Contacts of the strand formed by residues 588 - 594 (chain A) in PDB entry 4JPB
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 GLU 588 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A VAL* 3.1 4.2 - - - -
585A ILE* 2.8 40.6 + - - +
586A ARG 2.7 7.0 + - - +
587A GLY* 1.3 78.9 - - - +
589A VAL* 1.3 62.8 + - - +
590A ILE* 3.4 15.3 - - + +
621A LYS* 3.2 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A VAL* 5.8 2.5 - - + -
582A VAL* 4.1 28.0 - - + -
583A ILE 3.8 3.1 - - - -
584A VAL* 4.4 15.9 - - + +
587A GLY 3.8 6.2 + - - +
588A GLU* 1.3 76.5 - - - +
590A ILE* 1.3 64.7 + - - +
591A PRO* 3.7 8.3 - - + +
621A LYS* 5.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A VAL* 4.1 2.9 - - - -
583A ILE* 2.8 48.8 + - + +
585A ILE* 4.0 20.9 - - + -
588A GLU* 3.4 49.4 - - + +
589A VAL* 1.3 75.5 - - - +
591A PRO* 1.3 63.7 - - - +
592A VAL 3.6 0.2 + - - -
614A ILE* 4.0 17.9 - - + -
621A LYS* 4.1 24.9 - - + +
622A TYR* 3.7 6.3 - - - -
623A GLY* 3.2 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A ARG* 4.5 10.8 - - + -
581A ASP 3.3 11.2 - - - +
582A VAL* 3.7 11.6 - - + -
589A VAL* 3.7 9.9 - - + +
590A ILE* 1.3 81.7 - - - +
592A VAL* 1.3 61.4 + - - +
593A TYR* 3.7 18.9 - - + +
620A ARG* 4.5 7.2 - - - +
621A LYS 4.0 11.0 - - - +
622A TYR* 3.5 18.2 - - + +
623A GLY 2.9 20.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A ILE* 4.6 4.5 - - + -
574A ILE* 4.3 13.7 - - + -
580A ARG* 5.3 1.7 - - - +
581A ASP* 2.8 26.7 + - + +
582A VAL 4.0 2.2 - - - -
583A ILE* 3.7 43.7 - - + +
590A ILE* 5.3 0.4 - - + -
591A PRO* 1.3 72.2 - - - +
593A TYR* 1.3 69.5 + - - +
594A ARG* 3.9 23.8 + - - +
623A GLY* 3.8 10.3 - - - +
625A VAL* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A ARG* 3.9 28.1 + - + -
591A PRO* 3.7 33.6 - - + +
592A VAL* 1.3 81.6 - - - +
594A ARG* 1.3 64.8 + - - +
598A VAL* 3.8 21.1 - - + -
620A ARG* 4.4 6.6 + - - -
622A TYR* 4.4 11.9 - + + -
623A GLY 3.2 12.5 + - - +
624A ILE* 3.4 10.4 - - + +
625A VAL 3.0 21.5 + - - -
670A ILE* 3.8 26.5 - - + -
671A VAL* 3.5 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A LYS* 3.6 18.8 - - - +
574A ILE* 3.7 22.2 - - - +
581A ASP* 3.1 36.1 + - - +
592A VAL* 3.9 15.2 + - - +
593A TYR* 1.3 74.1 - - - +
595A LEU* 1.3 66.0 + - - +
596A TRP* 3.2 43.3 - - + +
597A GLU* 3.4 28.3 + - - +
598A VAL* 3.0 22.5 + - - +
606A GLU* 2.8 25.9 + - - +
610A MET* 5.2 0.7 - - - -
625A VAL* 4.1 12.5 - - + +
----------------------------------------------------------
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