Contacts of the helix formed by residues 572 - 586 (chain A) in PDB entry 6FEQ
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 572 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A MET* 3.7 39.1 + - - -
551A PHE* 4.4 11.2 - - - +
568A LEU 4.9 2.9 - - - -
569A GLN 3.7 9.1 + - - -
570A TYR 3.3 2.6 + - - -
571A PHE* 1.3 78.8 - - - +
573A ILE* 1.3 65.1 + - - +
574A PRO* 4.2 1.8 - - - -
575A ARG* 3.2 23.0 + - - +
576A TYR* 3.2 21.1 - - - -
636A MET* 5.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A CYS* 4.6 5.4 - - - -
516A VAL* 3.9 18.1 - - + +
519A SER* 3.3 53.2 - - - +
520A ALA* 3.9 12.1 - - + +
523A MET* 3.9 28.7 - - + -
545A PHE* 4.8 1.8 - - + -
548A MET* 3.8 7.6 - - + -
571A PHE 4.1 1.0 + - - -
572A SER* 1.3 70.5 - - - +
574A PRO* 1.3 71.5 - - + +
575A ARG 3.1 1.4 + - - -
576A TYR* 3.2 19.1 + - - +
577A GLY 3.6 6.4 + - - -
633A LEU* 4.0 6.1 - - + +
636A MET* 3.7 16.4 - - + -
640A PHE* 4.3 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A THR* 4.6 5.9 - - - +
435A THR* 4.8 16.6 - - + -
438A CYS* 3.6 26.9 - - + -
439A PHE* 6.5 0.9 - - + -
516A VAL* 4.8 5.6 - - + -
545A PHE* 5.3 2.9 - - + +
548A MET* 3.6 31.9 - - + +
549A MET* 4.9 2.9 - - - +
552A SER* 4.6 13.7 - - - -
572A SER* 3.6 4.3 - - - -
573A ILE* 1.3 91.6 - - + +
575A ARG* 1.3 61.9 + - - +
577A GLY 3.9 1.6 - - - +
578A PHE* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A PHE 4.1 11.0 - - - +
552A SER* 4.1 23.8 - - - +
558A LEU* 4.3 10.5 - - + +
569A GLN* 2.7 67.6 + - - +
570A TYR* 3.9 13.0 - - - -
572A SER* 3.2 22.0 + - - +
573A ILE 3.1 1.4 + - - -
574A PRO* 1.3 80.1 - - - +
576A TYR* 1.3 78.1 + - - +
578A PHE* 3.7 0.4 - - - -
579A THR* 2.6 55.1 + - - +
618A GLY 4.8 11.1 + - - -
619A ILE* 6.2 1.0 - - - +
628A LYS* 6.0 2.0 - - - +
629A ASN* 5.0 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A TYR* 2.7 51.1 + + - +
572A SER 3.2 25.6 - - - -
573A ILE 3.2 4.4 + - - -
575A ARG* 1.3 94.1 - - - +
577A GLY* 1.3 61.8 + - - +
580A ALA* 3.4 11.8 + - - +
628A LYS* 5.5 2.9 - - + -
629A ASN* 3.3 42.3 - - + +
632A ALA* 3.7 28.8 - - + +
633A LEU* 3.8 31.2 - - + +
636A MET* 4.3 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A THR* 3.9 12.1 - - - -
512A THR* 4.0 14.3 - - - +
516A VAL* 4.5 16.6 - - - -
573A ILE 3.6 5.9 + - - -
574A PRO 3.6 4.1 + - - -
575A ARG 3.2 0.4 - - - -
576A TYR* 1.3 79.0 - - - +
578A PHE* 1.3 56.4 + - - +
580A ALA* 2.9 19.4 + - - +
581A LEU* 3.0 17.2 + - - +
633A LEU* 4.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ALA* 3.7 13.0 - - + -
430A LEU* 3.6 25.6 - - + -
431A PHE* 3.5 36.8 - + + -
434A THR* 3.6 15.1 - - + +
552A SER* 3.5 28.9 - - - +
553A GLY* 4.4 14.4 - - - -
554A LEU* 4.4 11.2 - - + -
574A PRO* 3.0 19.6 + - + +
575A ARG 4.1 1.1 - - - +
577A GLY* 1.3 74.7 - - - +
579A THR* 1.3 63.4 + - - +
581A LEU* 4.1 2.1 - - - +
582A GLN* 3.1 61.2 + - - +
617A GLN* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A SER 4.9 2.9 + - - -
