Contacts of the helix formed by residues 540 - 555 (chain O) in PDB entry 5A31
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 540 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 3.9 24.0 - - - -
82A GLU 4.6 9.4 + - - -
84A GLY 5.7 0.3 + - - -
89A TYR* 6.0 0.9 - - - -
536O THR* 2.8 33.7 + - - +
537O ALA 5.4 1.6 - - - -
538O LEU 3.9 0.4 - - - -
539O ASN* 1.3 68.7 - - - +
541O ILE* 1.3 70.5 + - - +
542O GLU 3.4 0.4 - - - -
543O GLY 3.4 1.1 + - - +
544O VAL* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 541 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE 5.7 1.1 - - - +
2D SER* 5.3 1.8 - - - +
539O ASN* 2.6 12.2 + - - +
540O SER* 1.3 82.5 + - - +
542O GLU* 1.3 64.5 + - - +
544O VAL* 3.1 18.4 + - + +
545O TYR* 3.1 10.6 + - - +
567O LEU* 4.1 15.9 - - + -
570O HIS* 3.3 38.6 - - + +
571O CYS* 4.2 6.3 - - - -
574O LEU* 3.8 16.2 - - + -
576O ASN* 5.3 7.0 - - - +
579O MET* 4.0 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 542 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SER* 4.4 18.0 + - - -
509O LEU* 5.1 0.2 - - - -
513O LYS* 2.6 55.4 + - - +
535O ILE* 4.0 6.7 - - + +
539O ASN* 2.9 32.8 + - + +
540O SER 3.4 0.4 - - - -
541O ILE* 1.3 78.3 - - - +
543O GLY* 1.3 68.0 + - - +
545O TYR* 3.2 8.2 + - + +
546O ARG* 2.9 47.6 + - + +
579O MET* 5.1 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 543 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532O VAL* 3.3 7.9 - - - +
535O ILE* 4.2 11.9 - - - +
536O THR* 3.6 36.4 - - - +
539O ASN* 4.5 0.2 - - - +
540O SER 3.4 6.0 + - - +
541O ILE 3.3 0.8 - - - -
542O GLU* 1.3 79.3 - - - +
544O VAL* 1.3 57.1 + - - +
546O ARG* 4.6 0.9 - - - -
547O LYS* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 544 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER* 5.2 3.4 - - - +
84A GLY* 4.6 15.0 - - - -
86A ASP* 4.3 20.4 - - + +
87A VAL 5.0 6.1 - - - +
536O THR* 4.7 6.5 - - - +
540O SER 3.1 14.3 + - - +
541O ILE* 3.1 14.3 + - - +
543O GLY* 1.3 73.8 - - - +
545O TYR* 1.3 65.2 + - - +
547O LYS* 3.0 8.6 + - + +
548O ALA* 2.8 30.7 + - - +
563O LEU* 3.9 18.4 - - + +
567O LEU* 3.3 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 545 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541O ILE 3.1 9.0 + - - +
542O GLU* 3.2 7.6 + - + +
544O VAL* 1.3 82.8 - - - +
546O ARG* 1.3 89.1 + - - +
548O ALA* 3.3 3.4 + - + +
549O VAL* 3.2 27.2 + - + +
564O LEU* 4.5 6.1 - - + -
567O LEU* 3.7 22.0 - - + -
579O MET* 3.7 33.9 - - + -
582O SER* 3.9 31.2 + - - -
583O VAL* 4.4 3.4 - - - -
586O SER* 3.8 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 546 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475O GLU* 5.5 1.6 + - - -
513O LYS* 3.8 22.8 - - - +
516O PHE* 3.2 47.1 - - + -
517O ASP* 4.4 13.7 + - - -
532O VAL* 3.9 10.8 - - + -
535O ILE* 4.0 11.7 - - + -
542O GLU* 2.9 51.8 + - + +
543O GLY 3.7 4.0 - - - +
545O TYR* 1.3 106.9 - - - +
547O LYS* 1.3 65.6 + - - +
549O VAL* 3.1 12.2 - - - +
550O VAL* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 547 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP* 5.4 11.2 - - + +
88A ASP* 4.5 17.9 - - - +
529O ASP* 3.6 21.6 + - - -
532O VAL* 3.5 17.7 - - + +
543O GLY 2.8 15.2 + - - +
544O VAL* 3.0 14.6 + - + +
546O ARG* 1.3 75.8 - - - +
548O ALA* 1.3 64.2 + - - +
550O VAL* 3.0 15.1 - - + +
551O LEU* 2.9 49.1 + - - +
554O GLN* 4.4 1.6 + - - -
