Contacts of the helix formed by residues 297 - 320 (chain C) in PDB entry 3HB1
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 ASP 297 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C ALA* 4.1 0.8 - - - +
296C LYS* 1.3 73.0 - - - +
298C THR* 1.3 58.4 + - - +
299C THR* 3.0 17.1 + - - -
300C THR* 2.6 44.6 + - - +
301C SER* 2.9 28.4 + - - -
420C LEU* 4.2 3.4 - - + +
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Residues in contact with THR 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C GLY 4.9 3.4 - - - +
291C ALA* 4.1 9.4 - - + -
292C SER 5.1 0.7 - - - +
296C LYS 3.3 7.8 + - - +
297C ASP* 1.3 72.8 + - - +
299C THR* 1.3 71.6 + - - +
301C SER* 3.2 9.1 + - - -
302C VAL* 2.9 27.9 + - - +
412D GLN* 4.3 2.8 + - - -
415D ALA* 3.7 37.5 - - + +
416D GLU* 4.2 17.2 - - - +
419D ALA* 4.0 18.4 - - + -
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Residues in contact with THR 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ASP* 3.0 14.8 + - - +
298C THR* 1.3 82.3 + - - +
300C THR* 1.3 61.4 + - - +
303C ARG* 3.0 24.9 + - + +
412D GLN* 3.4 29.3 + - - +
416D GLU* 5.9 0.9 - - - +
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Residues in contact with THR 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ASP* 2.6 34.5 + - - +
299C THR* 1.3 70.6 - - - +
301C SER* 1.3 68.5 + - - +
303C ARG* 3.1 33.4 + - - +
304C ILE* 2.9 34.8 + - + +
416C GLU* 4.9 2.7 - - + +
420C LEU* 3.8 16.8 - - + -
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Residues in contact with SER 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C SER 4.6 1.2 + - - -
285C LEU* 2.7 44.6 + - - +
288C GLY* 4.6 2.5 - - - -
291C ALA* 3.7 23.0 + - - +
297C ASP 2.9 14.8 + - - -
298C THR* 3.2 10.8 - - - -
300C THR* 1.3 77.4 - - - +
302C VAL* 1.3 57.3 + - - -
304C ILE* 3.3 4.4 + - - +
305C GLY 2.9 23.0 + - - -
420C LEU* 3.8 16.8 - - - +
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Residues in contact with VAL 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LEU 3.7 16.8 - - - +
286C LEU* 4.1 13.5 - - + +
298C THR 2.9 16.5 + - - +
301C SER* 1.3 73.1 - - - +
303C ARG* 1.3 65.4 + - - +
305C GLY* 3.1 0.9 + - - +
306C LEU* 2.9 44.1 + - + +
408D GLU 5.1 0.2 - - - +
411D LEU* 4.2 20.4 - - + +
412D GLN* 3.0 31.6 - - + +
415D ALA* 3.7 23.3 - - + -
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Residues in contact with ARG 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C THR* 3.0 20.4 + - + +
300C THR* 3.4 23.8 + - - +
302C VAL* 1.3 78.5 - - - +
304C ILE* 1.3 89.1 + - - +
306C LEU* 3.3 8.2 + - - +
307C MET* 3.0 47.1 + - + +
416C GLU* 2.7 28.7 + - - -
412D GLN* 4.3 1.1 - - - +
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Residues in contact with ILE 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LEU* 4.5 3.4 - - + -
300C THR* 2.9 23.1 + - + +
301C SER* 3.5 7.0 - - - +
303C ARG* 1.3 115.8 - - - +
305C GLY* 1.3 57.3 + - - +
307C MET* 3.1 5.2 + - - +
308C MET* 2.9 29.9 + - + +
413C LEU* 3.8 19.2 - - + +
416C GLU* 3.5 23.1 - - + +
417C LEU* 3.3 38.8 - - + -
420C LEU* 4.9 4.9 - - + -
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Residues in contact with GLY 305 (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 PHE* 3.5 8.5 - - - -
285C LEU* 4.0 18.6 - - - +
