Contacts of the helix formed by residues 493 - 504 (chain H) in PDB entry 4P0S
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 493 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487H GLN* 3.6 3.6 - - - +
491H ARG 4.1 1.6 + - - -
492H VAL* 1.3 75.6 - - - +
494H LEU* 1.3 56.5 + - - +
495H GLU* 3.8 5.8 + - - +
496H MET* 3.4 22.2 + - - +
497H ALA* 2.8 34.8 + - - +
51P C 3.0 48.5 + - - -
52P A 3.6 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 494 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483H ARG* 3.2 39.3 - - - +
487H GLN* 3.3 16.3 - - - +
493H SER* 1.3 73.0 - - - +
495H GLU* 1.3 68.2 + - + +
497H ALA* 3.6 2.8 - - - +
498H SER* 2.7 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 495 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493H SER* 3.3 6.5 + - - +
494H LEU* 1.3 88.2 - - + +
496H MET* 1.3 66.9 + - - +
498H SER* 3.7 4.6 + - - -
499H ALA* 3.5 19.9 + - - +
532H VAL* 3.9 22.1 - - + +
533H ARG* 3.6 45.3 + - + +
534H ARG* 4.7 8.2 + - - -
51P C 4.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 496 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486H ILE* 5.4 0.2 - - - -
491H ARG 4.5 12.8 - - - +
492H VAL* 4.8 4.0 - - + -
493H SER* 3.4 23.1 + - - +
494H LEU 3.3 0.2 - - - -
495H GLU* 1.3 78.0 - - - +
497H ALA* 1.3 63.1 + - - +
499H ALA* 3.3 13.4 + - - +
500H VAL* 3.4 17.9 + - + +
532H VAL* 4.4 9.9 - - + -
541H THR* 4.1 19.1 - - + -
544H ARG 4.4 12.1 - - - +
545H ILE* 3.9 27.2 - - + +
549H LEU* 4.1 22.4 - - + -
50P G 4.0 11.2 - - - +
51P C 3.4 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 497 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483H ARG* 3.9 15.0 - - + +
486H ILE* 3.8 25.1 - - + +
487H GLN* 3.6 23.3 - - + -
492H VAL* 4.0 1.9 - - + +
493H SER 2.8 20.9 + - - +
494H LEU* 3.6 4.9 - - - +
496H MET* 1.3 77.3 - - - +
498H SER* 1.3 62.7 + - - +
500H VAL* 3.7 2.4 + - - +
501H VAL* 3.3 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 498 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483H ARG* 3.7 24.2 - - - +
494H LEU* 2.7 31.1 + - - +
495H GLU* 4.1 5.8 - - - -
497H ALA* 1.3 72.3 - - - +
499H ALA* 1.3 52.2 + - - +
501H VAL* 3.2 6.2 + - - +
502H ASN* 2.9 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 499 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495H GLU 3.5 10.8 + - - +
496H MET* 3.3 12.1 + - - +
498H SER* 1.3 75.8 - - - +
500H VAL* 1.3 65.6 + - - +
501H VAL 3.5 0.2 + - - -
502H ASN* 3.7 15.1 + - - +
503H ALA* 3.7 10.2 + - - +
530H ILE* 3.7 30.7 - - + +
531H GLN 3.9 15.9 - - - +
532H VAL* 4.7 6.5 - - + -
545H ILE* 4.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 500 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482H TRP* 6.1 2.9 - - + -
486H ILE* 4.5 26.0 - - + -
496H MET 3.4 13.3 + - - +
497H ALA 4.1 5.8 - - - +
498H SER 3.5 0.2 - - - -
499H ALA* 1.3 78.7 - - - +
501H VAL* 1.3 61.5 + - + +
503H ALA* 3.5 5.5 + - - +
504H TYR* 3.5 22.3 + - + +
510H LEU* 5.7 6.5 - - + -
527H LEU* 3.8 27.1 - - + -
530H ILE* 4.3 8.7 - - + -
545H ILE* 4.3 18.2 - - + -
549H LEU* 6.2 0.4 - - + -
553H ILE* 4.2 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 501 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479H ALA* 5.0 4.0 - - + +
482H TRP* 3.9 24.5 - - + +
483H ARG* 3.5 37.0 - - + +
486H ILE* 3.6 16.6 - - + -
497H ALA 3.3 13.9 + - - +
498H SER* 3.2 11.6 + - - +
500H VAL* 1.3 73.6 - - - +
502H ASN* 1.3 68.1 + - - +
503H ALA 3.2 1.8 - - - -
504H TYR 3.2 5.3 - - - -
505H PRO* 3.1 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 502 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498H SER* 2.9 31.9 + - - +
499H ALA* 4.2 9.2 - - - +
500H VAL 3.6 0.4 - - - -
501H VAL* 1.3 75.4 - - - +
503H ALA* 1.3 59.9 + - - +
505H PRO* 4.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 503 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499H ALA 3.7 8.0 + - - +
500H VAL 3.5 10.7 + - - +
501H VAL 3.2 0.4 - - - -
502H ASN* 1.3 82.3 - - - +
504H TYR* 1.3 85.3 + - + +
505H PRO* 3.7 5.2 - - - +
509H LEU* 5.8 0.7 - - - +
530H ILE* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 504 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482H TRP* 2.9 18.4 + - + -
500H VAL* 3.5 11.5 + - + +
501H VAL* 3.2 6.1 + - - +
503H ALA* 1.3 100.3 - - + +
505H PRO* 1.3 53.6 - - - +
506H SER 2.7 21.3 + - - +
509H LEU* 3.8 25.4 - - + -
510H LEU* 4.0 27.1 - - + +
513H ALA* 3.7 19.4 - - + +
526H LEU* 3.2 41.5 + - + +
527H LEU* 3.8 14.1 - - + -
530H ILE* 5.2 0.7 - - + -
----------------------------------------------------------
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