Contacts of the helix formed by residues 435 - 456 (chain D) in PDB entry 5NTI
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 GLU 435 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D GLU 5.2 0.2 - - - +
344D LEU* 4.7 1.0 - - - +
345D CYS* 3.8 37.2 + - - +
348D ASP* 3.0 14.6 + - - +
434D GLN* 1.3 87.3 + - + +
436D LYS* 1.3 63.3 + - - +
437D ARG* 3.2 4.3 - - + -
438D LYS* 3.0 49.1 + - + +
439D VAL* 3.2 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 436 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428D ALA* 3.6 27.6 - - + +
429D HIS* 5.6 1.1 - - - +
433D LEU* 4.5 22.7 - - + +
434D GLN 3.6 4.8 + - - +
435D GLU* 1.3 75.0 - - - +
437D ARG* 1.3 57.9 + - - +
439D VAL* 3.3 4.5 + - - +
440D GLU* 2.9 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 437 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D GLU* 5.0 1.1 - - - -
436D LYS* 1.3 78.9 - - - +
438D LYS* 1.3 56.9 + - - +
440D GLU* 3.5 16.7 + - - +
441D GLN* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 438 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D GLU* 4.3 18.8 + - + +
344D LEU* 4.1 20.5 - - + +
435D GLU* 3.0 41.9 + - + +
437D ARG* 1.3 76.4 - - - +
439D VAL* 1.3 64.0 + - - +
441D GLN* 3.6 6.7 + - + +
442D LEU* 3.3 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 439 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D LEU* 4.2 21.8 - - + -
348D ASP* 3.9 15.5 - - - +
352D LEU* 4.2 9.9 - - + -
426D ILE* 3.8 19.1 - - + +
427D ASN 4.2 4.0 - - - -
428D ALA* 4.0 24.5 - - + +
433D LEU* 4.2 22.0 - - + -
435D GLU 3.2 13.2 + - - +
436D LYS 3.8 5.2 - - - +
438D LYS* 1.3 74.6 - - - +
440D GLU* 1.3 60.7 + - - +
442D LEU* 3.3 3.7 + - - -
443D GLN* 2.8 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 440 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428D ALA* 3.6 22.9 - - + -
436D LYS* 2.9 40.4 + - + +
437D ARG* 3.5 18.7 - - - +
439D VAL* 1.3 77.1 - - - +
441D GLN* 1.3 57.0 + - - +
443D GLN* 3.4 9.1 + - - +
444D TYR* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 441 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D TYR* 4.8 21.3 + - - +
437D ARG 3.1 16.1 + - - +
438D LYS* 3.9 9.0 - - + +
439D VAL 3.2 0.4 - - - -
440D GLU* 1.3 75.0 - - - +
442D LEU* 1.3 59.5 + - - +
444D TYR* 3.9 12.6 - - - +
445D ASN* 3.1 49.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 442 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D LEU* 4.6 16.6 - - + -
339D SER 4.0 8.5 - - - +
340D GLY* 3.6 43.1 - - - +
341D PHE 4.0 0.7 - - - +
344D LEU* 4.4 8.5 - - + -
426D ILE* 3.8 34.3 - - + -
438D LYS 3.3 15.0 + - - +
439D VAL* 3.3 4.2 + - - +
441D GLN* 1.3 75.9 - - - +
443D GLN* 1.3 65.0 + - - +
445D ASN* 3.5 7.7 + - + +
446D LEU* 3.1 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 443 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D LEU* 3.5 14.0 - - + +
426D ILE* 3.5 25.9 - - - +
427D ASN* 3.6 0.9 - - - -
428D ALA* 3.2 34.8 + - - +
429D HIS* 4.8 4.3 + - - -
439D VAL 2.8 17.3 + - - +
440D GLU* 3.6 10.5 + - - +
441D GLN 3.3 0.2 - - - -
442D LEU* 1.3 76.8 - - - +
444D TYR* 1.3 56.3 - - - +
446D LEU* 3.4 3.9 + - - -
447D GLU* 2.9 43.3 + - - +
469D LYS* 3.3 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 444 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D GLU 3.0 17.6 + - - +
441D GLN* 3.9 13.7 - - - +
442D LEU 3.3 0.2 - - - -
443D GLN* 1.3 78.0 - - - +
445D ASN* 1.3 61.2 + - - +
447D GLU* 3.0 25.5 + - + +
448D LEU* 2.8 63.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 445 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D TYR 6.0 0.4 - - - +
265D ALA* 4.0 28.4 + - - +
270D ILE* 3.7 4.9 - - + +
273D LEU* 3.6 19.8 - - + +
441D GLN* 3.1 39.3 + - - +
442D LEU* 3.9 10.4 - - + +
444D TYR* 1.3 75.9 - - - +
446D LEU* 1.3 52.7 + - - +
448D LEU* 3.2 21.4 + - - +
449D ALA* 2.7 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D LEU* 3.8 20.4 - - + -
277D VAL* 3.7 31.0 - - + -
