Contacts of the helix formed by residues 424 - 439 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414D ARG* 6.0 0.4 - - - +
414E ARG* 5.9 4.6 - - - -
415E LYS 4.7 4.0 - - - +
417E GLY* 4.5 5.5 + - - -
418E ARG 3.4 20.2 + - - -
420E ASN* 4.0 22.8 - - + +
421E PHE* 3.1 28.7 + - + +
422E GLY 3.5 1.0 - - - -
423E GLY* 1.3 76.4 - - - +
425E SER* 1.3 60.8 + - - +
426E GLU 3.2 2.9 + - - -
427E GLN* 3.3 25.4 + - + +
428E GLU* 3.0 40.0 + - - +
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Residues in contact with SER 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D ARG* 4.3 21.1 + - - +
421D PHE* 5.4 12.3 - - - -
421E PHE 4.3 2.3 + - - -
423E GLY* 3.3 1.6 - - - +
424E GLN* 1.3 77.3 - - - +
426E GLU* 1.3 59.5 + - - +
428E GLU* 3.8 15.6 + - - +
429E ASN* 2.9 31.7 + - - +
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Residues in contact with GLU 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378E LEU* 4.9 10.1 - - + -
379E GLU 4.7 7.9 - - - +
381E PHE 3.9 14.0 - - - +
382E VAL* 3.3 16.1 - - - +
383E GLY* 2.9 37.4 + - - -
384E VAL 3.8 0.5 + - - -
385E GLY* 3.6 15.5 + - - +
386E PRO* 3.7 6.9 - - - +
423E GLY* 3.7 14.1 + - - +
424E GLN 3.2 1.8 - - - -
425E SER* 1.3 76.8 - - - +
427E GLN* 1.3 61.8 + - - +
428E GLU 3.3 0.2 - - - -
429E ASN* 3.4 10.1 + - - +
430E THR* 3.0 30.0 + - - +
2G ALA* 4.9 12.0 - - + +
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Residues in contact with GLN 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378E LEU* 4.2 19.6 - - + +
411E ALA 3.8 19.5 - - - +
412E VAL* 3.2 20.8 + - - +
413E GLY* 4.0 0.2 - - - -
414E ARG* 3.0 55.7 + - + +
415E LYS 4.8 1.2 - - - +
423E GLY 4.2 3.8 + - - +
424E GLN* 3.3 31.1 + - + +
426E GLU* 1.3 79.1 - - - +
428E GLU* 1.3 61.8 + - - +
430E THR* 3.3 3.3 + - - -
431E LEU* 2.9 28.8 + - - +
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Residues in contact with GLU 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D ARG* 3.8 17.2 + - - -
455D ARG* 3.4 26.3 + - - +
416E ARG* 3.8 24.4 - - + +
417E GLY 2.9 32.1 + - - +
424E GLN* 3.0 36.1 + - - +
425E SER* 4.0 11.8 + - - +
426E GLU 3.3 0.8 - - - -
427E GLN* 1.3 78.6 - - - +
429E ASN* 1.3 63.1 + - - +
431E LEU* 4.0 2.3 - - - +
432E ASN* 2.9 35.9 + - - +
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Residues in contact with ASN 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D SER* 3.1 22.3 + - - +
378D LEU* 5.0 14.3 - - - +
411D ALA* 3.3 34.2 + - - +
382E VAL* 5.1 2.2 - - - +
383E GLY* 5.5 2.3 - - - +
386E PRO* 3.3 21.2 - - + +
425E SER* 2.9 24.8 + - - +
426E GLU* 3.4 22.4 + - - +
427E GLN 3.3 0.6 - - - -
428E GLU* 1.3 79.7 - - - +
430E THR* 1.3 61.6 + - - +
432E ASN* 3.4 1.0 + - - +
433E GLN 3.1 11.8 + - - -
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Residues in contact with THR 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E PHE* 3.9 23.6 - - + -
378E LEU* 4.4 5.5 - - - +
385E GLY* 3.3 38.7 - - - +
386E PRO* 3.4 8.3 - - - +
389E VAL* 3.9 13.1 - - + +
412E VAL* 4.2 13.6 - - + +
426E GLU* 3.0 19.6 + - - -
427E GLN* 3.3 7.4 + - - -
429E ASN* 1.3 76.1 - - - +
431E LEU* 1.3 61.7 + - - +
433E GLN 3.6 0.2 + - - -
434E LEU* 3.3 20.6 + - - +
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Residues in contact with LEU 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412E VAL 3.4 18.8 + - - +
413E GLY* 3.9 1.1 - - - -
414E ARG 3.4 25.6 - - - +
416E ARG* 3.7 19.3 - - + +
427E GLN* 2.9 18.4 + - - +
428E GLU* 4.0 5.8 - - - +
430E THR* 1.3 76.3 - - - +
432E ASN* 1.3 58.6 + - - +
434E LEU* 3.0 13.2 + - + +
435E LEU* 3.0 27.4 + - + +
460E ASP* 3.3 27.4 - - + +
463E LEU* 3.8 35.9 - - + -
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Residues in contact with ASN 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D SER* 4.5 0.6 + - - -
375D SER* 3.9 13.7 - - - +
408D GLN* 3.6 28.9 - - + +
410D ASP* 4.2 11.5 - - - +
