Contacts of the helix formed by residues 478 - 493 (chain A) in PDB entry 1SL1
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 GLY 478 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ALA 3.6 3.6 + - - -
477A SER* 1.3 70.3 - - - +
479A LEU* 1.3 64.2 + - - +
480A GLU* 3.4 4.0 - - - -
481A LEU* 3.2 11.3 + - - +
482A ARG* 3.1 25.0 + - - +
526A TYR* 5.0 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ALA* 4.0 18.9 + - + -
477A SER 3.0 6.2 + - - +
478A GLY* 1.3 74.8 - - - +
480A GLU* 1.3 60.3 + - - +
482A ARG* 3.1 4.2 + - - +
483A CYS* 2.8 39.3 + - - -
618A GLY* 3.6 26.2 - - - +
621A ILE* 4.0 23.1 - - + -
622A CYS* 3.2 35.7 - - - -
654A ASP* 3.8 17.2 + - - +
677A MET* 5.3 2.2 - - - -
690A LEU* 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG* 3.8 20.0 + - - +
478A GLY* 3.4 1.4 - - - -
479A LEU* 1.3 82.4 + - - +
481A LEU* 1.3 63.1 + - - +
483A CYS* 3.2 10.2 + - - +
484A LEU* 3.1 20.4 + - - +
526A TYR* 5.8 3.3 - - + -
529A LEU* 3.4 30.1 - - + +
614A LEU* 4.8 14.4 - - + +
615A GLN* 5.6 3.8 - - - -
618A GLY* 4.3 3.3 - - - -
654A ASP* 3.0 29.1 - - - +
22P 2DA 5.5 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLY* 3.2 11.6 + - - +
480A GLU* 1.3 77.6 - - - +
482A ARG* 1.3 58.1 + - + +
484A LEU* 3.1 14.4 + - + +
485A ALA* 2.9 25.5 + - - +
496A TYR* 3.7 36.1 - - + +
500A ILE* 4.0 13.2 - - + -
505A ILE* 4.2 14.8 - - + -
506A HIS* 4.1 18.2 - - + -
509A ASN* 5.2 0.2 - - - +
525A ILE* 4.1 23.3 - - + -
526A TYR* 4.0 28.2 - - + +
529A LEU* 3.6 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A SER* 3.1 35.8 + - - -
478A GLY* 3.1 12.6 + - - +
479A LEU* 3.5 7.6 - - - +
481A LEU* 1.3 73.2 - - - +
483A CYS* 1.3 61.4 + - - +
485A ALA* 3.2 4.0 + - - +
486A HIS* 2.9 28.1 + - - +
500A ILE* 4.2 20.2 + - + +
501A LEU* 4.1 14.8 - - - +
686A PHE* 4.5 1.6 - - - -
688A CYS* 3.6 23.7 - - - +
689A LEU 2.8 27.0 + - - -
690A LEU* 4.1 18.2 - - + +
691A ASP* 2.8 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A LEU* 2.8 22.3 + - - -
480A GLU* 3.2 9.8 + - - +
482A ARG* 1.3 76.1 - - - +
484A LEU* 1.3 63.8 + - - +
486A HIS* 3.3 1.7 + - - +
487A PHE* 3.1 31.2 + - - -
614A LEU* 4.2 11.7 - - + +
617A ALA* 3.7 31.4 - - + -
618A GLY* 3.8 17.7 - - - -
621A ILE* 3.9 10.3 - - - -
686A PHE* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A GLU 3.1 12.2 + - - +
481A LEU* 3.1 14.8 + - + +
483A CYS* 1.3 77.0 - - - +
485A ALA* 1.3 63.5 + - - +
487A PHE* 3.3 2.6 + - - -
488A MET* 3.0 45.0 + - + +
496A TYR* 4.2 17.5 - - + +
525A ILE* 4.6 5.4 - - + -
528A PHE* 5.3 3.8 - - + -
529A LEU* 3.9 18.6 - - + -
562A ILE* 4.1 30.1 - - + -
565A LEU* 4.0 16.8 - - + -
610A LEU* 4.8 3.8 - - + -
614A LEU* 3.8 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LEU 2.9 12.3 + - - +
482A ARG 3.4 8.7 - - - +
484A LEU* 1.3 76.7 - - - +
