Contacts of the helix formed by residues 428 - 442 (chain A) in PDB entry 5ULM
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 THR 428 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A SER* 3.8 15.1 + - - +
423A PHE* 3.5 8.9 - - - -
426A GLU* 3.2 27.6 + - + +
427A PRO* 1.3 79.1 - - - +
429A LEU* 1.3 63.9 + - - +
430A GLN* 3.8 8.3 + - - +
431A SER* 3.3 23.1 + - - -
432A GLY 3.1 17.8 + - - -
462A LEU* 3.5 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A THR* 1.3 73.2 - - - +
430A GLN* 1.3 58.8 + - - +
432A GLY 3.2 0.2 + - - -
433A ILE* 2.7 38.4 + - + +
459A LEU* 3.6 33.7 - - + +
462A LEU* 3.8 23.2 - - + +
463A LEU* 4.1 20.0 - - + +
466A LYS* 4.4 25.5 - - + +
477A GLU* 5.4 2.0 - - - +
480A PHE* 3.9 37.9 - - + +
481A PHE* 4.1 3.6 - - + +
484A ALA* 4.0 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A SER* 5.0 2.1 + - - -
388A ASP* 4.2 15.5 + - - +
391A CYS* 3.6 32.3 - - - +
419A PHE* 5.5 0.6 - - + -
428A THR* 3.2 9.3 + - - +
429A LEU* 1.3 80.8 - - - +
431A SER* 1.3 60.4 + - - +
433A ILE* 3.5 1.8 - - - +
434A ASN* 2.8 38.3 + - - +
480A PHE* 3.5 55.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A SER* 4.7 0.4 - - - -
391A CYS* 3.8 10.5 - - - -
419A PHE* 3.7 19.8 - - - +
422A ALA* 3.6 27.4 - - - -
423A PHE* 3.3 24.9 + - - -
426A GLU 4.2 0.9 + - - -
428A THR* 3.3 16.2 + - - -
429A LEU 3.4 0.2 - - - -
430A GLN* 1.3 76.0 - - - +
432A GLY* 1.3 62.0 + - - +
434A ASN 3.5 0.2 + - - -
435A TYR* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A PHE* 3.4 30.7 - - - -
428A THR 3.1 9.8 + - - -
429A LEU 3.6 2.2 - - - -
431A SER* 1.3 79.4 + - - +
433A ILE* 1.3 56.1 - - - +
435A TYR* 3.4 1.7 + - - +
436A ALA* 3.0 30.3 + - - +
455A VAL* 3.6 6.8 - - - +
459A LEU* 4.0 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU 2.7 26.4 + - - +
430A GLN 3.5 6.7 - - - +
432A GLY* 1.3 71.0 - - - -
434A ASN* 1.3 65.6 + - - +
436A ALA* 3.4 1.6 + - - +
437A VAL* 2.9 36.5 + - - +
459A LEU* 4.2 11.0 - - + -
479A GLY 5.2 0.4 - - - +
480A PHE* 4.2 27.1 - - + +
483A GLY* 3.8 23.6 - - - +
484A ALA* 3.6 35.0 - - + +
487A LEU* 3.9 19.1 - - + -
514A ILE* 5.3 4.3 - - + -
517A THR* 4.5 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LYS* 3.4 20.4 + - - +
419A PHE* 3.5 38.3 - - + -
430A GLN* 2.8 37.2 + - - +
433A ILE* 1.3 85.8 - - - +
435A TYR* 1.3 61.3 + - - +
437A VAL* 3.6 5.4 + - - +
438A LEU* 3.2 30.0 + - - +
480A PHE* 5.4 2.6 - - - -
517A THR* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA* 3.5 24.9 - - + +
419A PHE* 3.9 12.3 - - + +
420A LYS* 2.9 56.3 + - + +
423A PHE* 4.6 11.2 - + + -
431A SER 2.9 19.7 + - - +
432A GLY* 3.6 3.4 - - - +
434A ASN* 1.3 72.1 - - - +
436A ALA* 1.3 64.1 + - - +
438A LEU* 3.2 5.6 + - - +
439A LEU* 3.0 48.4 + - + +
451A GLU* 3.4 18.7 + - + +
455A VAL* 3.5 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLY 3.0 14.1 + - - +
435A TYR* 1.3 75.7 - - - +
437A VAL* 1.3 56.5 + - - +
439A LEU* 3.2 7.7 + - - +
440A LEU* 2.8 33.5 + - + +
452A LEU* 3.7 23.6 - - + +
455A VAL* 4.2 12.8 - - + -
459A LEU* 4.9 0.9 - - + -
487A LEU* 3.3 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LYS* 6.2 1.3 - - + -
433A ILE 2.9 21.3 + - - +
434A ASN* 3.9 5.8 - - - +
436A ALA* 1.3 77.2 - - - +
438A LEU* 1.3 61.2 + - + +
440A LEU* 3.3 12.6 + - + +
441A ALA* 2.9 25.8 + - - +
487A LEU* 3.8 24.9 - - + -
517A THR* 3.8 28.0 - - + +
520A ILE* 3.5 39.0 - - + +
521A TYR* 4.0 13.7 - - + +
524A PHE* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LYS* 4.6 22.2 - - + -
401A PHE* 4.0 29.4 - - + -
412A ARG* 3.9 20.0 - - + +
415A GLY* 3.6 11.2 - - - -
416A ALA* 3.4 38.1 - - + +
419A PHE* 3.9 14.8 - - + -
434A ASN 3.2 16.9 + - - +
435A TYR 3.2 4.9 + - - +
437A VAL* 1.3 77.5 - - + +
439A LEU* 1.3 61.4 + - - +
441A ALA* 3.3 3.8 + - - +
442A ALA* 2.9 28.2 + - - +
520A ILE* 4.6 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA* 4.9 6.7 - - + +
435A TYR* 3.0 62.1 + - + +
436A ALA* 3.5 6.1 - - - +
438A LEU* 1.3 73.5 - - - +
440A LEU* 1.3 65.7 + - - +
442A ALA* 3.0 10.4 + - + +
443A GLY 3.2 0.9 + - - -
444A HIS* 3.0 57.8 + - + +
451A GLU* 3.9 18.4 - - + -
452A LEU* 4.1 22.9 - - + +
455A VAL* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ALA 2.8 21.7 + - - +
437A VAL* 3.3 16.8 - - + +
439A LEU* 1.3 70.3 - - - +
441A ALA* 1.3 61.9 + - - +
443A GLY* 3.2 13.7 + - - -
444A HIS 3.6 14.9 - - - +
452A LEU* 3.6 27.1 - - + +
487A LEU* 5.1 6.3 - - + -
521A TYR* 3.6 39.0 - - + -
524A PHE* 4.0 21.4 - - + +
525A VAL* 5.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A PHE* 3.8 21.3 - - + -
412A ARG* 3.6 14.8 + - - -
437A VAL 2.9 13.7 + - - +
438A LEU* 3.6 9.6 - - - +
439A LEU 3.2 0.4 - - - -
440A LEU* 1.3 75.7 - - - +
442A ALA* 1.3 57.5 + - - +
443A GLY 3.2 1.4 + - - -
520A ILE* 4.1 2.7 - - + -
524A PHE* 3.4 51.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ARG* 3.6 32.2 + - - +
413A ASP* 4.2 5.4 - - - +
438A LEU 2.9 15.7 + - - +
439A LEU* 3.0 9.1 + - + +
441A ALA* 1.3 74.5 - - - +
443A GLY* 1.3 57.7 + - - +
444A HIS* 3.6 13.0 - - + +
----------------------------------------------------------
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