411D ALA* 4.4 8.5 - - + +
455D ARG* 3.7 21.8 - - - +
416E ARG* 3.2 30.2 + - - +
428E GLU 2.9 22.7 + - - +
429E ASN* 4.7 1.8 + - - +
431E LEU* 1.3 75.5 - - - +
433E GLN* 1.3 61.0 + - - +
435E LEU* 3.5 8.2 + - - +
436E VAL* 3.3 27.5 + - - +
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Residues in contact with GLN 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D SER* 3.6 23.7 + - - -
375D SER* 3.4 13.5 + - - -
376D GLU* 3.9 1.8 + - - +
386E PRO* 3.5 32.8 - - + +
389E VAL* 3.7 13.0 - - + +
390E ARG* 3.3 32.1 + - + +
429E ASN 3.1 16.1 + - - +
430E THR 4.0 3.1 - - - +
431E LEU 3.2 0.4 - - - -
432E ASN* 1.3 74.1 - - - +
434E LEU* 1.3 64.5 + - - +
436E VAL* 3.5 3.8 + - - +
437E GLU* 3.2 50.2 + - - +
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Residues in contact with LEU 434 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E PHE* 5.5 5.4 - - + -
389E VAL* 3.8 13.9 - - + +
392E LEU* 5.8 0.2 - - + -
393E PHE* 3.6 30.5 - - + -
406E ILE* 4.3 14.6 - - + -
409E ILE* 4.2 23.6 - - + -
412E VAL* 5.0 12.1 - - + -
430E THR 3.3 13.1 + - - +
431E LEU* 3.0 18.9 + - + +
433E GLN* 1.3 75.8 - - - +
435E LEU* 1.3 62.2 + - - +
436E VAL 3.5 0.3 + - - -
437E GLU* 3.7 0.9 + - - +
438E MET* 3.3 41.5 + - - +
463E LEU* 3.9 21.3 - - + -
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Residues in contact with LEU 435 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D GLN* 4.2 17.0 - - + +
454D ASN* 4.6 0.2 - - - +
416E ARG* 3.3 30.1 - - - +
431E LEU* 3.0 17.9 + - + +
432E ASN* 3.6 18.4 - - - +
433E GLN 3.3 0.4 - - - -
434E LEU* 1.3 77.7 - - - +
436E VAL* 1.3 61.4 + - - +
438E MET* 3.7 0.3 + - - +
439E ASP 3.4 16.8 + - - +
460E ASP* 4.9 0.2 - - - +
462E ALA* 3.7 23.8 - - + +
463E LEU* 3.8 24.2 - - + +
468E ARG* 3.2 49.3 + - + +
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Residues in contact with VAL 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371D THR* 6.5 0.9 - - + -
372D VAL 6.0 0.4 - - - -
373D SER* 3.4 33.2 - - - +
376D GLU* 5.8 0.7 - - - +
407D ASP* 3.9 24.9 - - + +
408D GLN* 3.7 20.9 - - + -
432E ASN 3.3 18.3 + - - +
433E GLN* 4.0 8.7 - - - +
434E LEU 3.3 0.2 - - - -
435E LEU* 1.3 79.3 - - - +
437E GLU* 1.3 67.2 + - - +
438E MET 3.2 1.0 + - - -
439E ASP 4.7 2.0 - - - -
440E GLY* 3.5 20.2 + - - -
441E PHE* 4.0 15.2 - - + +
468E ARG* 5.2 0.2 - - - +
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Residues in contact with GLU 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D GLU* 4.8 4.3 - - - +
389E VAL* 4.3 6.1 - - + +
390E ARG* 4.1 13.7 - - + +
393E PHE* 3.5 41.4 - - + +
397E ARG* 3.0 47.5 + - - +
433E GLN* 3.2 38.7 + - - +
434E LEU 4.4 0.4 - - - +
435E LEU 3.4 0.2 - - - -
436E VAL* 1.3 80.8 - - - +
438E MET* 1.3 60.9 + - - +
441E PHE 5.4 2.7 - - - -
442E ASN* 4.5 9.6 - - - +
443E THR* 4.6 3.5 + - - +
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Residues in contact with MET 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342E LYS* 2.9 28.6 + - + +
393E PHE* 3.7 21.8 - - + -
406E ILE* 5.9 0.4 - - - -
434E LEU* 3.3 40.1 + - - +
435E LEU 4.2 0.4 - - - +
436E VAL 3.1 0.6 - - - -
437E GLU* 1.3 79.1 - - - +
439E ASP* 1.3 60.8 + - - +
440E GLY 3.9 0.9 - - - -
443E THR* 3.3 11.2 - - - +
449E ILE* 3.9 17.3 - - + -
463E LEU* 4.6 6.7 - - - -
468E ARG* 3.3 49.8 - - + +
469E PHE* 3.6 26.5 - - + -
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Residues in contact with ASP 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D LYS* 4.9 6.8 + - - -
801D ANP 3.4 31.9 + - - +
802D MG 3.3 17.5 - - - -
342E LYS* 3.6 15.2 + - - +
435E LEU 3.4 11.8 + - - +
436E VAL* 3.8 3.5 - - - +
438E MET* 1.3 77.5 - - - +
440E GLY* 1.3 58.9 + - - +
443E THR* 5.1 0.2 + - - -
465E ARG* 2.5 26.5 + - - +
467E GLY* 3.8 16.1 - - - +
468E ARG* 3.4 23.6 + - - +
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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