3 58.7 + - - +
302C TRP* 3.8 15.8 - - + +
391C PRO* 5.0 17.5 - - + -
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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
------------------------------------------------------------
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