Contacts of the helix formed by residues 287 - 301 (chain C) in PDB entry 4OE5
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 287 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209C PRO* 5.5 1.8 - - - +
284C PHE* 3.6 9.3 - - - -
286C GLY* 1.3 74.5 - - - -
288C VAL* 1.3 63.0 + - - +
289C PRO* 3.5 13.8 - - - +
290C THR* 2.8 31.1 + - - -
291C PHE* 3.0 17.5 + - - +
315C CYS* 4.1 1.6 - - - -
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Residues in contact with VAL 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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287C SER* 1.3 69.1 - - - +
289C PRO* 1.4 70.5 - - + +
291C PHE* 3.1 3.3 + - + +
292C LYS* 2.8 59.1 + - + +
315C CYS* 3.6 29.3 - - + +
316C GLY 4.9 7.6 - - - +
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Residues in contact with PRO 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C SER* 3.5 15.3 - - - +
288C VAL* 1.4 94.8 - - + +
290C THR* 1.3 54.5 + - - +
292C LYS* 3.8 9.0 - - + +
293C HIS* 2.9 29.3 + - - +
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Residues in contact with THR 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ILE* 6.1 0.7 - - + -
209C PRO* 6.5 1.1 - - + -
284C PHE* 3.6 26.9 - - + -
287C SER* 2.8 26.7 + - - -
289C PRO* 1.3 76.4 - - - +
291C PHE* 1.3 64.2 + - - +
293C HIS* 3.1 11.6 + - + +
294C LEU* 2.9 30.2 + - + +
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Residues in contact with PHE 291 (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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282C ILE* 5.3 0.4 - - + -
284C PHE* 3.7 32.3 - + + -
287C SER 3.0 16.3 + - - +
288C VAL* 3.7 4.5 - - + +
290C THR* 1.3 76.0 - - - +
292C LYS* 1.3 62.9 + - + +
294C LEU* 3.2 10.3 + - + +
295C TRP* 2.9 55.4 + + - +
311C LEU* 4.0 31.6 - - + -
312C ALA 3.7 11.2 - - - -
313C GLY* 3.4 31.9 - - - -
315C CYS* 3.9 16.6 - - - -
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Residues in contact with LYS 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C VAL* 2.8 44.1 + - + +
289C PRO* 3.8 7.9 - - + +
291C PHE* 1.3 76.8 - - + +
293C HIS* 1.3 57.3 + - - +
295C TRP* 3.3 13.2 + - + +
296C LYS* 2.9 44.9 + - + +
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Residues in contact with HIS 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C PRO* 6.2 5.8 - - + +
270C GLY* 6.5 0.4 - - - -
271C ASP* 4.5 3.8 + - - -
289C PRO 2.9 15.5 + - - +
290C THR* 3.3 14.1 - - + +
292C LYS* 1.3 76.1 - - - +
294C LEU* 1.3 60.7 + - + +
296C LYS* 3.2 14.2 + - - +
297C GLN* 2.9 67.6 + - + +
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Residues in contact with LEU 294 (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 ILE* 4.1 21.3 - - + -
270C GLY* 3.9 27.8 - - - -
273C VAL* 5.4 0.2 - - + -
274C THR* 4.3 10.2 - - + +
282C ILE* 4.3 15.7 - - + -
284C PHE* 3.7 35.9 - - + -
290C THR* 2.9 23.0 + - + +
291C PHE* 3.6 9.6 - - + +
293C HIS* 1.3 79.8 - - + +
295C TRP* 1.3 63.7 + - - +
297C GLN* 3.1 15.1 + - - +
298C VAL* 2.9 28.9 + - - +
311C LEU* 4.9 4.3 - - + -
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Residues in contact with TRP 295 (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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291C PHE* 2.9 41.7 + + + +
292C LYS* 3.4 16.2 - - + +
294C LEU* 1.3 75.8 - - - +
296C LYS* 1.3 61.3 + - + +
298C VAL* 3.2 4.6 + - + +
299C ALA* 2.9 32.7 + - + +
311C LEU* 3.9 29.8 - - + +
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Residues in contact with LYS 296 (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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292C LYS* 2.9 30.3 + - + +
293C HIS* 3.5 12.3 - - - +
295C TRP* 1.3 75.7 - - + +
297C GLN* 1.3 66.7 + - + +
299C ALA* 3.2 8.1 + - - +
300C GLN* 2.9 25.1 + - - +
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Residues in contact with GLN 297 (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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270C GLY* 3.5 14.9 - - - +
271C ASP* 2.6 31.9 + - - +
274C THR* 3.4 28.6 + - - +
293C HIS* 2.9 47.0 + - + +
294C LEU* 3.1 13.7 + - - +
296C LYS* 1.3 78.7 - - + +
298C VAL* 1.3 63.0 + - - +
300C GLN* 3.4 6.3 + - - +
301C ASN* 3.2 27.6 + - - +
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Residues in contact with VAL 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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274C THR* 4.0 6.7 - - + -
279C LEU* 3.9 25.4 - - + -
282C ILE* 3.9 16.2 - - + -
294C LEU 2.9 16.5 + - - +
295C TRP* 3.5 8.3 - - + +
297C GLN* 1.3 77.0 - - - +
299C ALA* 1.3 63.2 + - - +
301C ASN 3.1 10.0 + - - -
302C LEU* 3.1 17.1 + - + +
305C PHE* 3.2 28.4 - - + -
309C PRO* 4.0 21.5 - - + +
311C LEU* 4.4 17.7 - - + -
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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
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295C TRP* 2.9 22.0 + - + +
296C LYS* 3.5 12.1 - - - +
297C GLN 3.2 0.2 - - - -
298C VAL* 1.3 79.1 - - - +
300C GLN* 1.3 61.7 + - - +
302C LEU* 3.1 31.5 + - + +
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Residues in contact with GLN 300 (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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300A GLN 4.7 16.2 - - - +
301A ASN* 3.8 8.9 - - - +
303A ASP* 5.5 12.6 - - + +
304A ARG* 3.2 20.3 + - - +
296C LYS 2.9 16.1 + - - +
297C GLN* 3.7 7.6 - - - +
299C ALA* 1.3 75.2 - - - +
301C ASN* 1.3 63.5 + - - +
302C LEU 3.3 2.1 + - - -
303C ASP 5.1 0.9 + - - -
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Residues in contact with ASN 301 (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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304A ARG* 2.6 41.7 + - - +
274C THR* 2.8 37.2 + - - +
275C SER* 3.5 15.4 + - - +
297C GLN* 3.2 12.8 + - - +
298C VAL 3.1 5.5 + - - -
300C GLN* 1.3 79.5 - - - +
302C LEU* 1.3 63.7 + - - +
303C ASP* 3.1 3.1 + - - -
304C ARG* 3.1 37.9 + - - +
305C PHE* 3.2 10.6 - - + -
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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