Contacts of the helix formed by residues 409 - 433 (chain C) in PDB entry 6I53
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 LYS 409 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C ARG* 3.8 38.5 - - + +
407C ILE 3.2 1.2 - - - -
408C ALA* 1.3 79.7 - - + +
410C MET* 1.3 60.2 + - - +
411C ASP 3.4 2.5 - - - +
412C SER* 3.4 25.0 + - - +
413C TYR* 3.5 39.2 + - + -
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Residues in contact with MET 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C GLU* 3.3 42.4 - - + +
316C THR* 3.8 17.5 - - + -
317C LEU* 3.8 10.0 - - + +
406C ARG 5.2 3.6 - - - +
407C ILE* 3.3 48.1 + - + +
408C ALA 3.4 1.6 - - - -
409C LYS* 1.3 75.9 - - - +
411C ASP* 1.3 61.8 + - - +
413C TYR* 3.0 12.3 + - + +
414C ALA* 2.7 28.1 + - + +
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Residues in contact with ASP 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C PHE* 3.7 31.5 - - - +
257C ILE 4.9 0.7 - - - +
258C ASN* 5.8 0.2 - - - -
259C LYS* 5.0 5.4 + - - +
265C ARG* 3.7 22.9 + - - -
313C GLU* 3.1 18.2 - - - +
317C LEU* 3.4 22.0 - - + +
408C ALA 5.0 1.5 + - - +
409C LYS* 3.4 0.6 - - - +
410C MET* 1.3 74.5 - - - +
412C SER* 1.3 63.9 + - - +
413C TYR 3.2 0.2 - - - -
414C ALA* 4.3 3.1 - - - +
415C ARG* 3.2 38.2 + - - +
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Residues in contact with SER 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C LYS* 3.4 25.6 + - - +
410C MET 3.2 0.8 - - - -
411C ASP* 1.3 77.7 - - - +
413C TYR* 1.3 67.5 + - - +
415C ARG* 4.3 11.9 + - - +
416C ILE* 3.8 23.6 - - - +
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Residues in contact with TYR 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C ARG 4.7 23.5 + - - -
409C LYS* 3.5 36.1 + - + -
410C MET* 3.0 12.6 + - + +
412C SER* 1.3 88.4 - - - +
414C ALA* 1.3 58.0 + - - +
415C ARG 3.3 0.7 - - - -
416C ILE* 3.3 8.3 + - + +
417C PHE* 2.9 31.2 + - + +
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Residues in contact with ALA 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C PHE* 3.6 37.6 - - + -
313C GLU* 4.2 10.5 - - + +
410C MET* 2.7 21.6 + - + +
411C ASP* 3.7 1.3 + - - -
412C SER 3.6 0.2 - - - -
413C TYR* 1.3 69.4 - - - +
415C ARG* 1.3 64.3 + - - +
416C ILE 3.2 1.8 - - - -
417C PHE* 4.0 6.3 - - - +
418C PHE* 3.4 34.8 + - + +
419C PRO* 3.8 1.2 - - - +
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Residues in contact with ARG 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C PHE* 2.7 43.6 + - + -
256C TRP* 3.5 67.4 + - + +
257C ILE 5.4 0.8 + - - -
258C ASN* 5.9 2.2 - - - +
411C ASP* 3.2 25.6 + - - +
412C SER* 4.6 10.4 + - - +
413C TYR 3.3 0.6 - - - -
414C ALA* 1.3 76.5 - - - +
416C ILE* 1.3 61.8 + - + +
419C PRO* 3.3 22.0 - - - +
309D TYR* 3.7 18.6 + - - -
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Residues in contact with ILE 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C SER 3.8 18.4 - - - +
413C TYR* 3.3 9.3 + - + +
414C ALA 3.2 0.2 - - - -
415C ARG* 1.3 82.8 - - + +
417C PHE* 1.3 60.1 + - - +
418C PHE 3.5 0.4 - - - -
419C PRO* 3.7 2.6 - - - +
420C THR* 2.6 39.8 + - - +
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Residues in contact with PHE 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C TYR* 2.9 20.7 + - + +
