Contacts of the strand formed by residues 602 - 610 (chain A) in PDB entry 5JAJ
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 TRP 602 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A VAL* 4.8 0.4 - - + -
571A GLU* 2.9 28.7 + - - -
574A HIS* 3.6 23.8 - + - -
595A PHE* 4.4 0.9 - + - -
599A PHE* 3.4 65.5 + + + +
600A ARG 3.7 0.8 - - - -
601A ASP* 1.3 84.2 - - + +
603A GLU* 1.3 83.1 + - - +
604A PRO* 3.8 23.8 - - + -
619A MET* 4.2 14.1 - - + -
621A MET* 3.6 36.3 - - + +
622A ILE 3.1 14.6 - - - +
623A TYR* 3.8 20.9 - + + -
624A ARG 4.7 0.2 - - - +
630A ILE* 5.8 0.9 - - + -
1X G 3.8 15.9 - - - -
10Y C 3.5 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A LYS* 3.0 32.0 + - - +
599A PHE* 5.0 1.1 - - - +
602A TRP* 1.3 82.9 - - - +
604A PRO* 1.3 73.0 - - + +
622A ILE* 2.8 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A LYS* 2.9 29.4 + - - +
593A ILE* 3.5 32.3 - - + +
595A PHE* 3.6 48.7 - - + +
597A ARG 6.0 0.2 - - - +
599A PHE* 5.0 2.9 - - + -
602A TRP* 3.8 7.4 - - + -
603A GLU* 1.3 89.1 - - + +
605A GLY* 1.3 60.2 + - - +
619A MET* 4.3 8.1 - - - -
620A GLU 3.5 9.2 - - - +
622A ILE* 3.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A LYS* 4.1 5.6 - - - -
593A ILE* 2.8 34.5 + - - +
603A GLU 3.7 1.4 + - - -
604A PRO* 1.3 72.1 - - - +
606A CYS* 1.3 64.8 + - - -
619A MET* 5.7 0.4 - - - -
620A GLU* 2.9 25.2 + - - -
622A ILE* 3.9 17.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
588A VAL* 3.5 21.3 - - + -
590A SER 3.2 27.1 - - - +
591A GLY* 3.5 22.2 - - - +
592A LYS* 3.7 6.3 - - - -
593A ILE* 4.4 2.2 - - - -
605A GLY* 1.3 75.5 - - - -
607A ARG* 1.3 63.5 + - - +
619A MET* 3.4 1.5 - - - -
620A GLU* 2.8 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LYS* 5.8 3.6 - - - +
588A VAL* 3.5 2.4 - - - -
589A SER* 2.9 38.2 + - - +
590A SER* 3.0 29.2 + - - +
591A GLY 4.4 0.4 + - - -
593A ILE* 2.9 45.8 - - + +
606A CYS* 1.3 76.1 - - - +
608A ILE* 1.3 64.5 + - - +
609A VAL* 5.5 0.9 - - + -
616A GLU* 4.6 16.7 + - + -
618A GLY 3.7 9.6 - - - +
619A MET* 4.2 3.8 - - + +
1X G 5.5 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A TYR* 3.5 39.9 - - + -
587A THR 3.3 4.5 - - - +
588A VAL* 4.4 4.7 - - + -
606A CYS 4.0 0.9 - - - +
607A ARG* 1.3 80.1 - - - +
609A VAL* 1.3 67.6 + - - +
616A GLU* 3.9 1.7 - - - +
617A TRP* 3.0 26.4 + - + -
618A GLY 3.0 29.7 + - - +
619A MET 3.6 1.8 - - - +
620A GLU* 4.0 21.8 - - + +
629A PRO* 3.6 28.7 - - + -
630A ILE 4.2 12.1 - - - +
631A LEU* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A TYR* 3.2 5.6 - - - -
587A THR* 2.8 49.9 + - + +
589A SER* 3.2 32.1 - - - +
607A ARG* 5.5 0.9 - - + -
608A ILE* 1.3 77.6 - - - +
610A CYS* 1.3 68.8 + - - +
614A ARG* 3.5 30.1 - - + +
615A GLN 3.2 12.3 - - - +
616A GLU* 4.0 13.7 - - + -
617A TRP* 4.2 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A CYS* 3.9 0.2 - - - -
557A CYS* 3.9 2.5 - - - -
559A VAL* 4.2 5.2 - - - -
585A TYR 4.8 0.7 - - - -
609A VAL* 1.3 73.8 - - - +
611A SER* 1.3 62.0 + - - +
612A GLU* 3.4 22.4 - - - -
613A CYS* 3.5 9.2 - - - -
614A ARG* 2.9 27.4 + - - +
615A GLN 2.9 13.7 + - - +
617A TRP* 3.5 40.0 - - + +
701A ZN 2.4 36.3 - - - -
----------------------------------------------------------
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