Contacts of the helix formed by residues 421 - 439 (chain C) in PDB entry 6NYY
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 PHE 421 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B ARG* 5.9 0.7 + - - -
420C ASN* 1.3 80.4 - - + +
422C GLY* 1.3 67.3 + - - +
423C GLY* 3.3 33.4 - - - -
424C GLN* 3.1 31.4 + - + +
425C SER* 4.0 3.8 + - - -
422D GLY* 3.6 42.8 - - - +
425D SER* 5.7 1.1 - - - -
1G ALA* 5.6 7.9 - - + -
2G ALA 3.5 21.5 - - - -
3G ALA* 3.6 13.0 - - + -
4G ALA* 3.5 28.5 - - + -
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Residues in contact with GLY 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B GLN* 6.0 2.9 - - - -
420C ASN 3.7 2.8 + - - -
421C PHE* 1.3 80.7 - - - +
423C GLY* 1.3 60.8 + - - +
424C GLN 3.5 0.3 + - - -
425C SER* 3.6 17.2 + - - -
426C GLU* 4.4 6.1 + - - +
4G ALA 5.0 1.8 - - - -
6G ALA* 5.4 3.8 - - - +
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Residues in contact with GLY 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C PHE* 3.3 23.3 - - - -
422C GLY* 1.3 76.2 - - - +
424C GLN* 1.3 60.0 + - - +
425C SER 3.3 1.0 + - - -
426C GLU* 3.8 12.7 + - - +
427C GLN* 4.0 8.1 + - - +
382D VAL* 4.6 14.1 - - - +
425D SER* 5.2 7.7 + - - -
426D GLU* 5.3 2.1 - - - +
4G ALA 4.1 15.2 + - - -
6G ALA* 5.8 1.1 - - - -
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Residues in contact with GLN 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ARG* 5.8 0.7 - - - +
414C ARG* 5.8 7.0 - - - +
415C LYS 4.3 7.3 + - - -
417C GLY* 3.3 33.2 - - - +
418C ARG 4.9 1.6 - - - -
420C ASN* 3.3 28.7 + - - +
421C PHE* 3.1 24.9 + - + +
423C GLY* 1.3 75.6 - - - +
425C SER* 1.3 63.8 + - - +
427C GLN* 3.4 13.0 + - - +
428C GLU* 3.3 31.4 + - + +
425D SER* 5.9 2.5 - - - -
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Residues in contact with SER 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 5.9 0.5 - - - +
414B ARG* 3.9 32.2 + - - +
427B GLN* 5.7 3.1 - - - +
421C PHE 4.0 3.0 + - - -
422C GLY* 3.6 13.1 + - - -
423C GLY 3.3 1.2 - - - -
424C GLN* 1.3 79.9 - - - +
426C GLU* 1.3 61.5 + - - +
428C GLU* 3.2 12.4 + - - +
429C ASN* 2.9 40.5 + - - +
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Residues in contact with GLU 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 4.8 2.6 - - - +
423B GLY 5.5 2.1 - - - +
378C LEU* 3.7 13.6 - - + +
381C PHE 4.0 4.8 - - - +
382C VAL* 2.9 56.6 - - - +
384C VAL 4.1 5.4 - - - +
386C PRO* 4.7 3.3 - - - +
422C GLY 5.0 5.2 - - - +
423C GLY* 3.8 7.9 + - - +
424C GLN 3.3 0.4 - - - -
425C SER* 1.3 76.2 + - - +
427C GLN* 1.3 63.0 + - - +
428C GLU 3.3 0.2 - - - -
429C ASN* 3.7 13.4 + - - +
430C THR* 2.9 28.6 + - - -
382D VAL* 5.2 7.2 - - + -
6G ALA* 3.8 24.6 - - + +
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Residues in contact with GLN 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C LEU* 4.5 17.8 - - + +
411C ALA 4.1 16.2 - - - +
412C VAL* 2.9 30.7 + - + +
414C ARG* 3.0 53.0 + - + +
415C LYS 4.7 2.4 - - - +
423C GLY 4.0 6.2 + - - +
424C GLN* 3.4 17.3 + - + +
425C SER 3.2 0.4 - - - -
426C GLU* 1.3 79.0 - - - +
428C GLU* 1.3 68.6 + - - +
430C THR* 3.4 4.1 + - - -
431C LEU* 3.0 25.5 + - - +
425D SER* 5.7 6.1 - - - +
