Contacts of the helix formed by residues 287 - 300 (chain C) in PDB entry 5I94
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 VAL 287 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C LEU* 3.9 22.8 - - + +
284C GLN 2.9 18.5 + - - +
286C CYS* 1.3 77.7 - - - +
288C LYS* 1.3 63.6 + - + +
289C PRO 3.4 0.4 - - - -
290C LEU* 3.1 17.1 + - + -
291C LYS* 2.9 56.3 + - + +
357C VAL* 5.9 1.1 - - + -
361C LEU* 4.7 4.3 - - + -
416C LEU* 3.7 33.0 - - + +
417C CYS* 4.5 4.0 - - - -
419C ILE* 4.4 10.3 - - + -
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Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C SER* 3.1 41.9 + - - +
287C VAL* 1.3 79.5 - - + +
289C PRO* 1.3 66.1 - - + +
291C LYS* 3.6 13.4 - - - +
292C TYR* 3.1 24.1 + - - +
331C PRO 3.9 9.5 - - - +
332C MET* 3.4 35.2 - - - +
333C VAL 4.1 3.1 - - - -
334C ASN* 3.5 19.5 + - - -
337C ALA* 3.5 28.7 - - + -
340C VAL* 5.8 0.2 - - - +
413C TYR* 3.2 25.4 + - - -
417C CYS* 4.8 5.9 - - - -
465C TYR* 6.4 0.7 - - - -
480C LYS* 4.3 1.6 - - - -
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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
----------------------------------------------------------
286C CYS 3.2 18.4 - - - +
288C LYS* 1.3 93.7 - - + +
290C LEU* 1.3 58.6 + - + +
292C TYR* 3.4 1.4 + - + +
293C ALA* 2.9 25.5 + - - +
332C MET* 3.8 9.6 - - + -
433C LEU* 5.4 0.9 - - + -
455C THR* 3.4 32.9 - - + +
459C MET* 3.7 19.7 - - + -
480C LYS* 3.6 32.1 - - + -
488C LEU* 4.4 8.7 - - + -
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Residues in contact with LEU 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU* 4.1 23.1 - - + -
286C CYS 3.7 14.4 - - - +
287C VAL* 3.1 10.7 + - + +
289C PRO* 1.3 78.5 - - - +
291C LYS* 1.3 60.7 + - - +
293C ALA* 3.2 9.0 + - - +
294C ILE* 3.1 27.8 + - - +
361C LEU* 3.7 31.2 - - + -
364C MET* 4.4 16.5 - - + +
429C MET* 3.9 25.4 - - + +
433C LEU* 4.6 14.1 - - + -
488C LEU* 4.2 22.7 - - + -
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Residues in contact with LYS 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C VAL* 2.9 38.7 + - + +
288C LYS* 3.6 11.9 - - - +
290C LEU* 1.3 75.5 - - - +
292C TYR* 1.3 67.1 + - - +
294C ILE* 3.6 12.0 + - + +
295C ALA* 3.2 21.3 + - - +
337C ALA* 3.7 23.0 - - - +
340C VAL* 3.8 9.2 - - + +
341C THR* 3.3 16.6 + - - +
344C ILE* 3.6 19.7 - - + +
357C VAL* 5.5 4.0 - - + -
413C TYR* 3.3 34.2 + - - -
416C LEU* 3.6 29.7 - - + +
417C CYS* 4.9 1.0 - - - -
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Residues in contact with TYR 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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288C LYS 3.1 20.2 + - - +
289C PRO* 3.6 4.0 - - + +
291C LYS* 1.3 76.8 - - - +
293C ALA* 1.3 64.0 + - - +
295C ALA* 3.1 5.2 + - - +
296C VAL* 3.0 29.9 + - + +
304C VAL* 3.8 23.3 - - + -
305C HIS* 2.5 28.5 + - - -
331C PRO* 3.3 34.5 - - + -
332C MET* 4.6 3.1 - - + -
340C VAL* 4.1 16.6 - - + -
454C ASN* 3.3 27.3 + - + -
455C THR* 3.6 26.9 - - + -
458C LEU* 3.5 24.4 - - + +
473D PHE* 3.7 1.4 - - - -
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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
----------------------------------------------------------
289C PRO 2.9 14.1 + - - +
