Contacts of the helix formed by residues 542 - 560 (chain A) in PDB entry 4WGK
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 THR 542 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ASN* 3.5 5.4 - - - +
351A GLY* 4.0 4.5 - - - -
352A ASP* 3.5 26.2 - - + +
540A GLU 4.9 1.3 - - - +
541A PHE* 1.3 76.9 - - - +
543A THR* 1.3 65.1 + - - +
545A SER* 2.8 27.1 + - - -
546A GLY 3.0 16.3 + - - -
580A ILE 3.1 14.4 + - - +
581A THR* 3.6 22.0 - - + -
585A GLU* 2.8 20.2 + - - +
592A GLU* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ASN* 4.7 0.2 - - - -
262A TYR* 4.6 3.6 - - + -
276A ASN 3.3 24.1 + - - +
277A THR* 3.8 7.0 - - - -
278A ASP* 3.9 7.9 + - - +
349A ASN* 3.1 24.0 + - - +
352A ASP* 2.8 30.3 + - - -
353A VAL* 3.6 14.9 - - - +
542A THR* 1.3 72.3 - - - +
544A MET* 1.3 63.4 + - - +
547A ARG* 3.1 53.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 3.6 33.8 - - + +
265A ASN* 3.5 12.3 - - - +
269A GLU* 3.4 47.8 - - + +
270A ARG* 3.7 21.8 - - + -
273A TYR* 3.9 5.6 - - + -
542A THR* 4.1 1.2 + - - -
543A THR* 1.3 76.2 - - - +
545A SER* 1.3 60.7 + - - +
547A ARG* 3.5 21.9 - - - +
548A ARG* 3.0 29.2 + - - +
582A THR* 3.8 8.3 - - + -
585A GLU* 3.5 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A PHE* 3.6 19.3 - - - -
542A THR* 2.8 30.1 + - - -
543A THR 3.3 0.6 - - - -
544A MET* 1.3 79.4 - - - +
546A GLY* 1.3 60.3 + - - +
548A ARG* 3.4 2.4 + - - +
549A LEU* 3.1 19.6 + - - +
580A ILE 3.1 18.1 + - - -
581A THR 3.2 2.3 - - - -
582A THR* 3.2 19.3 + - - +
603A LEU* 3.6 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ASN* 3.8 15.3 - - - -
541A PHE* 3.7 8.9 - - - -
542A THR 3.0 10.7 + - - -
545A SER* 1.3 74.2 - - - +
547A ARG* 1.3 60.6 + - - +
550A ARG* 2.9 42.5 + - - +
569A ILE* 3.8 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 2.8 34.6 + - - -
273A TYR* 3.3 57.1 - - + +
275A SER* 2.8 21.4 + - - +
277A THR 3.3 15.6 + - - -
278A ASP* 2.8 21.0 + - - +
543A THR* 3.1 26.0 + - - +
544A MET* 3.5 18.1 - - - +
546A GLY* 1.3 76.3 - - - +
548A ARG* 1.3 61.6 + - - +
550A ARG* 3.2 24.4 - - - +
551A GLU* 3.2 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASN* 3.5 8.7 + - - -
266A PRO* 3.6 5.9 - - - +
269A GLU* 2.7 42.6 + - - +
273A TYR* 6.1 0.4 - - - +
544A MET* 3.0 19.1 + - - +
545A SER 3.8 4.7 - - - +
546A GLY 3.3 0.2 - - - -
547A ARG* 1.3 78.2 - - - +
549A LEU* 1.3 57.4 + - - +
551A GLU* 3.9 5.6 - - - +
552A ALA* 3.0 31.6 + - - +
582A THR* 3.6 18.3 - - - +
583A TYR* 4.4 5.3 - - - +
584A GLU* 3.0 39.1 + - - -
603A LEU* 4.1 15.3 - - + +
607A ILE* 3.9 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A THR* 3.8 19.5 - - + +
537A ILE* 4.3 2.2 - - + -
541A PHE* 3.6 28.5 - - + -
545A SER 3.1 15.2 + - - +
546A GLY 4.1 1.8 - - - +
548A ARG* 1.3 76.4 - - - +
550A ARG* 1.3 66.9 + - - +
552A ALA* 4.4 1.3 - - - -
553A VAL* 2.9 48.1 + - + +
569A ILE* 3.7 21.3 - - + -
606A TYR* 4.0 1.3 - - + +
607A ILE* 4.0 31.4 - - + +
610A PHE* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASP* 2.6 35.9 + - - +
348A SER* 4.5 3.8 + - - -
349A ASN* 3.5 18.0 + - - +
546A GLY 2.9 21.2 + - - +
547A ARG* 3.2 30.8 - - - +
549A LEU* 1.3 78.3 - - - +