414C ALA* 4.6 2.7 - - - -
416C ILE* 1.3 79.6 - - - +
418C PHE* 1.3 79.4 + + - +
420C THR* 3.1 9.9 + - + -
421C ALA* 2.7 51.0 + - + +
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Residues in contact with PHE 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C TRP* 3.3 33.5 - + + +
255C PHE* 3.4 36.6 - + + -
306C PHE* 4.4 23.5 - + + -
309C SER* 3.4 39.5 - - - -
310C ALA* 4.6 1.6 - - + -
313C GLU* 4.5 9.0 - - + -
414C ALA* 3.4 15.7 + - + +
417C PHE* 1.3 103.2 - + + +
419C PRO* 1.3 70.9 - - + +
421C ALA* 4.4 1.3 - - - +
422C PHE* 3.3 15.2 + - - +
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Residues in contact with PRO 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C TRP* 3.7 34.5 - - + -
414C ALA 3.8 3.4 - - - +
415C ARG* 3.3 28.0 - - - +
416C ILE 3.7 4.5 - - - +
418C PHE* 1.3 92.5 - - + +
420C THR* 1.3 60.4 + - - +
423C CYS* 3.3 30.9 + - - +
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Residues in contact with THR 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C ILE* 2.6 31.3 + - - +
417C PHE* 3.1 12.8 + - + -
419C PRO* 1.3 76.6 - - - +
421C ALA* 1.3 54.9 + - - +
423C CYS* 3.3 2.7 + - - +
424C LEU* 2.8 45.9 + - + +
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Residues in contact with ALA 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C PHE* 3.3 28.7 - - + -
417C PHE* 2.7 45.0 + - + +
418C PHE 4.5 0.4 - - - +
420C THR* 1.3 73.3 - - - +
422C PHE* 1.3 57.9 + - - +
424C LEU* 4.1 11.2 - - + +
425C PHE* 3.5 14.9 + - - +
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Residues in contact with PHE 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C THR* 3.8 39.3 - - + -
248C VAL* 4.2 14.6 - - + -
249C VAL* 5.4 3.1 - - + -
252C TRP* 3.6 26.5 - + + -
299C PHE* 4.6 3.8 - + - -
302C VAL* 5.7 0.2 - - + -
303C CYS* 4.2 19.7 - - - -
306C PHE* 3.8 28.9 - + + -
418C PHE 3.3 18.5 + - - +
420C THR 3.2 0.4 - - - -
421C ALA* 1.3 77.9 - - - +
423C CYS* 1.3 65.6 + - - +
424C LEU 3.3 0.4 - - - -
425C PHE* 3.3 13.0 + + - +
426C ASN* 3.2 50.2 + - - -
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Residues in contact with CYS 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C TRP* 5.5 3.1 - - - -
419C PRO* 3.3 21.8 + - - +
420C THR* 3.3 3.8 + - - +
422C PHE* 1.3 83.7 - - - +
424C LEU* 1.3 63.2 + - - +
425C PHE 3.3 0.2 - - - -
426C ASN* 3.5 10.5 + - - +
427C LEU* 3.2 19.9 + - - +
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Residues in contact with LEU 424 (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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420C THR* 2.8 27.1 + - + +
421C ALA* 4.3 9.4 - - + +
423C CYS* 1.3 75.2 - - - +
425C PHE* 1.3 62.9 + - - +
427C LEU* 3.3 24.0 + - + +
428C VAL* 3.2 30.5 + - + +
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Residues in contact with PHE 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C LEU* 4.5 11.4 - - + -
299C PHE* 3.9 26.9 - + - -
302C VAL* 3.6 48.2 - - + -
303C CYS* 5.9 0.2 - - - -
306C PHE* 4.8 3.6 - + + -
421C ALA 3.5 15.6 + - - +
422C PHE* 3.3 18.5 + + - +
423C CYS 3.3 0.6 - - - -
424C LEU* 1.3 80.0 - - - +
426C ASN* 1.3 59.7 + - - +
428C VAL* 3.0 12.2 + - + +