559O GLU* 5.4 4.9 + - - -
563O LEU* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 548 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544O VAL 2.8 12.0 + - - +
545O TYR* 3.6 7.6 - - + +
546O ARG 3.1 0.2 - - - -
547O LYS* 1.3 77.6 - - - +
549O VAL* 1.3 56.8 + - - +
551O LEU* 3.2 5.4 + - - +
552O GLN* 3.0 32.7 + - - +
560O ALA* 4.0 4.4 - - - +
563O LEU* 3.8 18.8 - - + +
564O LEU* 3.5 41.5 - - + -
586O SER* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 549 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516O PHE* 4.0 14.1 - - + -
520O MET* 4.9 14.0 - - + +
545O TYR* 3.2 22.9 + - + +
546O ARG* 3.1 24.9 - - - +
548O ALA* 1.3 77.4 - - - +
550O VAL* 1.3 63.2 + - - +
552O GLN* 3.4 17.5 + - + +
553O ALA* 3.3 19.8 + - + +
586O SER* 4.5 13.6 + - - +
589O GLU* 5.1 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 550 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516O PHE* 4.1 15.2 - - + -
520O MET* 4.3 9.6 - - - -
525O TYR* 3.7 29.8 - - + +
528O ALA* 4.4 5.2 - - + -
529O ASP* 3.9 17.0 - - + +
532O VAL* 4.6 9.6 - - + -
546O ARG 2.9 16.3 + - - +
547O LYS* 3.0 37.2 - - + +
549O VAL* 1.3 76.7 - - - +
551O LEU* 1.3 57.1 + - - +
553O ALA* 3.3 3.2 + - - +
554O GLN* 2.9 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 551 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547O LYS* 2.9 32.3 + - - +
548O ALA 3.4 5.4 - - - +
550O VAL* 1.3 76.6 - - + +
552O GLN* 1.3 62.4 + - - +
554O GLN* 3.5 18.4 + - - +
555O ASN 3.1 3.5 + - - -
556O GLN* 3.0 69.0 + - + +
559O GLU* 3.8 22.9 - - + +
560O ALA* 3.7 26.0 - - + +
563O LEU* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 552 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548O ALA 3.0 19.3 + - - +
549O VAL* 3.5 15.2 + - - +
551O LEU* 1.3 75.7 - - - +
553O ALA* 1.3 58.8 + - - +
555O ASN* 2.9 16.7 + - - +
556O GLN 4.9 1.1 - - - +
557O MET* 5.1 4.3 - - - -
560O ALA* 4.3 8.9 - - + +
564O LEU* 4.2 6.1 - - - +
586O SER* 3.5 31.5 + - - +
589O GLU* 3.5 32.9 + - - +
590O LEU* 3.8 31.1 - - + +
593O ARG* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 553 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520O MET* 3.7 14.8 - - + -
525O TYR* 3.4 49.9 + - + +
549O VAL 3.3 7.0 + - - +
550O VAL 3.8 6.3 - - - +
552O GLN* 1.3 80.2 - - - +
554O GLN* 1.3 61.0 + - - +
555O ASN* 3.1 4.5 + - - +
593O ARG* 4.9 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 554 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 5.5 0.4 - - - +
611A GLU* 4.3 12.0 + - - -
614A THR* 3.3 44.5 - - + +
615A SER* 3.7 6.1 + - - -
525O TYR* 4.2 18.8 - - + -
526O HIS* 4.5 13.9 - - - +
529O ASP* 3.3 32.6 + - - +
547O LYS* 4.4 1.6 + - - -
550O VAL* 2.9 26.2 + - - +
551O LEU* 3.7 26.2 - - + +
552O GLN 3.3 0.4 - - - -
553O ALA* 1.3 73.2 - - - +
555O ASN* 1.3 67.9 + - - +
556O GLN* 3.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 555 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A THR 4.7 0.2 - - - -
615A SER* 4.2 12.4 + - - +
616A GLU* 3.6 15.5 + - - +
617A LEU* 6.2 2.4 - - - +
781A GLU* 5.1 7.0 + - - +
551O LEU 3.1 0.2 + - - -
552O GLN 2.9 15.5 + - - +
553O ALA 4.1 4.3 - - - +
554O GLN* 1.3 82.9 - - - +
556O GLN* 1.3 61.2 + - - +
557O MET* 3.3 36.6 + - - +
593O ARG* 3.8 11.7 + - - +
----------------------------------------------------------
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