Contacts of the helix formed by residues 284 - 305 (chain C) in PDB entry 5KX8
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 284 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282C PRO 3.5 3.6 + - - -
283C LEU* 1.3 78.1 - - - +
285C TRP* 1.3 59.3 + - - +
286C HIS* 3.5 7.3 + - - +
287C MET* 3.0 30.7 + - - +
288C ARG* 2.9 28.1 + - - +
418C MET* 4.8 4.0 - - - +
419C ASN* 6.3 0.2 - - - -
420C ASP* 3.5 19.0 + - - -
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Residues in contact with TRP 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C SER* 1.3 68.6 - - - +
286C HIS* 1.3 61.5 + - - +
288C ARG* 3.0 12.8 + - + +
289C CYS* 2.8 54.7 + - - -
380C ILE* 4.5 1.1 - - + -
381C ILE* 4.3 19.5 - - + -
418C MET* 3.8 24.4 - - + -
420C ASP* 2.8 31.2 + - - +
421C ALA* 3.7 20.9 - - + -
422C ASP* 4.5 2.7 - - - -
425C SER* 2.8 29.2 + - - -
426C VAL* 3.6 42.0 - - + -
429C MET* 3.6 35.2 - - + -
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Residues in contact with HIS 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C SER* 3.3 4.4 + - - +
285C TRP* 1.3 80.7 - - - +
287C MET* 1.3 85.1 + - + +
289C CYS* 3.5 6.3 + - - +
290C LYS* 3.3 24.4 + - + +
420C ASP* 3.1 18.4 + - - +
419D ASN* 5.9 0.8 + - - -
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Residues in contact with MET 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU* 4.4 17.3 - - + -
284C SER* 3.0 29.8 + - - +
286C HIS* 1.3 95.3 - - + +
288C ARG* 1.3 63.5 + - - +
290C LYS* 3.3 18.7 + - - +
291C ILE* 3.0 31.3 + - + +
322C ALA* 4.1 12.6 - - - +
323C PHE* 3.9 31.4 - - + -
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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
----------------------------------------------------------
270C LEU* 6.1 0.7 - - + -
274C LEU* 3.7 20.5 + - + +
282C PRO* 4.5 3.2 - - - +
283C LEU* 2.8 50.0 + - + +
284C SER 2.9 11.3 + - - +
285C TRP* 3.0 15.2 + - + +
287C MET* 1.3 77.0 - - - +
289C CYS* 1.3 55.4 + - - +
291C ILE* 3.2 9.2 + - + +
292C ALA* 3.0 28.8 + - - +
380C ILE* 2.8 58.9 + - + +
383C GLY 4.3 1.0 - - - +
415C ASP* 2.8 37.2 + - - +
417C LYS* 3.9 6.3 + - - +
418C MET* 3.4 29.9 - - - +
429C MET* 4.6 0.9 - - - -
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Residues in contact with CYS 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C TRP* 2.8 61.9 + - - +
286C HIS* 3.8 6.5 - - - +
288C ARG* 1.3 71.0 - - - +
290C LYS* 1.3 63.6 + - - +
292C ALA* 3.3 2.3 + - - +
293C GLN* 3.0 31.0 + - - +
425C SER* 5.2 1.1 - - - -
429C MET* 4.1 7.6 - - - -
457C MET* 3.8 24.2 - - + +
458C THR* 4.0 18.4 - - + -
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Residues in contact with LYS 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PRO* 5.9 1.4 - - - +
286C HIS* 3.3 16.8 + - + +
287C MET* 3.3 22.8 + - - +
289C CYS* 1.3 79.9 - - - +
291C ILE* 1.3 56.4 + - - +
293C GLN* 3.5 12.7 + - - +
294C GLY* 3.0 25.8 + - - -
322C ALA* 2.7 35.7 + - - +
323C PHE 3.7 15.0 - - - +
324C THR* 3.8 18.2 + - - +
325C ALA 5.5 1.1 + - - -
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Residues in contact with ILE 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LEU* 4.1 31.0 - - + -
283C LEU* 3.9 33.7 - - + -
287C MET* 3.0 26.6 + - + +
288C ARG* 3.2 8.9 + - - +
290C LYS* 1.3 72.4 - - - +
292C ALA* 1.3 61.4 + - - +
