Contacts of the helix formed by residues 438 - 456 (chain B) in PDB entry 1NYX
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 438 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASP* 3.2 22.7 + - - -
370B PHE* 3.8 7.8 - - + -
373B LYS* 4.4 26.0 - - - +
374B PHE* 3.8 33.7 - - + +
377B LEU* 4.1 16.8 - - + -
387B PHE* 5.0 1.6 - - + -
434B LYS* 3.4 18.6 - - + +
435B LEU* 3.0 15.7 + - + +
437B GLN* 1.3 81.0 + - + +
439B MET* 1.3 60.1 + - - +
440B THR 3.2 0.9 - - - -
441B ASP* 2.9 40.4 + - - +
442B LEU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLN* 3.1 36.3 - - + +
440A THR* 4.2 4.9 - - - +
324B GLU* 6.5 0.2 - - - -
387B PHE* 3.9 32.8 - - + -
390B VAL* 5.2 6.1 - - + -
391B ILE* 4.3 26.7 - - + -
394B SER* 5.3 2.5 - - - +
410B GLN* 5.1 4.5 - - - +
436B LEU* 3.4 28.0 - - - +
438B LYS* 1.3 75.8 - - - +
440B THR* 1.3 56.1 + - - +
441B ASP 2.9 5.4 - - - -
442B LEU* 3.8 8.4 - - + +
443B ARG* 3.0 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LEU 4.0 5.7 + - - -
437A GLN* 4.3 1.9 + - - -
439A MET* 3.6 23.7 - - + +
440A THR* 3.4 40.7 + - - +
443A ARG* 4.6 14.4 - - + -
436B LEU 5.0 0.2 + - - -
437B GLN* 3.4 17.5 + - - -
438B LYS 3.2 0.4 - - - -
439B MET* 1.3 77.6 - - - +
441B ASP* 1.3 60.8 + - - +
443B ARG* 4.3 2.1 - - - +
444B GLN* 3.7 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASP* 4.0 13.0 - - - +
370B PHE* 3.8 19.1 - - + -
373B LYS* 4.9 6.6 + - - -
437B GLN 2.9 22.5 - - - +
438B LYS* 2.9 38.2 + - - +
439B MET 2.9 0.2 - - - -
440B THR* 1.3 83.4 - - - +
442B LEU* 1.3 62.7 + - - +
443B ARG 3.3 0.2 - - - -
444B GLN* 3.3 7.9 + - - +
445B ILE* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLU* 3.6 29.6 - - + +
327B TYR* 4.1 17.3 - - + -
328B THR* 2.9 26.7 - - - +
370B PHE* 3.3 33.9 - - + -
374B PHE* 5.8 0.2 - - + -
387B PHE* 4.5 7.6 - - + -
391B ILE* 3.7 20.6 - - + -
438B LYS 2.9 15.4 + - - +
439B MET* 3.3 10.7 + - + +
441B ASP* 1.3 74.9 - - - +
443B ARG* 1.3 60.5 + - - +
445B ILE* 3.1 5.5 + - + +
446B VAL* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLN* 5.4 1.4 + - - -
440A THR* 3.2 39.1 + - + +
444A GLN* 4.3 6.3 - - - +
324B GLU* 2.9 34.4 + - - +
394B SER* 3.5 10.9 + - - -
396B ASP* 2.7 31.5 + - - -
397B ARG* 3.2 29.9 - - - +
439B MET* 3.0 39.8 + - - +
440B THR 4.5 1.6 - - - +
442B LEU* 1.3 77.4 - - - +
444B GLN* 1.3 56.4 + - - +
446B VAL* 3.5 3.7 + - - +
447B THR* 2.8 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ARG* 3.6 38.3 + - + +
444A GLN* 4.2 12.8 + - - +
447A THR* 4.1 14.5 + - - +
476A LEU* 6.2 1.8 - - - +
440B THR 3.7 15.0 + - - +
441B ASP* 3.3 10.8 + - - +
442B LEU 3.2 0.2 - - - -
443B ARG* 1.3 78.0 - - - +
445B ILE* 1.3 61.0 + - + +
447B THR* 4.3 9.5 - - - +
448B GLU* 2.9 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TYR* 4.0 20.9 - - + -
366B PRO* 3.4 36.8 - - + +
367B LYS* 3.1 36.6 + - + +
370B PHE* 4.3 20.2 - - + -
441B ASP 3.1 18.2 + - - +
442B LEU* 3.1 9.8 + - + +
444B GLN* 1.3 78.1 - - + +
446B VAL* 1.3 53.8 + - - +
448B GLU* 3.2 6.1 + - - +
449B HIS* 2.6 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TYR 5.7 1.6 - - - +
323B HIS* 3.4 40.4 - - + -
324B GLU* 3.5 27.8 - - + +
327B TYR* 4.0 15.7 - - + -
442B LEU* 2.9 17.9 + - + +