575A ARG* 2.6 42.8 + - - +
576A TYR 4.2 0.2 - - - -
578A PHE* 1.3 76.9 - - - +
580A ALA* 1.3 59.1 + - - +
582A GLN* 3.3 9.6 + - - +
583A HIS* 2.8 27.5 + - - +
619A ILE* 3.7 38.7 - - + +
625A GLY 5.2 1.3 - - - +
629A ASN* 3.7 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A THR* 3.7 19.3 - - + +
576A TYR 3.4 13.2 + - - +
577A GLY 2.9 9.5 + - - +
579A THR* 1.3 79.8 - - - +
581A LEU* 1.3 59.2 + - - +
583A HIS* 3.2 1.5 + - - -
584A ASN* 2.9 29.9 + - - +
626A LEU* 3.7 12.4 - - + +
629A ASN* 3.7 13.6 - - + +
630A HIS* 4.2 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 3.8 38.1 - - + +
433A LEU* 4.8 4.5 - - + -
434A THR* 3.7 26.5 - - + -
509A MET* 3.8 37.0 - - + -
512A THR* 4.1 12.6 - - + +
513A LEU* 3.7 23.1 - - + -
577A GLY 3.0 15.7 + - - +
578A PHE* 4.3 3.6 - - - +
580A ALA* 1.3 72.2 - - - +
582A GLN* 1.3 67.4 + - - +
584A ASN* 3.4 6.5 + - + +
585A GLU* 3.4 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ALA* 4.1 5.0 - - + +
430A LEU* 4.6 4.5 - - + -
578A PHE* 3.1 61.7 + - + +
579A THR* 3.6 4.0 - - - +
581A LEU* 1.3 78.5 - - - +
583A HIS* 1.3 60.2 + - - +
586A PHE* 3.2 49.3 + - + +
613A TYR* 3.4 34.8 + - - -
614A LEU* 3.8 13.0 - - + +
617A GLN* 4.8 5.7 - - - +
619A ILE* 3.4 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A THR* 2.8 21.6 + - + +
580A ALA* 3.2 4.7 + - - +
582A GLN* 1.3 73.8 - - - +
584A ASN* 1.3 64.1 + - - +
585A GLU 3.4 0.2 + - - -
587A LEU* 3.4 40.0 - - + +
614A LEU* 4.0 13.6 - - + +
619A ILE* 4.1 8.1 - - + +
620A ASP 3.1 29.1 + - - -
621A LEU* 3.8 13.2 + - - -
622A SER 3.5 22.8 + - - -
623A PRO* 4.8 2.2 - - - +
625A GLY 4.6 1.5 - - - +
626A LEU* 3.4 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A LYS* 3.5 20.7 - - - +
505A ALA* 3.3 30.5 + - - +
508A VAL* 3.4 23.6 - - + +
509A MET* 3.2 36.0 - - - +
512A THR* 6.1 0.2 - - - +
580A ALA 2.9 17.3 + - - +
581A LEU* 3.8 10.6 - - + +
582A GLN 3.3 0.4 - - - -
583A HIS* 1.3 78.9 - - - +
585A GLU* 1.3 57.8 + - + +
587A LEU* 5.0 4.2 - - - +
626A LEU* 4.4 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ARG* 2.5 47.1 + - - +
430A LEU* 4.2 9.2 - - + +
499A LEU* 3.8 32.5 - - + +
500A LYS* 3.7 18.9 + - + +
581A LEU 3.4 16.2 + - - +
582A GLN 4.7 0.2 - - - +
583A HIS 3.2 0.2 - - - -
584A ASN* 1.3 80.7 - - + +
586A PHE* 1.3 80.9 + - - +
587A LEU 3.3 7.8 + - - -
589A GLN* 3.4 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ILE* 4.6 9.9 - - + -
426A ARG* 3.8 24.0 - - + -
427A ALA* 4.0 12.8 - - + -
430A LEU* 4.6 4.9 - - + -
582A GLN* 3.2 53.5 + - + +
585A GLU* 1.3 88.3 - - - +
587A LEU* 1.3 66.8 + - - +
588A GLY 3.8 0.4 - - - -
589A GLN* 4.4 5.8 - - - -
591A PHE* 3.9 33.4 - + - -
610A GLY* 3.2 32.2 - - - +
611A GLU 4.0 0.2 + - - -
613A TYR* 4.1 30.3 - + + -
614A LEU* 4.4 9.1 - - + +
----------------------------------------------------------
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