Contacts of the helix formed by residues 288 - 301 (chain C) in PDB entry 4PS1
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 THR 288 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246C LYS* 5.7 4.5 - - + -
286C ASP 5.4 0.7 - - - +
287C CYS* 1.3 75.5 - - - +
289C VAL* 1.3 66.1 + - - +
290C GLU* 3.7 9.0 + - - +
291C GLN* 3.0 38.9 + - - +
292C ILE* 2.9 21.5 + - - +
325C GLY* 4.1 1.1 - - - -
326C THR* 3.4 11.8 + - - +
327C ASP* 3.6 33.0 - - + +
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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
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288C THR* 1.3 73.4 - - - +
290C GLU* 1.3 65.1 + - - +
292C ILE* 3.0 10.9 + - + +
293C TYR* 3.0 50.6 + - + -
325C GLY* 3.6 12.3 - - - +
327C ASP* 3.3 5.4 + - - +
329C GLN* 3.2 49.6 - - + +
330C GLU 3.8 17.9 - - - +
331C ALA* 4.0 9.4 - - + +
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Residues in contact with GLU 290 (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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288C THR* 3.3 8.1 + - - +
289C VAL* 1.3 81.2 - - - +
291C GLN* 1.3 56.6 + - + +
293C TYR* 3.3 9.9 + - - +
294C GLU* 3.0 51.5 + - + +
327C ASP* 5.1 2.1 + - - +
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Residues in contact with GLN 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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286C ASP 3.7 7.3 - - - +
287C CYS* 3.4 16.9 - - + -
288C THR* 3.0 42.9 + - - +
290C GLU* 1.3 75.3 - - + +
292C ILE* 1.3 61.4 + - - +
294C GLU* 3.2 22.1 + - - +
295C ILE* 2.9 39.4 + - + +
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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
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239C ILE* 3.9 27.6 - - + -
241C ASN* 4.2 6.1 - - - +
287C CYS* 3.6 25.1 - - + +
288C THR 2.9 18.1 + - - +
289C VAL* 3.0 14.6 + - + +
291C GLN* 1.3 75.9 - - - +
293C TYR* 1.3 63.7 + - + +
295C ILE* 3.3 8.0 + - - +
296C LEU* 3.0 31.0 + - + +
314C ILE* 5.3 4.0 - - + -
323C ILE* 3.9 25.8 - - + -
325C GLY* 4.4 3.1 - - - +
331C ALA* 5.4 0.9 - - + -
336C LEU* 3.9 31.0 - - + -
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Residues in contact with TYR 293 (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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289C VAL* 3.0 39.8 + - + -
290C GLU* 3.7 9.0 - - - +
292C ILE* 1.3 79.8 - - + +
294C GLU* 1.3 56.8 + - + +
296C LEU* 3.9 5.7 - - + +
297C LYS* 2.9 30.7 + - - +
330C GLU 4.6 0.5 + - - -
331C ALA* 3.8 6.6 - - + -
332C PRO* 3.6 26.0 - - - +
335C GLU* 3.7 24.1 - - + +
336C LEU* 3.5 28.3 - - + -
339C GLN* 5.7 6.1 - - + -
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Residues in contact with GLU 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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290C GLU* 3.0 45.0 + - + +
291C GLN* 3.2 24.4 + - - +
293C TYR* 1.3 76.9 - - - +
295C ILE* 1.3 63.2 + - + +
297C LYS* 3.4 6.7 + - - +
298C ILE* 3.1 29.7 + - + +
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Residues in contact with ILE 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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237C LEU* 4.0 18.2 - - + -
239C ILE* 3.7 12.3 - - + -
284C HIS* 3.6 51.4 - - + +
287C CYS* 3.7 24.9 - - - -
291C GLN* 2.9 23.2 + - + +
292C ILE* 3.6 5.2 - - - +
294C GLU* 1.3 75.1 - - + +
296C LEU* 1.3 67.8 + - + +
298C ILE* 3.1 18.8 + - + +
299C TYR* 3.2 22.3 + - + -
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Residues in contact with LEU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C LEU* 3.8 25.1 - - + -
239C ILE* 5.7 2.5 - - + -
292C ILE* 3.0 25.7 + - + +
293C TYR* 3.9 5.4 - - + +
295C ILE* 1.3 78.2 - - + +
297C LYS* 1.3 52.6 + - - +
299C TYR* 3.3 1.4 + - - +
300C GLN* 2.7 36.9 + - - +
312C CYS* 4.3 14.8 - - - -
314C ILE* 5.7 1.3 - - + -
336C LEU* 3.7 55.6 - - + +
339C GLN* 4.6 11.4 - - + -
340C PHE* 3.5 23.5 - - + -
355C PHE* 5.1 2.7 - - + -
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Residues in contact with LYS 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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293C TYR 2.9 19.0 + - - +
294C GLU* 3.5 8.3 - - - +
295C ILE 3.2 0.2 - - - -
296C LEU* 1.3 75.6 - - - +
298C ILE* 1.3 66.3 + - + +
300C GLN* 3.2 28.3 + - - +
301C LEU* 3.0 51.2 + - + +
339C GLN* 5.9 2.0 - - - +
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Residues in contact with ILE 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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294C GLU* 3.1 18.9 + - + +
295C ILE* 3.1 11.6 + - + +
297C LYS* 1.3 79.2 - - + +
299C TYR* 1.3 69.1 + - + +
301C LEU* 3.4 6.2 + - - +
302C MET* 3.2 45.0 + - + +
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Residues in contact with TYR 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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235C TYR* 3.9 25.6 - + - -
237C LEU* 3.5 39.5 - - + -
282C LYS* 3.1 33.3 - - - +
284C HIS* 4.2 10.9 + + - -
295C ILE* 3.2 30.9 + - + -
296C LEU 3.9 4.7 - - - +
298C ILE* 1.3 81.2 - - + +
300C GLN* 1.3 64.9 + - - +
302C MET* 3.2 38.8 + - + +
304C HIS* 2.8 28.1 + + - +
310C PHE* 4.2 9.4 - + + -
340C PHE* 3.9 16.6 - - + -
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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
----------------------------------------------------------
296C LEU 2.7 21.6 + - - +
297C LYS* 3.3 36.5 + - - +
299C TYR* 1.3 73.1 - - - +
301C LEU* 1.3 75.9 + - - +
302C MET 3.7 1.4 + - - +
339C GLN* 3.2 38.8 - - + +
340C PHE* 3.7 13.1 - - + -
344C LYS* 2.9 38.8 + - - +
345C CYS* 3.5 17.5 - - + -
346C PRO* 5.6 0.3 - - - +
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Residues in contact with LEU 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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297C LYS* 3.0 45.2 + - + +
298C ILE* 3.8 5.8 - - - +
300C GLN* 1.3 99.2 - - - +
302C MET* 1.3 63.6 + - - +
303C ASP 4.0 0.3 + - - -
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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
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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