443B ARG* 3.9 4.7 - - - +
445B ILE* 1.3 75.9 - - - +
447B THR* 1.3 59.0 + - - +
449B HIS* 3.8 6.2 - - - +
450B VAL* 2.9 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLN* 3.5 26.2 + - - +
447A THR* 6.3 3.1 - - + -
443B ARG* 2.8 25.1 + - - +
444B GLN* 3.9 11.7 - - - +
446B VAL* 1.3 75.9 - - - +
448B GLU* 1.3 66.0 + - - +
449B HIS 3.1 1.3 - - - -
450B VAL* 2.9 27.8 - - + +
451B GLN* 3.3 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LEU* 3.7 26.3 - - - +
366B PRO* 4.4 19.3 - - + +
444B GLN* 2.9 29.3 + - - +
445B ILE* 3.9 5.8 - - + +
447B THR* 1.3 78.6 - - - +
449B HIS* 1.3 59.9 + - - +
451B GLN* 3.2 26.9 - - - +
452B LEU* 3.4 17.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLN* 5.7 1.5 + - - -
323B HIS* 4.5 7.7 + + - -
327B TYR* 2.1 40.1 + + - -
363B PHE* 3.9 29.5 - + - -
367B LYS* 3.3 19.8 + - - +
445B ILE 2.6 23.7 + - - +
446B VAL* 3.8 7.0 - - - +
448B GLU* 1.3 70.2 - - - +
450B VAL* 1.3 74.3 + - + +
451B GLN 2.9 5.5 + - - -
452B LEU* 3.0 12.3 + - - +
453B LEU* 2.9 43.1 + - + +
476B LEU 5.1 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B HIS* 4.4 17.0 - - + +
446B VAL* 2.9 30.7 - - + +
447B THR* 2.9 28.7 - - + +
449B HIS* 1.3 81.0 - - + +
451B GLN* 1.3 65.2 + - - +
453B LEU* 3.3 13.5 - - + +
454B GLN* 3.2 15.8 + - - +
475B ASP* 5.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B THR 3.3 8.7 + - - +
448B GLU* 3.2 24.1 + - - +
449B HIS 2.9 0.6 - - - -
450B VAL* 1.3 78.9 - - - +
452B LEU* 1.3 90.1 + - - +
453B LEU 3.0 0.9 - - - -
454B GLN* 2.5 59.4 + - - +
455B VAL* 3.6 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B PRO 4.8 4.5 - - - +
362B ASP* 3.5 52.7 - - + +
363B PHE* 4.2 15.5 - - + +
366B PRO* 5.5 3.1 - - + -
367B LYS* 6.3 0.9 - - - +
448B GLU* 3.4 15.2 + - + +
449B HIS* 3.0 10.6 + - - +
451B GLN* 1.3 98.0 + - - +
453B LEU* 1.3 57.1 + - - +
454B GLN 2.9 5.2 + - - -
455B VAL* 3.0 13.1 + - + +
456B ILE* 2.9 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 3.7 17.9 - - + -
286B GLN* 4.7 5.4 - - - +
323B HIS* 4.8 6.3 - - - +
363B PHE* 5.6 2.0 - - + -
449B HIS* 2.9 38.9 + - + +
450B VAL* 3.3 19.7 - - + +
452B LEU* 1.3 75.4 - - - +
454B GLN* 1.3 57.0 + - - +
456B ILE* 3.1 42.8 - - + +
457B LYS* 4.2 4.7 + - - +
475B ASP* 3.3 33.7 - - - +
476B LEU 4.4 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B VAL 3.2 7.5 + - - +
451B GLN* 2.5 49.3 + - - +
453B LEU* 1.3 69.6 - - - +
455B VAL* 1.3 75.5 + - + +
456B ILE 3.1 1.3 - - - -
457B LYS* 2.7 35.1 + - - +
458B LYS* 3.7 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B PRO* 5.9 7.6 - - + -
451B GLN* 3.6 23.3 - - - +
452B LEU* 3.0 13.7 + - + +
454B GLN* 1.3 98.0 - - + +
456B ILE* 1.3 52.2 + - - +
458B LYS* 2.7 51.7 + - + +
459B THR* 3.6 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 3.3 46.4 - - + -
359B PRO* 5.9 9.0 - - + +
360B PHE* 5.5 12.6 - - + -
363B PHE* 6.4 0.2 - - + -
452B LEU* 2.9 21.9 + - + +
453B LEU* 3.1 28.9 - - + +
454B GLN 3.1 0.4 - - - -
455B VAL* 1.3 76.6 - - - +
457B LYS* 1.3 77.1 + - + +
458B LYS 3.0 0.9 - - - -
459B THR* 3.2 10.0 + - - +
460B GLU* 2.8 33.5 + - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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