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Residues in contact with GLU 428 (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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414B ARG* 2.8 33.9 + - - +
455B ARG* 4.0 3.5 + - - -
416C ARG* 3.3 29.6 - - + -
417C GLY* 2.8 38.6 + - - +
418C ARG 4.8 0.5 - - - +
424C GLN* 3.4 23.2 + - + +
425C SER* 3.2 7.6 + - - +
427C GLN* 1.3 84.9 - - - +
429C ASN* 1.3 60.4 + - - +
431C LEU* 3.8 5.5 - - - +
432C ASN* 2.9 39.6 + - - +
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Residues in contact with ASN 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B SER* 3.4 18.8 - - - +
378B LEU* 4.0 22.8 - - + +
411B ALA* 3.3 42.0 + - - +
414B ARG* 5.8 1.8 - - - +
382C VAL 5.9 0.2 - - - +
386C PRO* 3.4 20.1 - - + +
425C SER* 2.9 29.7 + - - +
426C GLU* 4.1 13.8 - - - +
427C GLN 3.4 0.2 - - - -
428C GLU* 1.3 75.6 - - - +
430C THR* 1.3 60.3 + - - +
432C ASN* 4.5 1.6 - - - -
433C GLN* 3.1 21.3 + - - +
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Residues in contact with THR 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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377C PHE* 3.8 22.4 - - + -
378C LEU* 3.6 9.1 - - + +
385C GLY* 3.3 25.0 - - - +
386C PRO* 3.3 20.6 - - - +
389C VAL* 3.9 9.5 - - + +
412C VAL* 4.2 17.0 - - + +
426C GLU 2.9 17.6 + - - -
427C GLN* 3.8 4.5 - - - -
428C GLU 3.3 0.4 - - - -
429C ASN* 1.3 74.6 - - - +
431C LEU* 1.3 65.2 + - - +
433C GLN* 3.5 2.4 + - - +
434C LEU* 3.1 21.7 + - - +
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Residues in contact with LEU 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C VAL* 3.4 21.9 + - - +
413C GLY* 4.2 0.4 - - - -
414C ARG 3.4 25.6 - - - +
416C ARG* 3.9 17.3 - - + +
427C GLN* 3.0 18.1 + - - +
428C GLU* 3.8 4.9 - - - +
430C THR* 1.3 76.4 - - - +
432C ASN* 1.3 58.3 + - - +
434C LEU* 2.9 12.0 + - + +
435C LEU* 2.9 34.7 + - + +
460C ASP* 3.4 29.2 - - + +
463C LEU* 3.7 35.9 - - + -
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Residues in contact with ASN 432 (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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373B SER* 5.1 0.4 - - - -
375B SER* 4.1 4.4 + - - -
408B GLN* 3.6 23.1 - - + +
410B ASP* 3.7 23.1 + - - +
411B ALA* 4.1 19.2 - - + +
416C ARG* 3.4 36.1 + - - +
428C GLU* 2.9 28.8 + - - +
429C ASN* 4.1 4.7 - - - +
430C THR 3.4 0.2 - - - -
431C LEU* 1.3 75.8 - - - +
433C GLN* 1.3 60.5 + - - +
435C LEU* 3.6 7.8 + - - +
436C VAL* 3.3 28.6 + - - +
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Residues in contact with GLN 433 (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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373B SER* 3.2 14.9 + - - -
375B SER* 2.4 28.7 + - - +
376B GLU* 3.6 5.1 + - - +
386C PRO* 3.4 26.9 - - + +
389C VAL* 4.2 10.1 - - + -
390C ARG* 3.4 36.0 + - + +
429C ASN 3.1 16.0 + - - +
430C THR 3.8 4.9 - - - +
431C LEU 3.2 0.2 - - - -
432C ASN* 1.3 76.6 - - - +
434C LEU* 1.3 62.6 + - - +
436C VAL* 3.4 5.1 + - - +
437C GLU* 3.2 53.8 + - - +
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Residues in contact with LEU 434 (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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377C PHE* 5.8 3.1 - - + -
389C VAL* 3.7 26.9 - - + +
392C LEU* 5.7 1.3 - - + -
