Contacts of the helix formed by residues 424 - 439 (chain D) 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 GLN 424 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414C ARG* 5.0 0.4 + - - -
414D ARG* 5.7 5.7 - - - +
415D LYS 6.0 0.9 - - - -
417D GLY* 4.6 6.6 - - - -
418D ARG 4.1 4.9 - - - +
420D ASN* 3.4 31.9 + - + +
421D PHE* 3.3 42.9 + - + +
423D GLY* 1.3 75.2 - - - +
425D SER* 1.3 62.9 + - - +
427D GLN* 4.0 11.4 - - + +
428D GLU* 3.3 40.5 + - + +
419E GLY* 6.3 1.0 - - - -
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Residues in contact with SER 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ARG* 4.9 20.9 + - - +
421C PHE* 5.7 1.3 - - - -
423C GLY 5.2 7.8 + - - -
424C GLN* 5.9 1.9 - - - -
427C GLN* 5.7 6.6 - - - +
421D PHE 4.0 1.8 + - - -
422D GLY* 3.4 22.9 + - - -
423D GLY 3.2 1.2 - - - -
424D GLN* 1.3 77.6 - - - +
426D GLU* 1.3 70.4 + - - +
427D GLN 3.3 1.2 + - - -
428D GLU* 3.3 13.3 + - - +
429D ASN* 2.9 22.8 + - - +
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Residues in contact with GLU 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C LEU* 4.0 14.0 - - - +
423C GLY 5.3 2.8 - - - +
378D LEU* 3.3 14.3 - - + +
381D PHE 4.6 4.0 - - - +
382D VAL* 3.4 34.3 - - + +
383D GLY* 2.8 31.0 + - - -
385D GLY 5.2 0.9 + - - -
386D PRO* 4.5 2.8 - - - +
422D GLY 4.1 5.2 + - - +
423D GLY 4.2 2.1 + - - +
425D SER* 1.3 83.8 + - - +
427D GLN* 1.3 60.4 + - - +
429D ASN* 3.4 21.9 + - - +
430D THR* 2.9 24.1 + - - -
382E VAL* 5.7 5.2 - - + -
4G ALA* 4.4 13.5 - - + -
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Residues in contact with GLN 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D LEU* 4.3 18.3 - - + +
411D ALA 4.0 15.5 - - - +
412D VAL* 2.4 35.3 + - - +
414D ARG* 3.3 34.7 + - + +
415D LYS 4.7 2.4 - - - +
423D GLY 3.9 16.8 + - - +
424D GLN* 4.3 10.4 - - - +
425D SER 3.2 1.0 - - - -
426D GLU* 1.3 78.5 - - - +
428D GLU* 1.3 72.4 + - - +
429D ASN 3.2 0.4 - - - -
430D THR* 3.1 7.5 + - - -
431D LEU* 3.0 23.9 + - - +
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Residues in contact with GLU 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ARG* 2.8 29.3 + - - +
455C ARG* 3.2 17.4 + - - +
415D LYS 4.5 0.5 - - - +
416D ARG* 3.3 21.9 - - + -
417D GLY* 2.8 32.1 + - - +
418D ARG 5.1 0.7 - - - +
424D GLN* 3.3 26.7 - - - +
425D SER 3.3 5.1 + - - +
427D GLN* 1.3 86.8 - - - +
429D ASN* 1.3 61.5 + - - +
430D THR 3.2 0.2 - - - -
431D LEU* 3.7 7.1 - - - +
432D ASN* 2.8 38.7 + - - +
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Residues in contact with ASN 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C SER* 3.4 18.6 - - - +
378C LEU* 4.5 10.9 - - + +
411C ALA* 3.3 41.4 + - - +
414C ARG* 5.9 3.0 - - - +
386D PRO* 3.4 24.7 - - + +
425D SER* 2.9 23.8 + - - +
426D GLU* 3.4 28.0 - - - +
427D GLN 3.2 0.6 - - - -
428D GLU* 1.3 79.6 - - - +
430D THR* 1.3 61.4 + - - +
432D ASN* 4.7 1.1 - - - +
433D GLN 3.3 14.9 + - - -
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Residues in contact with THR 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D PHE* 3.9 14.8 - - + -
378D LEU* 3.3 8.3 - - + +
385D GLY* 3.3 37.6 - - - +
386D PRO* 3.5 6.5 - - - +
389D VAL* 3.7 14.3 - - + +
412D VAL* 4.1 17.2 - - + +
426D GLU 2.9 16.4 + - - -
427D GLN* 3.1 9.5 + - - -
429D ASN* 1.3 78.4 - - - +
431D LEU* 1.3 63.5 + - - +
433D GLN* 3.6 2.1 + - - +
434D LEU* 3.2 21.3 + - - +
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Residues in contact with LEU 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412D VAL* 3.6 27.7 - - + +
413D GLY* 3.8 12.8 - - - -
414D ARG 3.4 26.0 - - - +
416D ARG* 3.8 14.1 - - + +
427D GLN* 3.0 12.3 + - - +
428D GLU* 4.0 6.7 - - - +
429D ASN 3.4 0.2 - - - -
430D THR* 1.3 76.3 - - - +
432D ASN* 1.3 59.3 + - - +
434D LEU* 3.2 11.6 + - + +
435D LEU* 3.0 34.4 + - + +
460D ASP* 3.3 31.0 - - + +
463D LEU* 4.1 18.4 - - + -
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Residues in contact with ASN 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C SER* 4.2 7.2 - - - +