486A HIS* 1.3 62.9 + - - +
488A MET* 3.1 5.5 + - - +
489A ALA* 3.1 22.5 + - - +
492A ASP* 4.8 0.9 - - - +
494A GLY* 5.6 0.2 - - - -
496A TYR* 4.1 12.5 - - + +
497A ALA* 3.6 41.2 + - + +
500A ILE* 3.8 12.8 - - + -
688A CYS* 4.0 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ARG 2.9 14.2 + - - +
483A CYS 3.3 7.4 - - - +
484A LEU 3.2 0.2 - - - -
485A ALA* 1.3 78.4 - - - +
487A PHE* 1.3 90.0 + + - +
489A ALA* 3.2 16.1 + - - +
490A ARG 4.4 1.2 + - - -
596A LEU* 4.9 4.4 - - - +
684A TRP 4.6 3.1 + - - -
685A ASN 3.7 6.3 - - - -
686A PHE* 3.4 50.7 - + + -
687A ARG* 2.8 51.4 + - + +
688A CYS* 4.2 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A CYS* 3.1 24.2 + - + +
484A LEU* 4.0 1.3 - - - +
486A HIS* 1.3 103.2 - + - +
488A MET* 1.3 60.7 + - - +
490A ARG* 3.9 15.1 + - - +
491A PHE* 3.8 17.8 - - - -
565A LEU* 3.8 28.1 - - + +
596A LEU* 4.2 14.6 - - + -
613A LEU* 3.8 39.0 - - + -
614A LEU* 3.8 14.8 - - + -
617A ALA* 3.7 30.1 - - + -
686A PHE* 5.2 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A LEU* 3.0 44.2 + - + +
485A ALA* 3.1 5.5 + - - +
487A PHE* 1.3 72.6 - - - +
489A ALA* 1.3 54.2 + - - +
490A ARG 3.1 3.4 - - - -
491A PHE* 2.6 35.7 + - - +
492A ASP* 2.9 19.8 + - - +
496A TYR* 3.4 51.8 - - + -
559A THR* 4.0 4.5 - - + -
561A ALA* 3.4 29.8 - - + +
562A ILE* 3.7 22.9 - - + -
565A LEU* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ALA 3.1 9.6 + - - +
486A HIS 3.2 15.1 + - - +
488A MET* 1.3 75.4 - - - +
490A ARG* 1.3 61.1 + - - +
491A PHE 3.0 0.2 - - - -
492A ASP* 3.1 11.9 + - - -
493A ASN* 2.9 23.8 + - - -
494A GLY* 3.7 10.5 - - - +
687A ARG* 3.5 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A HIS 4.4 1.2 + - - -
487A PHE* 3.9 12.9 + - - +
488A MET 3.0 1.0 + - - -
489A ALA* 1.3 78.4 - - - +
491A PHE* 1.3 95.7 + - + +
493A ASN* 5.0 4.9 + - - -
568A SER* 5.5 3.6 + - - -
687A ARG* 4.6 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A PHE 3.8 17.9 - - - -
488A MET* 2.6 13.8 + - - +
490A ARG* 1.3 112.2 - - - +
492A ASP* 1.3 58.9 + - - +
493A ASN* 3.5 7.8 + - - +
561A ALA* 3.9 28.5 - - + -
564A ALA* 3.6 24.7 - - + -
565A LEU* 3.6 20.2 - - + -
568A SER* 3.3 27.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ALA 4.8 0.7 - - - +
488A MET* 2.9 22.2 + - - +
489A ALA* 3.1 13.0 + - - -
491A PHE* 1.3 72.8 - - - +
493A ASN* 1.3 72.9 + - - +
494A GLY* 2.9 14.2 + - - -
495A GLU* 3.3 23.3 + - + +
496A TYR* 2.7 37.2 + - - +
561A ALA* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ALA* 2.9 19.5 + - - -
490A ARG 5.0 4.9 + - - -
491A PHE 4.1 7.4 - - - +
492A ASP* 1.3 81.6 - - - +
494A GLY* 1.3 58.6 + - - +
495A GLU 3.7 0.3 + - - -
687A ARG* 4.7 11.9 + - - +
----------------------------------------------------------
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