Contacts of the helix formed by residues 558 - 578 (chain A) in PDB entry 4JWE
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 558 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A LYS 3.5 8.5 - - - +
557A LEU* 1.4 95.5 - - + +
559A ALA* 1.4 59.6 + - - +
560A ASP* 4.6 5.8 - - + +
561A ASP* 3.3 27.6 + - - +
562A LYS* 3.0 26.9 + - - +
597A LYS* 5.2 6.3 - - + -
601A ILE* 4.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU 3.9 0.4 + - - -
558A PRO* 1.4 71.3 - - - +
560A ASP* 1.4 55.7 + - - +
562A LYS* 3.2 11.4 + - - +
563A THR* 2.9 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A PRO* 3.5 4.3 - - + +
559A ALA* 1.4 76.8 - - - +
561A ASP* 1.4 63.7 + - - +
563A THR* 3.3 21.4 - - - +
564A ALA* 3.4 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 4.4 10.8 - - + -
558A PRO* 3.3 38.8 + - + +
559A ALA 3.3 0.4 - - - -
560A ASP* 1.4 78.0 - - - +
562A LYS* 1.4 56.2 - - - +
564A ALA* 3.3 7.5 + - - +
565A ILE* 3.0 39.7 + - + +
594A VAL 4.2 9.0 - - - +
597A LYS* 3.7 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A VAL* 4.8 11.7 - - + -
557A LEU* 3.8 26.1 - - + +
558A PRO 3.0 18.8 + - - +
559A ALA* 3.2 9.8 + - - +
561A ASP* 1.4 75.5 - - - +
563A THR* 1.4 60.3 + - - +
565A ILE* 3.4 4.9 + - + +
566A GLU* 3.0 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A ALA 2.9 20.7 + - - +
560A ASP* 3.3 24.7 - - - +
562A LYS* 1.4 76.3 - - - +
564A ALA* 1.4 63.3 + - - +
566A GLU* 3.5 7.2 + - - +
567A SER* 3.2 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A ASP 3.6 13.5 - - - +
561A ASP* 3.3 7.0 + - - +
563A THR* 1.4 80.2 - - + +
565A ILE* 1.4 57.8 + - - +
567A SER* 3.7 4.8 + - - -
568A ALA* 3.1 29.5 + - - +
594A VAL* 3.5 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A THR* 3.9 18.8 - - + -
550A VAL* 3.9 12.3 - - + -
557A LEU* 4.0 22.2 - - + -
561A ASP* 3.0 29.1 + - + +
562A LYS* 3.7 6.3 - - + +
564A ALA* 1.4 73.3 - - - +
566A GLU* 1.4 55.2 + - + +
568A ALA* 3.2 3.7 + - - +
569A LEU* 2.9 56.2 + - + +
591A LEU* 4.3 2.2 - - + -
594A VAL* 3.3 27.4 - - + +
595A SER* 3.7 10.8 - - - +
598A LEU* 4.1 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ARG* 5.8 0.2 + - - -
550A VAL* 6.2 3.1 - - + -
562A LYS* 3.0 49.5 + - + +
563A THR* 3.9 6.8 - - - +
564A ALA 3.5 0.2 - - - -
565A ILE* 1.4 76.5 - - + +
567A SER* 1.4 59.9 + - - +
569A LEU* 3.6 15.1 + - + +
570A THR* 3.0 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A THR* 3.2 19.0 + - - -
564A ALA* 4.0 5.6 - - - -
566A GLU* 1.4 72.9 - - - +
568A ALA* 1.4 59.7 + - - +
570A THR* 3.2 9.0 + - - -
571A ALA* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A ALA 3.1 19.7 + - - +
565A ILE 3.6 4.7 - - - +
567A SER* 1.4 72.1 - - - +
569A LEU* 1.4 59.4 + - - +
571A ALA* 3.5 8.6 + - - +
572A LEU* 3.0 28.4 + - - +
587A LYS 4.4 5.7 - - - +
590A GLU* 4.6 4.3 - - + -
591A LEU* 3.7 34.4 - - + +
594A VAL* 3.8 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A LEU* 3.5 36.4 - - + +