338D LEU* 5.8 2.0 - - + -
339D SER 5.6 1.3 - - - +
419D LEU* 5.0 7.6 - - + +
422D ALA* 3.9 18.6 - - + +
423D LEU* 3.7 15.7 - - + +
426D ILE* 3.6 35.0 - - + -
442D LEU* 3.1 29.6 + - + +
443D GLN* 3.7 4.9 - - - +
445D ASN* 1.3 72.4 - - - +
447D GLU* 1.3 60.0 - - - +
449D ALA* 3.5 7.1 - - + +
450D PHE* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 447 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D LEU* 3.6 22.8 - - + +
443D GLN* 2.9 33.5 + - - +
444D TYR* 3.0 34.7 + - + +
446D LEU* 1.3 76.6 - - - +
448D LEU* 1.3 57.4 + - + +
450D PHE* 3.4 6.0 + - - +
451D HIS* 2.9 41.9 + - + +
463D LEU* 5.7 1.1 - - + +
469D LYS* 5.6 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D ALA* 5.5 5.8 - - + +
270D ILE* 3.9 21.5 - - + +
444D TYR* 2.8 56.6 + - + +
445D ASN* 3.4 19.5 - - - +
447D GLU* 1.3 74.7 - - - +
449D ALA* 1.3 55.1 + - - +
451D HIS* 3.3 10.3 + - + +
452D HIS* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 449 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ILE* 3.7 15.4 - - + +
273D LEU* 4.1 15.3 - - + -
274D VAL* 3.5 25.5 - - + +
419D LEU* 4.0 10.7 - - + +
445D ASN 2.7 21.0 + - - +
446D LEU* 3.5 11.2 - - + +
448D LEU* 1.3 72.9 - - - +
450D PHE* 1.3 57.4 + - - +
452D HIS* 3.9 0.3 - - - +
453D HIS* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 450 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412D PHE* 4.2 16.2 - + - -
416D GLU* 3.5 32.1 - - + -
419D LEU* 3.6 24.2 - - + +
420D TYR* 3.8 24.2 - + + -
423D LEU* 4.0 15.0 - - + -
446D LEU 2.9 18.5 + - - +
447D GLU* 3.6 7.0 - - - +
448D LEU 3.2 0.2 - - - -
449D ALA* 1.3 74.1 - - - +
451D HIS* 1.3 65.1 + - - +
453D HIS* 3.5 0.3 + - - -
454D LEU* 3.0 47.9 + - + +
463D LEU* 3.7 27.1 - - + -
466D LEU* 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 451 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D GLU* 2.9 30.8 + - + +
448D LEU* 3.3 12.8 + - + +
450D PHE* 1.3 76.5 - - - +
452D HIS* 1.3 63.0 + - - +
454D LEU 3.4 0.2 + - - -
455D SER* 3.1 18.0 + - - -
460D GLN* 3.2 42.5 + - + +
463D LEU* 3.4 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 452 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D LEU* 3.7 35.2 - - + +
270D ILE* 4.3 16.4 - - + -
271D GLU* 3.4 30.5 + - + +
274D VAL* 5.1 3.4 - - + -
448D LEU 2.8 21.5 + - - +
449D ALA 3.9 3.6 - - - +
451D HIS* 1.3 72.7 - - - +
453D HIS* 1.3 62.8 + - - +
455D SER* 2.6 28.3 + - - -
456D LYS* 3.5 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 453 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D VAL* 3.9 14.5 - - + +
413D SER* 4.8 2.6 + - - -
415D ASP* 3.7 33.2 + - + +
416D GLU* 4.0 24.6 + - + +
419D LEU* 3.6 24.2 - - + -
449D ALA 3.1 18.8 + - - +
450D PHE 4.0 0.9 - - - +
452D HIS* 1.3 77.2 - - - +
454D LEU* 1.3 63.5 + - + +
456D LYS* 3.2 56.0 + - + +
457D THR* 4.3 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 454 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D GLU* 3.2 39.7 - - + +
450D PHE* 3.0 35.9 + - + +
451D HIS 3.9 3.6 - - - +
453D HIS* 1.3 77.1 - - - +
455D SER* 1.3 59.4 + - - +
456D LYS 3.4 0.3 + - - -
457D THR* 3.5 1.8 + - - -
458D HIS 3.3 3.8 + - - -
459D ARG* 2.9 59.5 + - + +
460D GLN* 3.9 4.5 - - + +
462D ILE* 3.8 19.5 - - + -
463D LEU* 3.6 35.9 - - + -
466D LEU* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 455 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D HIS 3.1 14.9 + - - -
452D HIS* 2.6 28.2 + - - -
454D LEU* 1.3 76.0 - - - +
456D LYS* 1.3 64.1 + - - +
457D THR 3.2 1.4 + - - -
458D HIS* 3.4 24.0 + - - +
460D GLN* 4.0 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 456 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D GLU* 3.1 35.1 + - - -
274D VAL* 4.3 3.8 - - - +
452D HIS* 3.7 26.5 - - + +
453D HIS* 3.2 46.2 + - + +
455D SER* 1.3 79.4 + - - +
457D THR* 1.3 65.9 + - + +
458D HIS* 3.6 6.0 - - - -
----------------------------------------------------------
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