393C PHE* 4.0 15.0 - - + -
406C ILE* 4.6 14.6 - - + -
409C ILE* 4.8 14.4 - - + -
412C VAL* 4.7 18.6 - - + +
430C THR 3.1 13.6 + - - +
431C LEU* 2.9 18.9 + - + +
433C GLN* 1.3 76.1 - - - +
435C LEU* 1.3 60.7 + - - +
437C GLU* 3.6 0.9 + - - +
438C MET* 3.3 49.2 + - - +
463C LEU* 4.1 21.1 - - + -
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Residues in contact with LEU 435 (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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408B GLN* 4.5 12.3 - - - +
416C ARG* 3.3 30.5 - - - +
431C LEU* 2.9 20.9 + - + +
432C ASN* 3.8 17.0 - - - +
433C GLN 3.2 0.4 - - - -
434C LEU* 1.3 76.6 - - - +
436C VAL* 1.3 63.5 + - - +
438C MET* 4.3 1.1 - - - -
439C ASP 3.3 9.5 + - - +
462C ALA* 3.3 42.6 - - + +
463C LEU* 3.7 23.3 - - + +
468C ARG* 2.8 39.8 + - + +
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Residues in contact with VAL 436 (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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372B VAL 5.4 1.8 - - - +
373B SER* 3.7 33.4 - - - +
376B GLU* 5.7 1.6 - - - +
407B ASP* 4.0 19.1 - - + +
408B GLN* 3.7 21.8 - - + +
432C ASN 3.3 18.0 + - - +
433C GLN* 3.4 8.5 + - - +
435C LEU* 1.3 77.1 - - - +
437C GLU* 1.3 66.7 + - - +
438C MET 3.3 1.0 + - - -
439C ASP 3.4 21.1 + - - -
440C GLY* 3.5 4.2 + - - -
441C PHE* 4.5 16.0 - - + +
443C THR* 3.7 3.3 + - - -
468C ARG* 4.9 0.4 - - - +
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Residues in contact with GLU 437 (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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376B GLU* 4.6 6.8 - - - +
389C VAL* 4.8 6.5 - - + -
390C ARG* 4.4 16.4 - - - +
393C PHE* 3.5 36.3 - - + +
397C ARG* 3.5 29.1 + - - -
433C GLN* 3.2 42.0 + - + +
434C LEU* 4.2 3.1 - - - +
435C LEU 3.4 0.2 - - - -
436C VAL* 1.3 80.9 - - - +
438C MET* 1.3 59.8 + - - +
441C PHE 5.6 3.7 - - - +
442C ASN* 5.0 4.8 - - - +
443C THR* 3.9 14.6 + - - +
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Residues in contact with MET 438 (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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342C LYS* 3.2 27.3 + - + +
393C PHE* 3.8 18.2 - - + -
406C ILE* 6.0 0.2 - - - -
434C LEU* 3.3 39.9 + - - +
435C LEU 4.3 0.2 - - - +
436C VAL 3.2 0.6 - - - -
437C GLU* 1.3 77.3 - - - +
439C ASP* 1.3 60.3 + - - +
443C THR* 3.3 5.8 - - - +
449C ILE* 3.8 19.7 - - + -
463C LEU* 4.3 10.1 - - + -
467C GLY 3.7 2.6 - - - +
468C ARG* 3.3 48.9 - - + +
469C PHE* 3.6 31.0 - - + -
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Residues in contact with ASP 439 (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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355B THR* 5.0 0.7 - - - +
359B LYS* 4.5 8.5 + - - -
407B ASP* 4.8 3.1 - - - +
801B ANP 3.5 27.9 + - - +
342C LYS* 4.8 4.6 + - - -
435C LEU 3.3 13.8 + - - +
436C VAL* 3.4 6.8 + - - +
438C MET* 1.3 82.7 - - - +
440C GLY* 1.3 61.6 + - - +
443C THR* 3.7 4.6 - - - +
465C ARG* 2.8 30.3 + - - -
467C GLY* 3.7 21.8 - - - +
468C ARG* 3.3 22.0 + - - +
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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
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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