286C LEU* 3.3 22.6 - - - +
301C SER 2.9 14.8 + - - -
302C VAL 3.1 0.6 + - - -
304C ILE* 1.3 76.3 - - - +
306C LEU* 1.3 56.0 + - - +
308C MET* 4.8 1.6 - - - -
309C GLU* 2.9 29.6 + - - +
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Residues in contact with LEU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C LEU* 3.8 7.6 - - + -
302C VAL* 2.9 34.5 + - + +
303C ARG* 3.6 6.7 - - - +
305C GLY* 1.3 73.6 - - - +
307C MET* 1.3 67.8 + - + +
309C GLU* 3.5 22.5 - - - +
310C GLU* 3.0 24.1 + - - +
407D ARG* 3.8 7.9 - - - +
408D GLU* 3.7 41.7 - - + +
411D LEU* 3.7 24.2 - - + -
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Residues in contact with MET 307 (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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303C ARG* 3.0 48.8 + - + +
304C ILE* 3.6 7.0 - - - +
306C LEU* 1.3 78.0 - - + +
308C MET* 1.3 62.7 + - - +
310C GLU* 3.4 6.5 - - - +
311C MET* 3.2 25.2 + - + +
409C THR* 4.0 26.9 - - + +
413C LEU* 3.7 28.3 - - + -
416C GLU* 5.0 3.8 - - - +
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Residues in contact with MET 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C PHE* 3.8 13.7 - - + -
285C LEU* 5.7 0.2 - - + -
304C ILE* 2.9 19.2 + - + +
305C GLY* 4.0 3.6 - - - +
307C MET* 1.3 74.1 - - - +
309C GLU* 1.3 66.7 + - - +
311C MET* 3.1 29.5 + - + -
312C ILE* 2.9 27.4 + - + +
410C TRP* 5.0 2.9 - - + -
413C LEU* 3.7 15.8 - - + +
414C ARG* 5.3 8.3 - - - -
417C LEU* 5.5 6.3 - - + -
460C LEU* 3.6 27.8 - - + +
461C TYR* 3.6 42.0 - - - +
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Residues in contact with GLU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C PHE* 3.4 23.9 - - + -
286C LEU* 4.3 7.6 - - + +
305C GLY 2.9 19.8 + - - +
306C LEU* 3.5 17.3 - - - +
307C MET 3.4 0.2 - - - -
308C MET* 1.3 77.2 - - - +
310C GLU* 1.3 63.4 + - - +
312C ILE* 3.1 4.0 + - - +
313C PHE* 3.0 48.5 + - + +
407D ARG* 3.0 44.1 + - - -
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Residues in contact with GLU 310 (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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306C LEU 3.0 13.8 + - - +
307C MET* 3.4 12.3 - - - +
308C MET 3.1 0.2 - - - -
309C GLU* 1.3 78.2 + - - +
311C MET* 1.3 56.3 + - + +
313C PHE* 3.2 5.9 + - - +
314C ASN* 2.6 54.2 + - + +
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Residues in contact with MET 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C MET 3.3 14.1 - - - +
308C MET* 3.1 20.3 + - + -
310C GLU* 1.3 81.4 - - + +
312C ILE* 1.3 62.9 + - - +
314C ASN* 4.0 6.2 - - - +
315C LEU* 2.9 27.7 + - - +
402C ILE* 4.8 10.3 - - + +
406C LYS* 3.6 45.3 - - + +
409C THR* 4.7 11.7 - - + -
410C TRP* 3.7 25.1 - - + +
413C LEU* 4.0 22.2 - - - -
460C LEU* 3.6 8.5 - - + +
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Residues in contact with ILE 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C PHE* 3.8 29.6 - - + -
308C MET* 2.9 33.6 + - + +
309C GLU 3.1 6.0 + - - +
311C MET* 1.3 77.1 - - - +
313C PHE* 1.3 71.7 + - + +
315C LEU* 3.7 0.3 - - - +
316C ALA* 3.1 22.3 + - - +
453C PRO* 3.8 12.8 - - + +
456C ALA* 3.4 26.4 - - + +
457C LYS* 3.6 28.3 - - + +
460C LEU* 3.4 19.5 - - + -
461C TYR* 4.5 4.7 - - + -