408C GLN* 3.3 27.7 - - + +
410C ASP* 3.9 13.6 + - - -
411C ALA* 4.4 11.8 - - + +
455C ARG* 4.2 6.9 - - - +
416D ARG* 2.7 45.6 + - - +
428D GLU* 2.8 26.2 + - - +
429D ASN* 4.5 4.2 - - - +
431D LEU* 1.3 72.8 - - - +
433D GLN* 1.3 64.5 + - - +
435D LEU* 3.5 6.3 + - - +
436D VAL* 3.2 28.5 + - - +
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Residues in contact with GLN 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C SER* 4.0 11.1 + - - -
375C SER* 3.1 23.6 + - - +
376C GLU* 3.4 16.5 - - - +
386D PRO* 3.4 26.0 - - + +
389D VAL* 4.0 9.0 - - + -
390D ARG* 3.1 36.3 - - + +
429D ASN 3.3 14.1 + - - +
430D THR 3.9 3.4 - - - +
431D LEU 3.3 0.6 - - - -
432D ASN* 1.3 75.6 - - - +
434D LEU* 1.3 65.9 + - - +
436D VAL* 3.4 6.3 + - - +
437D GLU* 3.2 35.9 + - - +
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Residues in contact with LEU 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D PHE* 5.8 5.4 - - + -
389D VAL* 3.8 15.6 - - + +
392D LEU* 5.8 0.7 - - + -
393D PHE* 3.7 30.5 - - + -
406D ILE* 4.6 15.3 - - + -
409D ILE* 4.8 14.6 - - + -
412D VAL* 4.3 18.8 - - + -
430D THR 3.2 11.8 + - - +
431D LEU* 3.2 13.8 + - + +
433D GLN* 1.3 78.3 - - - +
435D LEU* 1.3 56.3 + - - +
437D GLU* 2.9 6.3 + - - +
438D MET* 2.8 44.2 + - + +
463D LEU* 4.0 23.1 - - + -
469D PHE* 6.2 0.4 - - + -
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Residues in contact with LEU 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C GLN* 5.1 8.1 - - - +
416D ARG* 3.4 29.6 - - - +
431D LEU* 3.0 22.2 + - + +
432D ASN* 3.9 7.4 - - - +
433D GLN 3.4 0.2 - - - -
434D LEU* 1.3 73.9 - - - +
436D VAL* 1.3 61.7 + - - +
438D MET* 3.9 3.6 - - - -
439D ASP 3.4 10.9 + - - +
460D ASP* 4.2 3.8 - - - +
462D ALA* 3.4 37.9 - - + +
463D LEU* 3.7 23.8 - - + -
468D ARG* 3.1 45.8 + - + +
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Residues in contact with VAL 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C SER* 3.3 33.9 - - - +
376C GLU* 5.8 0.2 - - - +
407C ASP* 4.0 23.8 - - + +
408C GLN* 3.7 20.4 - - + -
432D ASN 3.2 18.3 + - - +
433D GLN* 3.8 9.6 - - - +
434D LEU 3.2 0.2 - - - -
435D LEU* 1.3 76.7 - - - +
437D GLU* 1.3 68.0 + - - +
439D ASP 4.4 3.1 - - - -
440D GLY* 3.3 26.3 + - - -
441D PHE 5.7 1.8 - - - +
442D ASN* 5.2 8.8 + - + +
443D THR* 3.9 1.4 + - - -
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Residues in contact with GLU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C GLU* 4.9 2.9 - - - +
389D VAL* 4.4 6.7 - - + +
390D ARG* 3.9 16.8 - - - +
393D PHE* 3.6 49.1 - - + +
397D ARG* 3.4 29.3 + - - -
433D GLN* 3.2 31.0 + - - +
434D LEU 2.9 7.4 + - - +
436D VAL* 1.3 79.7 - - - +
438D MET* 1.3 64.6 + - - +
442D ASN* 4.1 21.9 + - - +
443D THR* 3.6 11.0 + - - +
449D ILE* 5.3 1.0 - - - +
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Residues in contact with MET 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D LYS* 4.3 5.8 - - - +
393D PHE* 3.8 15.5 - - - -
406D ILE* 5.8 0.4 - - - -
434D LEU* 2.8 37.6 + - + +
435D LEU* 4.2 2.0 - - - +
436D VAL 3.3 0.2 - - - -
437D GLU* 1.3 78.4 - - - +
439D ASP* 1.3 59.4 + - - +
443D THR* 3.3 16.9 - - - +
449D ILE* 3.6 41.6 - - + +
463D LEU* 5.0 4.9 - - + -
467D GLY 4.1 7.8 - - - +
468D ARG* 3.3 54.7 - - + +
469D PHE* 3.7 24.7 - - + -
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Residues in contact with ASP 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C THR* 4.5 3.1 - - - +
359C LYS* 4.1 13.5 + - - -
407C ASP* 4.8 1.2 - - - +
801C MG 4.1 14.4 - - - -
803C ANP 3.7 21.8 + - - +
342D LYS* 3.6 20.9 + - - -
435D LEU 3.4 12.3 + - - +
436D VAL* 3.5 4.8 - - - +
438D MET* 1.3 80.7 - - - +
440D GLY* 1.3 59.2 + - - +
443D THR* 3.5 2.4 + - - -
465D ARG* 2.4 38.3 + - - +
467D GLY* 4.2 9.6 - - - +
468D ARG* 3.5 12.0 + - - +
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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
------------------------------------------------------------
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