Contacts of the helix formed by residues 287 - 301 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A PRO* 4.5 4.4 - - - +
212A PHE* 5.4 0.4 - - - -
284A PHE* 3.6 6.6 - - - -
286A GLY* 1.3 74.8 - - - +
288A VAL* 1.3 64.9 + - - +
289A PRO* 3.4 15.8 - - - +
290A THR* 3.1 25.5 + - - -
291A PHE* 3.1 17.2 + - - +
315A CYS* 4.1 0.4 - - - -
316A GLY 5.4 1.8 - - - +
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLY 3.8 0.8 + - - -
287A SER* 1.3 71.6 - - - +
289A PRO* 1.4 67.1 - - + +
291A PHE* 3.1 3.7 + - + +
292A LYS* 2.8 48.5 + - + +
315A CYS* 3.6 29.8 - - + +
316A GLY 4.1 13.9 - - - +
476A TYR* 4.8 12.8 - - + -
308B PHE* 4.4 15.0 - - + -
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Residues in contact with PRO 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A SER* 3.4 19.1 - - - +
288A VAL* 1.4 95.6 - - + +
290A THR* 1.3 56.0 + - - +
292A LYS* 3.4 10.0 + - + +
293A HIS* 3.0 26.5 + - - +
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Residues in contact with THR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 6.1 0.4 - - + -
209A PRO* 4.8 9.5 - - + +
284A PHE* 3.6 26.5 - - + -
287A SER* 3.1 21.6 + - - -
289A PRO* 1.3 75.2 - - - +
291A PHE* 1.3 66.6 + - - +
293A HIS* 3.1 11.9 + - + +
294A LEU* 3.0 27.6 + - + +
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Residues in contact with PHE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE* 5.3 0.7 - - + -
284A PHE* 3.7 37.6 - + + -
287A SER 3.1 9.1 + - - +
288A VAL* 3.5 6.5 - - - +
290A THR* 1.3 76.1 - - - +
292A LYS* 1.3 56.7 + - - +
294A LEU* 3.1 9.9 + - + +
295A TRP* 2.9 55.2 + + - +
311A LEU* 4.2 19.7 - - + -
312A ALA* 3.5 26.2 - - - -
313A GLY* 3.5 21.1 - - - -
315A CYS* 4.1 11.9 - - - -
308B PHE* 3.8 30.5 - + - -
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Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A VAL* 2.8 36.7 + - + +
289A PRO* 3.7 9.0 - - + +
291A PHE* 1.3 71.6 - - - +
293A HIS* 1.3 57.6 + - - +
295A TRP* 3.3 2.8 + - - +
296A LYS* 2.9 39.3 + - - +
302B LEU* 3.9 25.4 - - + +
303B ASP* 3.5 26.5 - - - +
308B PHE* 3.5 27.4 - - + -
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Residues in contact with HIS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ASP* 4.9 3.4 + - - -
289A PRO 3.0 15.5 + - - +
290A THR* 3.3 15.5 - - + +
292A LYS* 1.3 77.2 - - - +
294A LEU* 1.3 63.3 + - + +
296A LYS* 3.4 10.4 + - - +
297A GLN* 2.9 53.7 + - + +
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ILE* 4.1 21.8 - - + -
270A GLY* 4.2 19.7 - - - -
274A THR* 4.6 3.8 - - + -
282A ILE* 4.3 23.1 - - + -
284A PHE* 3.7 35.7 - - + -
290A THR* 3.0 21.4 + - + +
291A PHE* 3.1 7.8 + - + +
293A HIS* 1.3 79.0 - - + +
295A TRP* 1.3 60.6 + - - +
297A GLN* 3.2 19.5 + - - +
298A VAL* 2.9 34.0 + - - +
311A LEU* 4.2 5.4 - - + -
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Residues in contact with TRP 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A PHE* 2.9 43.4 + + - +
292A LYS* 3.4 9.9 - - - +
294A LEU* 1.3 77.9 - - - +
296A LYS* 1.3 60.9 + - - +
298A VAL* 3.4 3.1 + - - +
299A ALA* 3.1 17.8 + - - +
311A LEU* 3.8 29.5 + - + +
295B TRP* 4.0 25.6 + + - -
298B VAL* 3.8 20.2 - - + -
299B ALA* 3.6 35.7 - - + -
302B LEU* 3.9 25.1 - - + -
308B PHE* 4.3 11.6 - + - -
309B PRO* 4.5 12.3 - - + -
311B LEU* 4.0 16.2 - - + -
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LYS* 2.9 25.5 + - - +
293A HIS* 3.6 9.0 - - - +
295A TRP* 1.3 76.4 - - - +
297A GLN* 1.3 57.8 + - - +
299A ALA* 3.3 2.1 + - - +
300A GLN* 2.9 47.9 + - - +
299B ALA* 3.0 42.3 + - + +
300B GLN* 3.6 15.4 + - - +
302B LEU* 4.0 18.8 - - + +
303B ASP* 3.8 26.2 + - - +
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A GLY* 3.9 11.5 - - - +
271A ASP* 2.7 31.6 + - - +
274A THR* 3.1 30.6 + - + +
293A HIS* 2.9 40.5 + - + +
294A LEU* 3.2 15.3 + - - +
296A LYS* 1.3 77.9 - - - +
298A VAL* 1.3 61.4 + - - +
300A GLN* 3.4 10.1 + - - +
301A ASN* 2.6 38.6 + - - +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A THR* 3.9 11.2 - - + -
279A LEU* 4.1 8.7 - - + -
282A ILE* 3.8 25.4 - - + -
294A LEU 2.9 20.9 + - - +
295A TRP 3.8 4.0 - - - +
297A GLN* 1.3 74.4 - - - +
299A ALA* 1.3 64.3 + - - +
301A ASN 3.0 2.1 + - - -
302A LEU* 3.0 20.6 + - + -
305A PHE* 3.4 12.1 - - + -
309A PRO* 3.8 33.2 - - + -
311A LEU* 4.0 19.7 - - + -
295B TRP* 4.4 11.7 - - + +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A TRP 3.1 12.4 + - - +
296A LYS 3.7 2.0 - - - +
298A VAL* 1.3 79.1 - - - +
300A GLN* 1.3 61.1 + - + +
301A ASN 3.2 0.7 + - - -
302A LEU* 3.3 19.6 + - - +
295B TRP* 3.7 19.7 - - + +
296B LYS* 3.4 27.7 - - - +
299B ALA* 3.3 34.5 - - + -
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A LYS* 2.9 37.4 + - - +
297A GLN* 3.7 10.6 - - - +
298A VAL 3.3 0.2 - - - -
299A ALA* 1.3 77.2 - - + +
301A ASN* 1.3 64.8 + - - +
302A LEU 3.5 0.4 + - - -
303A ASP* 5.3 0.9 + - - +
296B LYS* 4.5 12.1 + - - +
299B ALA* 6.4 0.4 - - + -
300C GLN* 4.7 16.6 - - - +
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Residues in contact with ASN 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A THR* 3.5 25.5 + - - +
275A SER* 4.4 5.1 + - - -
297A GLN* 2.6 38.1 + - - +
298A VAL 3.0 6.5 + - - +
300A GLN* 1.3 86.1 + - - +
302A LEU* 1.3 62.7 + - - +
303A ASP* 3.0 5.1 + - - -
304A ARG* 2.6 57.3 + - - +
305A PHE* 3.2 6.5 - - + -
300C GLN* 3.8 8.9 - - - +
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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