295C ALA* 2.8 32.0 + - + +
317C ILE* 4.6 2.7 - - + -
319C LEU* 3.6 21.1 - - + -
323C PHE* 3.6 24.0 - - + +
325C ALA* 3.4 18.0 - - + +
380C ILE* 4.4 5.6 - - + -
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Residues in contact with ALA 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 ARG 3.0 13.0 + - - +
289C CYS 3.3 8.3 + - - +
291C ILE* 1.3 77.1 - - - +
293C GLN* 1.3 62.2 + - - +
295C ALA* 3.4 1.5 + - - -
296C ALA* 3.1 19.4 + - - +
373C PHE* 3.5 12.1 - - - -
377C LEU* 3.8 21.3 - - + -
380C ILE* 4.2 11.2 - - + +
429C MET* 3.8 22.7 - - + -
454C LEU* 3.9 10.3 - - + -
457C MET* 5.2 0.4 - - + -
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Residues in contact with GLN 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 CYS 3.0 21.4 + - - +
290C LYS* 3.7 12.7 - - - +
292C ALA* 1.3 76.7 - - - +
294C GLY* 1.3 56.9 + - - +
296C ALA* 3.2 4.7 + - - +
297C ASN* 3.0 38.5 + - - +
454C LEU* 3.0 45.7 + - + +
455C GLN* 3.9 13.7 - - + +
457C MET* 4.5 2.2 - - + +
458C THR* 3.0 34.3 + - - +
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Residues in contact with GLY 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ASN* 3.2 35.0 - - - +
290C LYS 3.0 17.3 + - - -
291C ILE 3.8 0.9 - - - -
293C GLN* 1.3 72.9 - - - +
295C ALA* 1.3 65.5 + - - +
297C ASN* 3.1 6.6 + - - -
298C GLY 3.1 17.5 + - - -
325C ALA* 3.9 6.1 - - - -
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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
----------------------------------------------------------
244C ASN* 5.3 0.2 - - - -
270C LEU* 6.4 0.2 - - + -
291C ILE* 2.8 24.2 + - + +
292C ALA* 3.7 1.8 - - - +
294C GLY* 1.3 71.2 - - - +
296C ALA* 1.4 57.2 + - - +
298C GLY* 3.1 3.8 + - - -
299C ILE* 3.0 30.8 + - - +
317C ILE* 4.4 13.0 - - + -
325C ALA* 3.5 12.7 - - + +
327C ILE* 3.6 20.3 - - + +
373C PHE* 3.6 24.5 - - + -
376C VAL* 5.7 0.4 - - + -
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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
----------------------------------------------------------
292C ALA 3.1 12.4 + - - +
293C GLN* 3.2 9.2 + - - +
295C ALA* 1.4 76.5 - - - +
297C ASN* 1.3 58.4 + - - +
299C ILE* 4.7 0.2 - - - -
300C ASN* 3.0 27.5 + - - +
373C PHE* 3.9 13.9 - - + -
447C ILE* 3.6 13.9 - - + +
450C VAL* 4.4 9.0 - - + -
451C GLN* 4.3 14.4 + - - -
454C LEU* 3.7 20.4 - - + -
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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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242C HIS* 3.9 12.0 + - + -
244C ASN* 3.4 22.1 + - - +
293C GLN* 3.0 21.6 + - - +
294C GLY* 3.1 6.9 + - - +
296C ALA* 1.3 75.8 - - - +
298C GLY* 1.3 59.2 + - - +
300C ASN* 3.4 3.5 + - - +
301C PHE* 3.0 27.4 + - - +
451C GLN* 3.0 35.4 + - - +
455C GLN* 4.4 10.1 + - - +
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Residues in contact with GLY 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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242C HIS* 4.4 3.8 - - - -
244C ASN* 3.7 26.6 - - - +
245C LEU* 3.9 7.7 - - - +
294C GLY 3.1 10.7 + - - -
295C ALA 3.1 3.7 + - - -
297C ASN* 1.3 74.3 - - - +
299C ILE* 1.4 63.2 + - - +
301C PHE* 3.3 4.5 + - - +
302C LEU* 3.1 25.9 + - - +
327C ILE* 4.0 8.5 - - - -
