Contacts of the helix formed by residues 285 - 306 (chain C) in PDB entry 3OLJ
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 285 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LYS 3.7 1.6 + - - -
284C PRO* 1.3 76.7 - - - +
286C GLU* 1.3 66.5 + - - +
287C GLU* 3.5 12.6 - - - +
288C ARG* 3.1 24.3 + - - +
289C VAL* 3.0 20.9 + - - +
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Residues in contact with GLU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C SER* 1.3 72.6 - - - +
287C GLU* 1.3 57.0 + - - +
289C VAL* 3.3 1.7 + - - +
290C ARG* 2.8 48.2 + - + +
332C MET* 4.5 1.2 - - - +
337C PHE* 3.4 45.8 - - + +
338C SER* 2.9 39.9 + - - +
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Residues in contact with GLU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C SER* 3.0 12.2 + - - +
286C GLU* 1.3 81.0 - - - +
288C ARG* 1.3 64.0 + - - +
290C ARG* 3.3 18.2 + - - +
291C GLU* 2.9 46.5 + - - +
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Residues in contact with ARG 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C TRP* 3.6 25.5 - - - -
216C ASP* 5.7 1.4 + - - -
219C ALA* 5.8 0.6 - - - +
223C GLU* 2.9 33.4 + - - +
284C PRO* 4.1 9.9 - - + -
285C SER* 3.1 23.1 + - - +
287C GLU* 1.3 79.3 + - - +
289C VAL* 1.3 59.1 + - - +
291C GLU* 3.0 52.7 + - - +
292C ILE* 3.1 31.0 + - + +
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Residues in contact with VAL 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C VAL* 4.2 11.0 - - + -
277C PHE* 4.3 4.3 - - + -
284C PRO* 3.9 24.0 - - + -
285C SER 3.0 13.1 + - - +
286C GLU 3.7 6.1 - - - +
288C ARG* 1.3 74.0 - - - +
290C ARG* 1.3 66.0 + - - +
292C ILE* 3.1 9.7 + - + +
293C ILE* 2.9 27.8 + - + +
332C MET* 3.7 22.2 - - - -
335C LEU* 4.1 15.0 - - + -
337C PHE* 3.6 31.9 - - + -
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Residues in contact with ARG 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C GLU* 2.8 39.4 + - + +
287C GLU* 3.4 17.7 + - - +
289C VAL* 1.3 71.7 - - - +
291C GLU* 1.3 54.9 + - - +
293C ILE* 3.9 3.1 - - - +
294C ILE* 2.8 56.5 + - + +
332C MET* 3.8 22.0 - - + -
338C SER* 5.1 2.0 + - - -
339C LYS 4.0 6.1 + - - -
340C VAL* 3.7 43.3 + - + +
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C GLU* 2.9 33.9 + - - +
288C ARG* 3.0 46.8 + - - +
290C ARG* 1.3 75.1 - - - +
292C ILE* 1.3 62.6 + - - +
294C ILE* 4.0 5.0 - - - +
295C ASN* 3.1 26.2 + - - +
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Residues in contact with ILE 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C TRP* 3.7 28.2 - - + -
213C TRP* 3.8 31.9 - - + -
223C GLU* 4.2 20.4 - - + +
226C VAL* 4.2 15.5 - - + -
227C ALA* 4.1 13.5 - - - -
284C PRO* 6.0 0.2 - - + -
288C ARG* 3.1 42.0 + - + +
289C VAL* 3.1 7.8 + - + +
291C GLU* 1.3 80.2 - - - +
293C ILE* 1.3 61.9 + - + +
295C ASN* 3.4 6.6 + - - +
296C ALA* 3.1 26.2 + - - +
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Residues in contact with ILE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C VAL* 4.0 16.2 - - + -
230C ALA* 3.8 20.6 - - + -
234C ILE* 3.9 4.2 - - + +
289C VAL* 2.9 25.1 + - + +
290C ARG* 3.9 2.2 - - - +
292C ILE* 1.3 74.6 - - + +
294C ILE* 1.3 61.0 + - + +
296C ALA* 3.3 4.7 + - - +
297C VAL* 3.0 28.2 + - + +
328C ALA* 3.8 28.0 - - + +
331C LEU* 3.8 26.9 - - + -
332C MET* 3.8 32.1 - - + -
335C LEU* 5.1 1.3 - - + -
340C VAL* 5.4 2.0 - - + -
341C PHE* 5.2 3.8 - - + -
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Residues in contact with ILE 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ARG* 2.8 47.8 + - + +
291C GLU* 4.0 4.5 - - - +
293C ILE* 1.3 68.2 - - + +
295C ASN* 1.3 67.8 + - - +
297C VAL* 3.2 8.3 + - - +
298C ARG* 3.0 44.4 + - + +
340C VAL* 3.9 31.6 - - + -
341C PHE* 4.0 11.9 - - + -
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Residues in contact with ASN 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C TRP* 2.9 30.8 - - - +
213C TRP* 6.2 0.4 - - - -
291C GLU 3.1 18.8 + - - +
292C ILE* 3.5 6.5 - - - +
294C ILE* 1.3 77.3 - - - +
296C ALA* 1.3 61.5 + - - +
298C ARG* 3.3 7.6 + - - +
299C ILE* 3.1 32.7 + - - +
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Residues in contact with ALA 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C TRP* 4.2 8.7 - - + -
230C ALA* 3.9 25.1 - - + -
234C ILE* 4.0 9.4 - - + -
235C PHE* 3.4 30.6 - - + -
292C ILE 3.1 13.8 + - - +
293C ILE 3.6 7.6 - - - +
294C ILE 3.2 0.2 - - - -