551A GLU* 1.3 61.0 + - + +
553A VAL* 3.4 2.1 + - - +
554A GLN* 2.9 29.7 + - - +
567A VAL* 3.1 46.1 - - + +
568A VAL* 4.5 2.9 - - - +
569A ILE* 3.8 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ARG* 2.6 28.8 + - - -
273A TYR* 2.5 33.5 + - - -
547A ARG* 3.2 18.3 + - - +
548A ARG* 4.1 4.9 - - - +
550A ARG* 1.3 81.1 + - + +
552A ALA* 1.3 60.6 + - - +
554A GLN* 3.6 16.0 - - - +
555A ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ARG 3.0 19.3 + - - +
549A LEU 3.8 2.7 - - - +
551A GLU* 1.3 74.2 - - - +
553A VAL* 1.3 61.8 + - + +
555A ALA* 3.4 7.2 + - - +
556A GLU* 3.1 26.9 + - - +
607A ILE* 3.6 29.2 - - + -
611A ARG* 3.8 16.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ILE* 4.3 7.4 - - + -
533A ALA* 5.2 0.2 - - + -
535A THR* 4.4 3.6 - - + -
549A LEU* 2.9 30.7 + - + +
550A ARG 3.8 2.9 - - - +
552A ALA* 1.3 74.0 - - + +
554A GLN* 1.3 65.8 + - - +
556A GLU* 3.3 7.8 + - - +
557A PHE* 3.1 46.9 + - + -
567A VAL* 4.1 18.2 - - + -
607A ILE* 5.3 0.9 - - - +
610A PHE* 3.8 36.8 - - + +
611A ARG* 4.3 4.0 - - + +
614A ALA* 4.0 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ARG 2.9 19.0 + - - +
551A GLU* 3.6 17.3 - - - +
553A VAL* 1.3 77.1 - - - +
555A ALA* 1.3 62.6 + - - +
557A PHE* 3.3 7.9 + - - +
558A ALA* 3.1 22.5 + - + +
562A MET 4.9 0.7 - - - +
564A ASN* 4.6 6.0 - - - +
565A MET* 2.8 36.9 + - - +
567A VAL* 3.9 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A GLU 2.9 18.5 + - - +
552A ALA* 3.6 8.1 - - - +
554A GLN* 1.3 76.6 - - - +
556A GLU* 1.3 58.1 + - - +
558A ALA* 3.2 9.0 + - - +
559A SER* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ALA 3.1 7.6 + - - +
553A VAL* 3.5 9.9 - - - +
554A GLN 3.3 0.2 - - - -
555A ALA* 1.3 72.7 - - - +
557A PHE* 1.3 66.0 + - - +
559A SER* 3.1 14.9 + - - -
560A HIS* 3.2 50.7 + - - -
611A ARG* 2.8 74.0 + - + +
614A ALA* 4.2 5.8 - - + -
615A LYS* 3.4 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ILE* 4.5 7.0 - - + -
528A THR* 3.9 18.6 - - + -
533A ALA* 3.9 16.2 - - + -
553A VAL* 3.1 42.9 + - + -
554A GLN* 3.6 7.4 - - - +
556A GLU* 1.3 77.5 - - - +
558A ALA* 1.3 61.8 + - - +
560A HIS* 3.2 8.0 + - - +
561A GLY 3.3 0.2 + - - -
562A MET* 2.8 76.0 + - + +
565A MET* 3.7 19.7 - - + -
567A VAL* 4.8 0.4 - - + -
614A ALA* 3.5 36.3 - - + +
617A ILE* 4.2 8.5 - - + -
618A ALA* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A GLN* 3.1 14.8 + - + +
555A ALA* 3.4 13.2 - - - +
557A PHE* 1.3 72.9 - - - +
559A SER* 1.3 61.7 + - - +
560A HIS 3.0 6.1 + - - -
561A GLY* 3.3 8.8 + - - -
562A MET 3.4 5.4 + - - +
563A GLN* 3.3 36.2 + - - +
564A ASN 5.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A ALA* 2.9 17.1 + - - +
556A GLU* 3.1 14.3 + - - -
558A ALA* 1.3 75.0 - - - +
560A HIS* 1.3 74.0 + - - +
561A GLY 3.6 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A GLU* 3.2 44.3 + - - +
557A PHE 3.2 2.0 + - - -
558A ALA 3.0 1.0 - - - -
559A SER* 1.3 90.6 + - - +
561A GLY* 1.3 58.5 + - - +
562A MET* 3.4 4.6 + - - +
615A LYS* 3.6 34.1 - - + +
618A ALA* 3.6 34.6 - - + +
619A THR* 3.5 20.6 - - + +
----------------------------------------------------------
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