429C TYR* 2.6 58.9 + + + +
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Residues in contact with ASN 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C THR* 5.2 3.6 - - - +
299C PHE* 3.7 19.1 - - - -
422C PHE* 3.2 44.9 + - - +
423C CYS* 4.0 10.4 - - - +
424C LEU 3.3 0.4 - - - -
425C PHE* 1.3 77.6 - - - +
427C LEU* 1.3 61.1 + - - +
428C VAL 3.3 0.2 - - - -
429C TYR* 4.2 0.9 - - - +
430C TRP* 3.1 59.3 + - + +
431C VAL* 5.2 0.2 - - - +
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Residues in contact with LEU 427 (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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423C CYS 3.2 13.8 + - - +
424C LEU* 3.5 27.8 - - + +
425C PHE 3.2 0.4 - - - -
426C ASN* 1.3 78.8 - - - +
428C VAL* 1.3 60.0 + - + +
431C VAL* 3.3 39.9 - - + +
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Residues in contact with VAL 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C LEU* 3.2 23.7 + - + +
425C PHE* 3.0 16.4 + - + +
427C LEU* 1.3 81.7 - - + +
429C TYR* 1.3 63.0 + - - +
431C VAL* 4.5 0.6 - - - +
432C SER* 3.1 36.2 + - - +
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Residues in contact with TYR 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C MET* 4.3 10.8 - - + +
241C TYR* 2.9 29.6 + + - -
295C ALA* 2.3 37.4 + - + +
298C LEU* 4.7 6.7 - - + -
299C PHE* 3.6 28.2 - + + +
425C PHE* 2.6 47.7 + + + +
426C ASN* 4.2 4.0 - - - -
428C VAL* 1.3 75.8 - - - +
430C TRP* 1.3 89.6 + + - +
431C VAL 3.3 1.4 + - - -
433C TYR* 3.2 59.3 + + - +
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Residues in contact with TRP 430 (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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160C MET* 3.6 26.9 - - + -
233C MET* 3.9 18.8 - - + -
237C THR* 5.4 5.4 - - + -
241C TYR* 3.8 45.8 - + + -
299C PHE* 4.6 4.1 - + - -
426C ASN* 3.1 56.8 + - + +
429C TYR* 1.3 88.3 - + - +
431C VAL* 1.3 60.1 + - + +
433C TYR* 4.3 2.7 - - - -
434C LEU* 3.4 43.1 - - + +
435C TYR* 5.0 1.0 - - - -
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Residues in contact with VAL 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C ASN 5.2 0.7 - - - +
427C LEU* 3.3 36.6 + - + +
428C VAL* 4.5 0.4 - - - +
429C TYR 3.2 0.8 - - - -
430C TRP* 1.3 79.7 - - + +
432C SER* 1.3 56.5 + - - +
433C TYR 3.1 4.9 + - - -
435C TYR* 2.7 49.2 + - + +
436C LEU* 3.9 25.4 - - + -
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Residues in contact with SER 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C VAL* 3.1 27.4 + - - +
429C TYR 3.4 2.0 + - - -
431C VAL* 1.3 77.7 - - - +
433C TYR* 1.3 74.4 + - - +
434C LEU 3.7 0.2 - - - -
435C TYR 3.9 10.0 - - - +
436C LEU* 4.6 15.3 - - - +
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Residues in contact with TYR 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ASN* 3.2 33.9 - - + +
160C MET* 3.3 38.4 - - + +
294C THR 5.4 0.3 + - - -
295C ALA* 3.6 25.3 - - + +
298C LEU* 3.4 23.5 - - + +
429C TYR* 3.2 56.7 + + - +
430C TRP 5.2 0.4 - - - +
431C VAL 3.1 0.6 - - - -
432C SER* 1.3 88.0 - - - +
434C LEU* 1.3 63.3 + - - +
435C TYR 4.7 0.7 - - - -
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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