295C ASN* 1.3 75.6 - - - +
297C VAL* 1.3 57.7 + - - +
299C ILE* 3.3 1.3 + - - -
300C GLU* 2.9 28.1 + - - +
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Residues in contact with VAL 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ILE* 4.0 15.2 - - + +
293C ILE 3.0 19.2 + - - +
294C ILE 3.2 6.9 + - - +
296C ALA* 1.3 74.7 - - - +
298C ARG* 1.3 61.9 + - - +
300C GLU* 3.3 2.4 + - - +
301C GLN* 2.8 55.0 + - - +
324C ILE* 3.9 10.1 - - + -
325C GLU* 3.8 15.3 - - + -
328C ALA* 3.4 31.2 - - + -
341C PHE* 4.0 16.2 - - + -
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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
----------------------------------------------------------
294C ILE* 3.0 31.3 + - + +
295C ASN* 3.7 9.6 - - - +
297C VAL* 1.3 73.3 - - - +
299C ILE* 1.3 62.2 + - + +
301C GLN* 2.9 27.1 + - - +
302C GLU* 3.0 29.8 + - - +
325C GLU* 3.0 22.4 + - - -
341C PHE* 3.7 26.3 - - - -
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Residues in contact with ILE 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C LYS* 4.1 29.8 - - + +
206C LYS* 3.5 37.5 - - + +
209C TRP* 3.5 37.0 - - + +
212C ARG* 5.7 1.1 - - - +
235C PHE* 4.0 8.1 - - + -
295C ASN* 3.1 25.9 + - - +
296C ALA 3.7 6.5 - - - +
298C ARG* 1.3 77.7 - - + +
300C GLU* 1.3 56.7 + - - +
302C GLU* 3.3 9.7 + - - +
303C PHE* 3.0 26.7 + - - +
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Residues in contact with GLU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C LYS* 2.7 31.3 + - - +
234C ILE* 3.4 23.6 - - + +
235C PHE* 3.2 13.7 - - + +
238C GLY* 3.0 32.6 + - - -
239C SER 4.0 2.1 + - - -
296C ALA 2.9 16.8 + - - +
297C VAL 3.6 3.6 - - - +
299C ILE* 1.3 78.6 - - - +
301C GLN* 1.3 62.0 + - - +
303C PHE* 3.2 3.8 + - - +
304C LEU* 3.0 37.2 + - + +
324C ILE* 3.8 20.2 - - + -
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Residues in contact with GLN 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C VAL* 2.8 27.0 + - + +
298C ARG* 2.9 34.6 + - - +
300C GLU* 1.3 71.6 - - - +
302C GLU* 1.3 54.0 + - - +
304C LEU* 3.4 5.9 + - - +
305C THR* 2.6 42.2 + - - +
321C LYS* 3.0 62.2 + - + +
324C ILE* 4.2 9.0 - - + -
325C GLU* 3.1 27.9 + - - +
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Residues in contact with GLU 302 (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 CYS 5.6 0.5 - - - +
205C LYS* 4.1 36.8 + - + +
298C ARG 3.0 18.1 + - - +
299C ILE* 3.4 8.9 - - - +
300C GLU 3.3 0.2 - - - -
301C GLN* 1.3 72.3 - - - +
303C PHE* 1.3 65.4 + - - +
305C THR* 4.0 4.3 - - - -
306C GLU* 2.8 56.4 + - + +
307C ALA* 3.1 19.9 + - - +
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Residues in contact with PHE 303 (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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130C VAL* 5.1 2.2 - - + -
133C PHE* 4.2 23.3 - + + -
202C CYS* 3.2 44.9 - - + +
203C VAL 4.7 0.4 - - - -
206C LYS* 3.2 39.7 - - + -
239C SER* 3.7 17.0 - - - -
299C ILE 3.0 13.2 + - - +
300C GLU* 3.2 7.2 + - - +
302C GLU* 1.3 79.0 + - - +
304C LEU* 1.3 78.2 + - + +
307C ALA* 3.8 10.1 - - + -
308C LEU* 2.8 59.6 + - + +
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Residues in contact with LEU 304 (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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126C PHE* 5.3 3.1 - - + -
238C GLY* 3.5 32.1 - - - +
239C SER* 4.3 1.1 - - - +
242C SER* 4.7 2.0 - - - +
300C GLU* 3.0 38.4 + - - +
301C GLN* 4.1 3.4 - - - +
303C PHE* 1.3 96.1 - - + +
305C THR* 1.3 62.0 + - + +
308C LEU 3.9 5.8 - - - +
310C VAL* 3.0 52.8 + - + +
317C CYS* 4.1 0.2 - - - -
320C MET* 3.7 19.7 - - + -
324C ILE* 3.6 20.2 - - + -
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Residues in contact with THR 305 (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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301C GLN 2.6 24.3 + - - +
302C GLU* 4.0 0.5 - - - -
304C LEU* 1.3 85.0 - - + +
306C GLU* 1.3 77.4 + - - +
309C PRO* 3.9 15.7 - - - +
311C LYS* 5.6 1.9 - - - -
317C CYS* 3.8 35.0 - - + +
320C MET* 5.5 0.4 - - + -
321C LYS* 3.7 40.6 + - + +
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Residues in contact with GLU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C GLU* 2.8 34.2 + - + +
305C THR* 1.3 93.9 - - - +
307C ALA* 1.3 64.4 + - - +
308C LEU 3.4 1.5 + - - -
309C PRO* 3.9 11.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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