Contacts of the helix formed by residues 608 - 625 (chain A) in PDB entry 5LUQ
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 PRO 608 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ARG* 4.3 17.0 + - - +
567A GLU* 4.6 12.6 - - + +
606A SER* 2.8 8.4 - - - +
607A ASP* 1.4 88.6 - - + +
609A ALA* 1.4 59.7 + - - +
610A ALA 2.9 0.4 - - - -
611A ASN* 2.5 25.3 + - + +
612A LEU* 3.0 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A LEU 3.7 21.5 - - - +
564A LEU* 4.1 1.6 - - - -
566A ASP* 4.5 2.9 - - + -
567A GLU* 3.9 9.1 - - + +
568A PHE* 3.4 32.3 - - + +
606A SER* 3.3 3.7 + - - +
608A PRO* 1.4 75.4 - - - +
610A ALA* 1.3 50.5 - - - +
612A LEU* 3.7 11.2 - - - -
613A HIS* 2.2 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A VAL* 3.0 32.1 - - + +
568A PHE* 3.7 12.9 - - + +
571A SER* 4.5 0.4 - - - +
604A PRO* 4.5 6.5 - - + -
606A SER 2.9 26.1 + - - +
607A ASP* 3.6 9.2 - - - +
609A ALA* 1.3 78.3 - - - +
611A ASN* 1.3 56.0 + - - +
613A HIS* 3.2 11.2 - - - -
614A PRO* 2.9 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ARG* 3.5 22.0 - - - +
491A CYS* 4.3 8.8 - - - -
492A SER* 4.5 11.7 - - - -
494A PRO* 6.2 2.0 - - - +
514A VAL* 5.1 2.3 - - - +
515A ARG 4.8 7.8 - - - +
516A THR* 5.8 1.9 - - - -
607A ASP* 2.6 36.0 + - - +
608A PRO* 2.5 12.9 + - + +
610A ALA* 1.3 74.2 - - - +
612A LEU* 1.3 60.6 + - - +
614A PRO* 3.0 18.7 - - - +
615A ALA* 3.9 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLN* 4.3 2.7 - - + +
488A ILE* 2.9 43.7 - - + +
489A ARG* 3.5 41.1 - - + +
491A CYS* 4.8 0.4 - - - -
563A LEU* 3.9 35.7 - - + -
608A PRO 3.0 6.3 + - - +
609A ALA* 3.6 25.1 - - + +
611A ASN* 1.3 75.7 - - - +
613A HIS* 1.3 86.3 + - + +
615A ALA* 2.8 22.1 - - - +
616A LYS* 2.9 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU* 3.6 17.8 + - - -
514A VAL* 4.1 1.6 - - + -
560A LEU* 6.4 0.7 - - + -
563A LEU* 5.3 2.2 - - + -
564A LEU* 3.7 44.0 - - + +
568A PHE* 3.0 50.5 - + - -
609A ALA 2.2 31.7 + - - +
610A ALA* 3.3 12.3 - - - -
612A LEU* 1.3 87.3 - - + +
614A PRO* 1.4 75.1 - - + +
616A LYS* 2.7 21.1 + - + -
617A PRO* 2.9 21.7 - - + +
656A GLN* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A ALA* 5.9 1.8 - - + +
513A GLU* 3.1 29.8 - - - +
514A VAL* 3.8 13.5 - - + -
610A ALA 2.9 20.9 - - - +
611A ASN* 3.0 17.9 - - - +
613A HIS* 1.4 105.7 - - + +
615A ALA* 1.3 51.8 + - - +
617A PRO* 3.6 3.3 - - + +
618A LYS* 2.7 39.9 + - - +
655A LEU* 4.7 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ILE* 4.1 4.9 - - - +
491A CYS* 3.3 30.0 - - + -
527A TYR* 1.9 56.6 + - + -
611A ASN 3.9 0.8 + - - -
612A LEU 2.8 15.5 + - - +
614A PRO* 1.3 78.8 - - - +
616A LYS* 1.3 63.3 + - - +
618A LYS* 2.8 9.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A HIS* 3.1 34.8 - - - -
488A ILE* 3.4 33.7 - - + +
556A SER* 2.5 29.2 + - - -
559A SER* 4.4 1.8 - - - -
560A LEU* 2.8 50.6 - - + +
563A LEU* 4.3 1.5 - - + +
612A LEU 2.9 7.2 + - - +
613A HIS* 2.7 24.0 + - + +
615A ALA* 1.3 71.0 - - - +
617A PRO* 1.3 64.5 - - + +
619A ASP* 4.6 0.7 - - - +
620A PHE* 2.6 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU* 4.9 4.5 - - - +
560A LEU* 4.8 3.4 - - + -
564A LEU* 5.2 5.6 - - + -
613A HIS* 2.9 32.5 - - + +
614A PRO* 3.8 4.9 - - + +