290C LEU* 3.2 12.5 + - - +
292C TYR* 1.3 77.5 - - - +
294C ILE* 1.3 51.9 + - - +
296C VAL* 3.2 1.1 + - - -
297C ASN* 2.7 36.4 + - - +
364C MET* 5.3 0.2 - - + -
433C LEU* 5.3 3.6 - - + -
447C LEU* 3.8 29.8 - - + -
451C ALA* 3.5 12.1 - - - +
455C THR* 3.5 19.3 - - + +
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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
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290C LEU 3.1 14.3 + - - +
291C LYS* 3.7 11.9 - - - +
293C ALA* 1.3 75.3 - - - +
295C ALA* 1.3 64.5 + - - +
297C ASN* 3.1 9.3 + - - +
298C ASP* 2.9 26.9 + - - +
344C ILE* 4.7 12.8 - - + -
356C TYR* 3.8 17.9 - - + -
357C VAL* 3.9 28.5 - - + -
360C PHE* 3.7 53.6 - - + -
361C LEU* 4.9 2.7 - - + -
364C MET* 4.1 10.1 - - + -
447C LEU* 4.2 2.0 - - - +
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Residues in contact with ALA 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 LYS 3.2 10.8 + - - +
292C TYR* 3.1 11.0 + - - +
294C ILE* 1.3 80.1 - - - +
296C VAL* 1.3 56.9 + - - +
298C ASP* 3.2 3.0 + - - -
299C LEU* 2.8 39.2 + - + +
304C VAL* 3.9 16.6 - - + -
340C VAL* 4.1 17.3 - - + -
343C LEU* 4.9 8.5 - - + -
344C ILE* 4.3 14.3 - - + +
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Residues in contact with VAL 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C TYR* 3.0 47.9 + - + +
293C ALA* 3.8 6.3 - - - +
295C ALA* 1.3 72.4 - - - +
297C ASN* 1.3 64.0 + - - +
300C GLY* 2.8 29.3 + - - +
301C THR* 4.0 17.7 - - - +
304C VAL* 3.9 16.4 - - + -
305C HIS* 5.0 0.2 - - - +
450C GLU* 3.9 16.2 - - - +
451C ALA* 3.6 29.6 - - - +
454C ASN* 4.4 4.9 - - - +
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Residues in contact with ASN 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 ALA 2.7 21.6 + - - +
294C ILE* 3.1 6.0 + - - +
296C VAL* 1.3 74.8 - - - +
298C ASP* 1.3 80.3 + - - +
360C PHE* 3.6 21.3 - - - -
445C ARG* 3.9 9.5 + - - +
446C VAL 4.1 1.9 + - - +
447C LEU* 3.7 15.1 - - + -
448C SER* 3.0 34.4 + - - -
451C ALA* 3.7 7.8 - - + +
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Residues in contact with ASP 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 ILE* 2.9 20.4 + - - +
295C ALA* 3.9 3.1 - - - +
297C ASN* 1.3 105.0 + - - +
299C LEU* 1.3 75.0 + - + +
344C ILE* 5.8 1.0 - - - +
345C LYS* 5.3 3.5 + - - +
356C TYR* 2.4 39.6 + - - -
360C PHE* 4.2 0.7 - - - -
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Residues in contact with LEU 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 ALA* 2.8 16.3 + - - +
298C ASP* 1.3 94.3 - - + +
300C GLY* 1.3 63.8 + - - +
303C TYR* 3.5 51.0 + - + +
304C VAL* 4.4 5.4 - - + -
343C LEU* 3.4 33.4 - - + +
344C ILE* 5.5 0.4 - - - -
346C GLN* 4.9 2.0 - - - +
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Residues in contact with GLY 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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296C VAL* 2.8 23.1 + - - -
298C ASP 3.8 0.2 - - - -
299C LEU* 1.3 83.7 - - - +
301C THR* 1.3 65.9 + - - -
302C GLU 3.3 2.5 - - - -
303C TYR 3.7 0.2 + - - -
304C VAL* 3.4 23.2 + - - +
450C GLU* 3.7 9.9 - - - -
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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