Contacts of the helix formed by residues 509 - 518 (chain A) in PDB entry 5UFL
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 LEU 509 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A PHE* 3.8 9.8 - - + -
479A ILE* 4.1 10.1 - - + -
480A LEU* 3.7 21.1 - - + -
483A LEU* 3.4 33.2 - - + -
503A ILE* 3.9 7.9 - - + +
504A LEU* 3.7 39.7 - - + +
506A ASP 3.1 14.5 + - - +
508A ARG* 1.3 78.5 - - - +
510A ILE* 1.3 63.4 + - + +
511A THR 3.3 0.8 + - - -
512A PRO* 3.3 6.3 - - + +
513A LEU* 3.1 34.0 + - + +
531A ILE* 4.3 8.1 - - + -
535A ALA* 5.2 1.3 - - + -
541A PHE* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ASP 5.3 1.8 - - - +
507A PRO* 3.4 21.1 - - + +
508A ARG 3.3 1.0 - - - -
509A LEU* 1.3 78.7 - - + +
511A THR* 1.3 60.0 + - - +
513A LEU* 3.4 8.0 + - + +
514A ALA* 3.0 25.8 + - - +
541A PHE* 3.8 33.2 - - + -
542A PRO* 4.0 23.3 - - + +
545A VAL* 3.9 25.6 - - + +
546A LEU* 3.6 35.5 - - + +
549A SER* 4.1 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ILE* 3.5 27.4 - - + -
459A ASP* 5.6 2.5 - - - +
465A LYS* 3.6 26.0 + - + +
507A PRO 4.8 0.2 + - - -
508A ARG 3.9 3.0 + - - -
510A ILE* 1.3 76.7 - - - +
512A PRO* 1.4 66.4 - - - +
514A ALA* 3.3 2.3 + - - +
515A PHE* 3.0 62.6 + - + -
549A SER* 4.1 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A PHE* 4.5 10.5 - - + -
458A ILE* 4.0 6.5 - - + -
476A ALA* 3.7 37.1 - - + +
479A ILE* 4.7 5.6 - - + -
480A LEU* 3.3 27.4 - - + +
508A ARG 3.2 20.0 - - - +
509A LEU* 3.3 9.2 - - + +
511A THR* 1.4 96.1 - - + +
513A LEU* 1.3 55.4 + - - +
515A PHE* 3.5 3.3 + - + +
516A ALA* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 4.2 8.5 - - + -
509A LEU* 3.1 38.6 + - + +
510A ILE* 3.6 11.0 - - + +
512A PRO* 1.3 73.4 - - - +
514A ALA* 1.3 60.6 + - - +
516A ALA* 3.3 1.3 + - - +
517A LEU* 2.9 40.5 + - + +
528A GLY* 3.4 31.0 - - - +
531A ILE* 4.0 15.3 - - + -
532A LEU* 4.0 21.1 - - + +
535A ALA* 5.3 1.1 - - + -
541A PHE* 4.4 25.4 - - + -
546A LEU* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A ILE 3.0 10.5 + - - +
511A THR 3.3 6.5 + - - +
513A LEU* 1.3 72.9 - - - +
515A PHE* 1.3 59.8 + - - +
517A LEU 4.0 0.4 - - - +
518A THR* 2.7 39.2 + - - +
546A LEU* 4.2 1.5 - - + +
549A SER* 3.2 40.8 - - - +
550A ILE* 3.9 14.6 - - + +
553A ASN* 3.6 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ILE* 5.2 1.1 - - + -
465A LYS* 4.0 12.8 - - + -
466A VAL 3.6 8.5 - - - -
467A ALA* 3.4 30.1 - - + -
472A CYS* 3.7 31.6 - - + -
473A LYS* 4.0 11.0 - - + +
476A ALA* 3.7 21.5 - - + -
511A THR* 3.0 41.2 + - + -
512A PRO* 3.6 9.2 - - + +
513A LEU 3.3 0.2 - - - -
514A ALA* 1.3 74.5 - - - +
516A ALA* 1.3 60.9 + - - +
518A THR* 3.4 7.6 + - - -
519A SER* 3.4 9.4 + - - -
524A GLN* 4.6 6.1 - - - +
553A ASN* 3.3 25.8 - - - -
557A ARG* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 3.4 33.2 - - + -
512A PRO 3.1 7.0 + - - +
513A LEU 3.6 3.6 - - - +
515A PHE* 1.3 77.0 - - - +
517A LEU* 1.3 61.7 + - - +
519A SER* 3.2 18.8 + - - -
524A GLN* 3.8 33.8 - - - +
525A VAL* 3.4 15.5 + - - +
528A GLY* 3.9 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A LEU* 2.9 33.2 + - + +
514A ALA 4.3 2.0 - - - +
515A PHE 3.5 0.2 - - - -
516A ALA* 1.3 73.1 - - - +
518A THR* 1.3 58.6 + - - +
519A SER 3.4 0.2 - - - -
525A VAL* 4.0 12.3 - - + +
528A GLY 4.5 3.8 - - - +
529A LEU* 3.6 44.9 - - + +
532A LEU* 3.6 28.3 - - + -
546A LEU* 4.8 1.1 - - + -
550A ILE* 3.9 29.4 - - + -
517B LEU 5.2 3.6 - - - +
518B THR* 5.1 0.7 - - - +
550B ILE* 3.2 20.8 - - + +
554B ASN* 2.9 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ALA 2.7 22.3 + - - +
515A PHE* 3.4 2.1 + - - -
517A LEU* 1.3 74.9 - - - +
519A SER* 1.3 59.5 + - - +
550A ILE* 3.4 30.1 - - + +
553A ASN* 3.6 10.9 - - + +
554A ASN* 3.2 26.7 - - - +
557A ARG* 2.9 30.7 + - - -
517B LEU 5.1 0.2 - - - +
554B ASN* 3.2 11.9 - - - +
558B GLN* 2.8 28.1 + - - -
----------------------------------------------------------
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