Contacts of the helix formed by residues 474 - 488 (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 SER 474 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A GLN* 1.3 77.0 - - - +
475A TYR* 1.3 65.8 + - - +
476A TRP* 3.1 49.2 + - - -
477A GLU* 3.1 20.5 + - - +
478A VAL* 3.2 12.3 + - - +
504A LEU* 4.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A GLN 3.5 3.4 + - - -
474A SER* 1.3 72.5 - - - +
476A TRP* 1.3 100.6 + + + +
478A VAL* 4.5 0.9 - - - -
479A GLY* 2.9 25.3 + - - -
501A LEU* 3.6 6.8 - - - +
504A LEU* 3.9 22.6 - - + +
505A LYS 5.6 0.2 - - - -
506A THR* 3.7 24.0 - - + +
507A PRO* 3.4 38.0 - - + +
509A TRP* 3.7 16.9 + + - -
510A TYR* 3.6 36.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A SER* 3.3 28.7 - - - -
475A TYR* 1.3 114.1 - + + +
477A GLU* 1.3 97.3 + - + +
480A PHE* 3.0 25.4 + + + -
510A TYR* 2.9 39.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU* 5.4 1.9 - - - +
466A LYS* 2.9 47.9 + - - +
472A LEU* 4.2 27.7 - - + +
474A SER* 3.1 17.8 + - - +
476A TRP* 1.3 98.8 + - + +
478A VAL* 1.3 60.1 + - - +
480A PHE* 3.5 4.9 + - - +
481A PHE* 3.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 4.2 11.0 - - + -
472A LEU* 3.5 31.6 - - + +
474A SER 3.2 11.9 + - - +
475A TYR 3.8 6.3 - - - +
477A GLU* 1.3 75.4 - - - +
479A GLY* 1.3 60.0 + - - +
481A PHE* 3.3 7.2 + - - +
482A LEU* 2.8 28.1 + - - +
497A ALA* 3.6 25.5 - - + +
500A LYS* 4.0 19.7 - - + -
501A LEU* 3.9 13.2 - - + +
504A LEU* 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A TYR 2.9 13.5 + - - -
478A VAL* 1.3 77.3 - - - +
480A PHE* 1.3 57.3 + - - +
482A LEU* 3.3 8.4 + - - +
483A GLY* 3.1 21.7 + - - -
501A LEU* 3.8 10.9 - - - +
510A TYR* 3.2 24.2 - - - -
514A ILE* 3.9 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU* 3.9 25.6 - - + +
430A GLN* 3.5 59.2 - - + -
433A ILE* 4.2 12.9 - - + +
434A ASN* 5.4 2.5 - - - -
476A TRP* 3.0 30.9 + + + +
477A GLU* 4.3 3.4 - - - +
479A GLY* 1.3 71.4 - - - +
481A PHE* 1.3 64.7 + - - +
483A GLY* 3.2 1.8 + - - +
484A ALA* 3.1 24.4 + - - +
510A TYR* 3.6 24.2 - + - -
513A SER* 5.7 2.5 - - - -
514A ILE* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU* 4.1 9.7 - - + +
463A LEU* 3.5 27.0 - - + +
466A LYS* 5.5 2.0 - - + -
467A GLY 4.2 16.2 - - - -
468A ASN* 5.6 0.2 - - - -
469A LEU* 3.7 38.8 - - + -
472A LEU* 3.8 20.6 - - + -
477A GLU 3.0 18.8 + - - +
478A VAL* 3.3 5.6 + - - +
480A PHE* 1.3 77.7 - - - +
482A LEU* 1.3 58.7 + - - +
484A ALA* 3.4 1.4 + - - +
485A SER* 2.7 45.9 + - - -
493A ARG* 3.5 31.9 - - + -
497A ALA* 3.8 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A VAL 2.8 14.6 + - - +
479A GLY 3.3 8.5 - - - +
480A PHE 3.2 0.2 - - - -
481A PHE* 1.3 75.5 - - - +
483A GLY* 1.3 59.7 + - - +
485A SER* 3.1 4.7 + - - -
486A VAL* 2.8 41.4 + - + +
494A VAL* 3.7 28.0 - - + +
497A ALA* 4.0 11.9 - - + -
498A SER* 3.4 24.2 - - - +
501A LEU* 3.7 26.9 - - + -
514A ILE* 4.2 14.1 - - + -
518A ILE* 4.4 5.8 - - + -
543A MET* 4.5 1.8 - - + -
546A LEU* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ILE* 3.8 22.9 - - - -
479A GLY 3.1 8.5 + - - -
480A PHE 3.2 3.1 + - - -
482A LEU* 1.3 81.4 - - - +
484A ALA* 1.3 56.4 + - - +
486A VAL* 3.4 7.1 + - - +
487A LEU* 3.0 34.5 + - - +
514A ILE* 5.4 6.1 - - - -
517A THR* 6.0 1.8 - - - -
518A ILE* 5.5 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU* 4.0 20.9 - - + -
433A ILE* 3.6 19.6 - - + +
459A LEU* 4.8 8.2 - - + +
463A LEU* 4.2 19.3 - - + +
480A PHE 3.1 15.6 + - - +
481A PHE 4.1 2.5 - - - +
483A GLY* 1.3 75.5 - - - +
485A SER* 1.3 56.7 + - - +
487A LEU* 3.3 5.9 + - - +
488A ALA* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LEU* 4.9 6.6 - - - +
481A PHE* 2.7 42.9 + - - -
482A LEU* 3.4 6.3 - - - -
484A ALA* 1.3 74.2 - - - +
486A VAL* 1.3 64.4 + - - +
488A ALA* 3.3 6.7 + - - +
489A ASN 3.2 2.9 + - - -
490A ASP* 2.9 31.9 + - - -
493A ARG* 3.8 18.1 - - - +
494A VAL* 3.7 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 2.8 34.2 + - + +
483A GLY* 3.5 9.2 - - - +
485A SER* 1.3 72.7 - - - +
487A LEU* 1.3 60.6 + - + +
489A ASN* 2.8 23.0 + - - +
494A VAL* 3.7 23.1 - - + -
518A ILE* 4.4 27.4 - - + -
521A TYR* 3.5 43.3 + - + -
522A LYS* 5.9 2.5 - - - +
543A MET* 4.5 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ILE* 3.9 25.1 - - + +
436A ALA* 3.3 34.1 - - + -
437A VAL* 3.8 24.5 - - + +
440A LEU* 5.1 4.0 - - + -
459A LEU* 4.3 12.1 - - + -
483A GLY* 3.0 26.6 + - - +
484A ALA* 3.3 9.6 + - - +
486A VAL* 1.3 79.9 - - + +
488A ALA* 1.3 60.9 + - - +
489A ASN* 3.1 1.6 + - - +
517A THR* 5.1 3.4 - - + -
521A TYR* 4.2 25.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LEU* 5.6 6.7 - - + -
484A ALA 2.9 17.5 + - - +
485A SER* 3.7 9.0 - - - +
486A VAL 3.1 0.4 - - - -
487A LEU* 1.3 74.8 - - - +
489A ASN* 1.3 70.4 + - - +
490A ASP* 3.4 9.8 + - + +
----------------------------------------------------------
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