Contacts of the strand formed by residues 593 - 606 (chain A) in PDB entry 2ZB5
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 HIS 593 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A NAG 3.1 40.0 + - + +
215A ASN* 4.3 5.1 - - - +
564A ILE* 4.0 23.9 - - + +
584A VAL* 4.3 11.0 - - + +
585A LEU 3.3 6.5 - - - +
586A ALA* 3.9 16.0 - - + +
591A GLY* 5.9 1.0 - - - -
592A GLY* 1.3 86.6 + - - -
594A ILE* 1.3 61.3 + - - +
595A THR* 4.2 1.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A PRO* 5.9 6.7 - - + -
560A LYS 5.8 3.1 - - - +
561A GLY* 6.3 0.2 - - - -
583A CYS 3.7 1.7 - - - +
584A VAL* 4.7 0.7 - - - -
585A LEU* 2.7 61.2 + - + +
586A ALA* 5.7 0.4 - - - -
587A ASP* 5.9 4.0 - - + +
592A GLY 4.1 1.2 + - - +
593A HIS* 1.3 74.6 - - - +
595A THR* 1.3 69.5 + - - +
596A HIS* 4.0 1.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 4.2 31.2 - - + +
216A VAL 3.8 17.0 + - - -
219A ILE* 4.6 7.4 - - + +
582A PHE* 4.5 17.7 - - + -
583A CYS 3.6 7.4 - - - +
584A VAL* 3.8 20.5 - - + +
593A HIS* 4.2 1.8 + - - +
594A ILE* 1.3 82.2 - - - +
596A HIS* 1.3 70.5 + - - +
597A SER* 4.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A VAL* 6.0 0.4 - - - +
553A TYR* 4.4 7.2 - + - -
555A PHE* 5.1 1.6 - - - +
556A ARG* 3.4 40.4 + - + +
558A PRO* 4.3 21.8 - - + -
581A HIS* 3.3 28.0 + + - -
582A PHE* 3.5 1.6 - - - -
583A CYS* 2.8 48.9 + - + +
585A LEU* 5.2 7.0 - - + -
594A ILE* 4.0 1.9 + - + -
595A THR* 1.3 73.4 - - - +
597A SER* 1.3 75.0 + - - +
598A GLY* 4.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASP* 5.5 0.3 + - - -
210A LEU* 3.8 27.5 - - - +
580A ARG* 3.3 23.8 + - - -
581A HIS 3.2 15.0 + - - -
582A PHE* 3.7 10.4 - - - -
595A THR 4.0 2.0 + - - -
596A HIS* 1.3 88.5 + - - +
598A GLY* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A TYR* 3.5 18.8 - - - -
579A CYS 3.9 0.2 - - - +
580A ARG* 3.2 11.9 + - - -
581A HIS* 2.9 44.7 + - - -
596A HIS* 4.6 0.4 - - - -
597A SER* 1.3 75.9 + - - +
599A MET* 1.3 59.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PHE* 3.7 9.4 - - - +
199A SER* 3.7 39.0 + - - +
201A MET 5.9 3.4 - - - +
268A PRO* 4.2 20.9 - - - +
270A PHE* 3.4 34.1 - - + -
553A TYR* 3.9 3.2 + - - -
571A PHE* 4.8 4.0 - - + -
578A TRP* 4.0 23.8 - - + -
579A CYS 3.1 17.5 - - - +
580A ARG* 3.2 48.4 - - + +
598A GLY* 1.3 74.2 - - - -
600A VAL* 1.3 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLY* 3.8 20.2 - - - -
197A GLN 3.3 12.8 - - - +
198A PHE* 3.4 28.0 - - + -
540A TYR* 3.9 30.5 - - + +
551A TYR* 4.1 8.3 - - + -
553A TYR* 3.9 8.1 - - + -
577A LEU 3.7 1.6 - - - +
578A TRP* 3.2 7.1 - - - -
579A CYS 2.9 34.6 + - - +
599A MET* 1.3 76.8 - - - +
601A GLY* 1.3 64.2 + - - +
602A MET* 4.2 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ARG 3.5 1.6 - - - +
197A GLN* 2.6 36.3 + - - +
576A LYS* 3.7 10.4 - - - +
577A LEU 3.9 0.4 - - - -
578A TRP* 3.4 34.8 - - - -
600A VAL* 1.3 73.1 - - - +
602A MET* 1.3 64.9 + - - -
603A GLY 3.5 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE* 3.9 11.2 - - + -
195A ARG 3.9 4.9 - - - -
196A GLY* 4.6 0.4 - - - -
540A TYR* 3.8 28.3 - - + -
542A VAL* 4.6 0.9 - - + -
549A PHE* 4.4 17.3 - - + -
551A TYR* 3.7 41.7 - - + -
576A LYS* 3.4 4.7 - - - +
577A LEU* 3.0 55.8 + - + +
579A CYS* 3.5 34.5 - - + -
600A VAL* 4.2 11.4 - - + -
601A GLY* 1.3 70.6 - - - -
603A GLY* 1.3 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE* 3.3 9.8 - - - -
195A ARG* 3.0 36.8 + - - +
575A GLN 4.9 2.7 - - - -
576A LYS* 4.0 21.3 - - - -
601A GLY 3.5 1.4 + - - -
602A MET* 1.3 76.7 - - - +
604A VAL* 1.3 62.2 + - - -
605A SER* 3.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASN* 3.6 35.6 - - + +
188A CYS* 4.7 5.1 - - - -
192A THR* 3.5 39.5 - - + +
193A THR 3.4 5.4 - - - +
194A ILE* 4.0 13.9 - - + +
575A GLN 5.5 3.5 + - - +
603A GLY* 1.3 71.7 - - - -
605A SER* 1.3 58.3 + - - +
606A CYS* 4.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A CYS* 4.1 2.0 - - - -
192A THR* 3.5 3.3 - - - -
193A THR* 2.9 40.9 + - - +
195A ARG* 3.2 41.7 + - - +
603A GLY 3.7 1.7 + - - -
604A VAL* 1.3 73.9 - - - +
606A CYS* 1.3 60.5 + - - +
607A THR* 3.2 7.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A CYS* 2.0 52.5 - - + -
191A PRO 4.1 5.4 - - - +
604A VAL 5.1 1.1 - - - -
605A SER* 1.3 70.1 - - - +
607A THR* 1.3 64.6 + - - +
----------------------------------------------------------
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