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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
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295C ALA 3.0 15.9 + - - +
298C GLY* 1.4 71.3 - - - +
300C ASN* 1.4 64.4 + - - +
302C LEU* 3.3 10.8 + - + +
303C HIS* 3.0 50.3 + - + +
312C ILE* 3.7 30.5 - - + -
327C ILE* 4.1 8.5 - - + -
369C ASP* 4.6 10.3 - - + +
370C ILE* 5.0 1.3 - - + -
373C PHE* 3.5 42.2 - - + -
447C ILE* 3.6 22.4 - - + -
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Residues in contact with ASN 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 ALA 3.0 20.5 + - - +
297C ASN 3.5 5.2 + - - +
298C GLY 3.2 0.2 - - - -
299C ILE* 1.4 77.2 - - - +
301C PHE* 1.3 52.6 + - - +
303C HIS* 3.3 1.9 + - - +
304C GLU* 2.8 62.8 + - - +
447C ILE* 3.5 23.8 - - + +
448C LYS* 3.5 23.6 - - - +
451C GLN* 3.3 28.5 + - - +
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Residues in contact with PHE 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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321A GLU* 3.2 29.4 - - - -
239C LYS 5.0 1.8 - - - -
240C CYS* 3.6 33.4 - - + -
241C GLN 3.3 25.6 - - - -
242C HIS* 3.3 34.1 - + + +
245C LEU* 3.8 12.3 - - + -
297C ASN 3.0 13.4 + - - +
298C GLY* 3.3 8.9 + - - +
300C ASN* 1.3 78.7 - - - +
302C LEU* 1.3 60.7 + - - +
304C GLU* 3.5 11.6 + - - -
305C ASN* 2.8 50.3 + - - +
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Residues in contact with LEU 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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236C VAL* 4.4 11.0 - - + -
240C CYS* 4.5 10.3 - - - -
245C LEU* 4.2 15.0 - - + -
298C GLY 3.1 16.0 + - - +
299C ILE* 3.3 15.7 + - + +
301C PHE* 1.3 77.9 - - - +
303C HIS* 1.3 63.4 + - + +
305C ASN* 3.2 11.4 + - - -
306C HIS 3.2 0.2 + - - -
307C HIS* 2.8 49.4 + - + +
309C HIS* 4.1 25.1 - - + +
327C ILE* 4.4 5.2 - - + -
330C PHE* 3.9 36.1 - - + -
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Residues in contact with HIS 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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299C ILE* 3.0 35.1 + - + +
302C LEU* 1.3 75.1 - - + +
304C GLU* 1.4 67.4 + - - +
306C HIS* 3.0 19.8 + - - -
307C HIS 3.3 19.5 - - - +
366C PRO* 3.5 40.6 - - + +
369C ASP* 3.0 26.4 + - + +
370C ILE* 4.1 9.8 - - + +
447C ILE* 3.5 28.6 + - + +
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Residues in contact with GLU 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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208A THR* 5.8 1.7 - - - +
321A GLU* 5.4 1.4 - - - +
300C ASN* 2.8 37.6 + - - +
301C PHE* 3.7 16.9 - - - +
302C LEU 3.4 0.2 - - - -
303C HIS* 1.4 72.9 - - - +
305C ASN* 1.3 62.1 + - - +
306C HIS* 3.4 20.7 + - - -
448C LYS* 3.1 29.8 + - + +
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Residues in contact with ASN 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C LYS* 3.9 29.4 + - - +
240C CYS* 3.9 22.5 - - - -
301C PHE* 2.8 51.1 + - - +
302C LEU 3.3 5.6 - - - +
303C HIS 3.2 0.6 - - - -
304C GLU* 1.3 82.3 + - - +
306C HIS* 1.4 72.9 + - - +
307C HIS* 3.2 14.9 + - + -
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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
------------------------------------------------------------
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