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Residues in contact with PHE 313 (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 PHE* 6.2 4.3 - + - -
309C GLU* 3.0 43.4 + - + +
310C GLU* 3.9 3.6 - - - +
312C ILE* 1.3 85.8 - - + +
314C ASN* 1.3 63.7 + - - +
316C ALA* 3.1 3.8 + - + +
317C ASP* 2.9 40.6 + - - +
322C PHE* 4.7 18.6 - + + -
453C PRO* 4.3 25.4 - - + -
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Residues in contact with ASN 314 (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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310C GLU* 2.6 40.0 + - + +
311C MET* 4.0 5.4 - - - +
313C PHE* 1.3 73.7 - - - +
315C LEU* 1.3 58.6 + - - +
317C ASP* 4.1 5.5 - - - +
318C THR* 2.7 34.5 + - - +
319C HIS* 5.9 0.5 - - - -
402C ILE* 5.7 1.2 - - - +
406C LYS* 3.5 34.2 + - - +
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Residues in contact with LEU 315 (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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311C MET 2.9 18.6 + - - +
312C ILE 3.7 2.7 - - - +
314C ASN* 1.3 76.3 - - - +
316C ALA* 1.3 67.8 + - - +
318C THR* 4.6 0.2 - - - -
319C HIS* 2.9 31.0 + - + +
320C LEU* 3.6 26.4 + - + -
398C VAL* 5.0 2.9 - - + -
401C LEU* 4.2 25.6 - - + -
402C ILE* 3.7 29.8 - - + -
456C ALA* 4.2 12.8 - - + +
459C LEU* 5.0 9.4 - - + -
460C LEU* 3.8 27.6 - - + -
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Residues in contact with ALA 316 (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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312C ILE 3.1 15.0 + - - +
313C PHE* 3.1 12.1 + - + +
315C LEU* 1.3 73.8 - - - +
317C ASP* 1.3 61.6 + - - +
320C LEU* 2.7 50.2 + - + +
322C PHE* 3.6 22.4 - - + -
452C ILE* 4.0 13.0 - - + +
453C PRO* 4.7 5.4 - - + -
456C ALA* 4.5 5.6 - - + -
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Residues in contact with ASP 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C PHE* 2.9 26.1 + - - +
314C ASN* 4.1 5.7 - - - +
316C ALA* 1.3 79.5 - - - +
318C THR* 1.3 65.8 + - - +
321C PHE* 3.6 14.7 + - - -
322C PHE* 3.5 28.4 + - - +
323C ASN* 3.7 26.4 + - + +
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Residues in contact with THR 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ASN* 2.7 32.0 + - - -
316C ALA 3.4 0.2 - - - -
317C ASP* 1.3 80.8 - - - +
319C HIS* 1.3 89.6 + - + +
321C PHE* 4.8 3.5 + - - -
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Residues in contact with HIS 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ASN* 5.9 0.7 - - - -
315C LEU* 2.9 20.0 + - + +
318C THR* 1.3 102.0 - - + +
320C LEU* 1.3 66.5 + - + +
321C PHE* 3.7 6.5 - - - -
390C MET* 2.9 36.5 - - - +
401C LEU* 3.3 55.3 + - + -
402C ILE* 4.6 20.4 + - + -
406C LYS* 6.3 1.8 - - + -
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LEU* 3.6 29.2 - - + -
316C ALA* 2.7 23.8 + - - +
319C HIS* 1.3 90.5 - - + +
321C PHE* 1.3 65.5 + - - +
322C PHE* 2.6 18.8 + - - -
325C LEU* 3.6 10.1 - - - +
387C VAL* 3.8 25.8 - - + +
390C MET* 4.4 10.5 - - + -
391C TYR 6.1 0.4 - - - +
401C LEU* 6.2 1.3 - - + -
452C ILE* 3.5 40.3 - - + +
455C LEU* 4.6 7.6 - - + -
456C ALA* 4.5 8.3 - - - +
459C LEU* 5.3 7.0 - - + -
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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