546A THR* 3.7 26.5 - - + -
547A ARG* 4.2 34.1 - - + +
550A VAL* 5.3 3.8 - - + -
565A ILE* 2.9 40.5 + - + +
566A GLU* 3.6 15.0 - - + +
567A SER 3.3 0.2 - - - -
568A ALA* 1.4 73.9 - - - +
570A THR* 1.4 57.4 + - - +
572A LEU* 3.4 2.7 + - - -
573A GLU* 2.9 28.6 + - - +
591A LEU* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ARG* 5.5 3.6 + - - +
566A GLU 3.0 13.7 + - - -
567A SER* 3.2 11.5 + - - -
569A LEU* 1.4 75.5 - - - +
571A ALA* 1.4 59.0 + - - +
573A GLU* 3.3 22.8 + - - +
574A THR* 3.0 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A SER 3.0 15.9 + - - +
568A ALA* 3.8 9.2 - - - +
569A LEU 3.4 0.2 - - - -
570A THR* 1.4 75.0 - - - +
572A LEU* 1.4 61.5 + - - +
574A THR* 3.6 7.0 + - - +
575A ALA* 3.1 23.7 + - - +
587A LYS* 3.7 30.5 - - + +
590A GLU* 5.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A GLY* 3.6 20.9 - - - +
542A LEU* 4.6 0.9 - - + -
543A LEU* 4.0 16.2 - - + +
568A ALA 3.0 18.3 + - - +
569A LEU* 3.7 4.9 - - - +
570A THR 3.3 0.2 - - - -
571A ALA* 1.4 73.1 - - - +
573A GLU* 1.4 65.0 + - - +
575A ALA* 3.2 2.4 + - - +
576A LEU* 3.0 46.0 + - + +
584A ILE* 3.6 29.8 - - + +
587A LYS* 3.8 13.4 - - + +
588A MET* 3.7 23.8 - - + +
591A LEU* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A LEU* 4.5 11.8 - - + +
547A ARG* 5.3 8.1 + - - +
569A LEU 2.9 15.0 + - - +
570A THR* 3.3 24.1 + - - +
572A LEU* 1.4 76.5 - - - +
574A THR* 1.4 75.8 + - - +
576A LEU* 3.3 25.3 + - - +
577A LYS* 3.6 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A THR* 3.0 20.7 + - - +
571A ALA* 3.8 7.6 - - - +
573A GLU* 1.4 85.7 + - - +
575A ALA* 1.4 62.8 + - - +
577A LYS* 3.2 25.8 + - + +
578A GLY* 3.8 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A ALA 3.1 18.0 + - - +
572A LEU 3.2 4.5 + - - +
574A THR* 1.4 75.0 - - - +
576A LEU* 1.4 56.7 - - - +
578A GLY* 3.0 23.0 + - - -
580A ASP 5.0 0.7 - - - +
583A ALA* 4.1 9.4 - - + +
584A ILE* 3.3 31.7 - - + +
587A LYS* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ARG* 3.1 68.7 + - + +
539A GLY* 3.9 15.7 - - - -
540A ASP* 4.5 4.3 - - + +
543A LEU* 4.5 13.9 - - + -
572A LEU* 3.0 39.2 + - + +
573A GLU* 3.4 14.4 - - - +
574A THR 3.3 0.6 - - - -
575A ALA* 1.4 76.4 - - - +
577A LYS* 1.4 57.6 + - + +
578A GLY 3.4 1.1 - - - +
584A ILE* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ARG* 3.5 9.7 + - - +
573A GLU* 3.8 35.4 + - - +
574A THR* 3.2 13.9 + - + +
576A LEU* 1.4 74.3 - - + +
578A GLY* 1.3 61.9 + - - +
518B ASP* 4.0 3.9 - - - +
521B ALA* 3.9 30.9 - - + +
522B ASN* 2.9 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU* 4.1 3.1 - - - +
536A ARG* 2.8 21.7 + - - -
574A THR 3.8 2.6 + - - -
575A ALA 3.0 17.1 + - - +
576A LEU 3.4 5.7 - - - +
577A LYS* 1.3 79.5 - - - +
579A GLU* 1.4 61.3 + - - -
580A ASP* 3.6 3.8 + - - -
584A ILE* 4.3 0.9 - - - +
522B ASN* 3.6 12.6 - - - -
----------------------------------------------------------
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