616A LYS* 1.3 84.2 - - + +
618A LYS* 1.3 56.9 + - - +
620A PHE* 2.4 32.2 + - + -
621A SER 3.0 6.8 + - - -
645A TRP* 4.5 16.6 - - + -
655A LEU* 4.3 19.1 - - + +
656A GLN* 5.1 2.7 - - - -
659A ARG* 3.1 35.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A VAL* 4.9 23.8 - - + -
506A GLU* 5.1 9.9 + - - -
509A ARG* 3.9 22.0 - - - +
527A TYR* 3.6 14.4 - - + +
614A PRO 2.7 28.1 + - - +
615A ALA* 2.8 6.9 + - - +
617A PRO* 1.3 70.8 - - - +
619A ASP* 1.3 57.7 + - - +
621A SER* 2.9 29.0 + - - -
622A ALA* 4.9 1.0 - - - +
655A LEU* 4.8 20.8 - - + +
659A ARG* 4.4 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A HIS* 5.3 4.9 - - - -
527A TYR* 2.2 35.7 + - - +
531A PHE* 2.8 55.6 - - + +
534A LEU* 5.6 0.2 - - - +
615A ALA 2.9 0.8 + - - +
616A LYS* 4.6 0.7 - - - +
618A LYS* 1.3 65.6 - - - +
620A PHE* 1.3 54.4 + - - +
621A SER 2.4 6.4 + - - -
622A ALA* 2.1 51.0 + - - +
623A PHE* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A HIS* 5.9 0.9 - - - -
553A VAL* 4.8 9.2 - - + -
556A SER* 5.1 2.0 - - - -
557A SER* 3.7 20.2 - - - -
560A LEU* 3.3 34.8 - - + -
616A LYS* 2.6 29.1 + - + +
617A PRO* 2.4 20.9 + - + +
619A ASP* 1.3 69.7 - - - +
621A SER* 1.3 54.4 + - - -
623A PHE* 3.6 37.7 - + - -
624A ILE* 2.9 43.0 + - + +
641A PHE* 4.4 14.6 - + - -
645A TRP* 4.2 21.1 - + - -
659A ARG* 4.3 5.8 - - + -
663A ILE* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A PRO 3.0 5.7 + - - -
618A LYS* 2.9 22.7 + - - -
619A ASP 2.4 9.0 + - - -
620A PHE* 1.3 71.7 - - - +
622A ALA* 1.3 66.1 + - - +
623A PHE 2.9 2.1 + - - -
624A ILE* 3.5 6.2 - - - +
625A ASN* 2.9 37.4 + - - +
659A ARG* 2.9 40.8 + - - +
662A LEU* 4.7 7.6 - - - -
666A PHE* 6.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PHE* 5.6 3.6 - - + -
535A LEU* 3.2 27.4 - - + +
618A LYS 4.9 0.4 - - - +
619A ASP* 2.1 34.6 + - + +
621A SER* 1.3 72.7 + - - +
623A PHE* 1.3 54.9 + - - -
625A ASN* 3.3 18.7 - - - +
626A LEU* 3.8 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A HIS* 4.9 13.5 - + - -
531A PHE* 5.5 0.7 - + + -
534A LEU* 4.6 25.6 - - + -
535A LEU* 3.4 19.8 - - + +
538A ASP* 4.4 14.8 - - - -
552A SER* 4.8 4.9 - - - -
553A VAL* 4.5 21.3 - - + -
556A SER* 4.0 24.0 - - - -
619A ASP* 3.0 26.6 + - - +
620A PHE* 3.6 34.3 - + - +
622A ALA* 1.3 77.2 - - - +
624A ILE* 1.3 63.2 + - + +
625A ASN 3.3 1.0 + - - -
626A LEU 3.7 0.9 + - - -
627A VAL* 3.1 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 624 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A VAL* 4.3 26.9 - - + -
620A PHE* 2.9 49.3 + - + +
621A SER* 3.5 8.5 - - - +
623A PHE* 1.3 73.3 - - + +
625A ASN* 1.3 65.1 + - + +
626A LEU 3.5 0.2 - - - -
627A VAL* 4.0 9.4 + - + +
628A GLU 5.7 2.7 - - - +
629A PHE* 3.0 43.2 - - + -
637A LYS* 4.9 12.1 - - + +
641A PHE* 5.3 3.8 - - + -
662A LEU* 6.1 1.1 - - + -
663A ILE* 3.8 30.1 - - + -
666A PHE* 6.2 2.0 - - + -
667A TYR* 4.9 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A SER* 2.9 18.1 + - - +
622A ALA* 3.3 26.9 - - - +
623A PHE 3.3 0.4 - - - -
624A ILE* 1.3 80.3 - - + +
626A LEU* 1.3 73.4 + - - +
629A PHE* 3.2 30.7 - - - +
666A PHE* 4.6 21.3 - - + -
----------------------------------------------------------
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