Contacts of the strand formed by residues 593 - 598 (chain A) in PDB entry 5ZR1
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 LEU 593 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A SER 4.2 1.0 + - - -
472A ALA* 3.4 7.4 - - + +
473A THR 3.2 24.9 + - - +
528A LEU* 5.5 2.5 - - + -
550A PHE* 3.8 35.9 - - + -
561A ILE* 3.4 23.8 - - + +
563A VAL* 3.8 22.2 - - + -
582A PHE* 4.2 3.1 - - + +
585A TRP* 3.8 28.0 - - + +
586A THR* 3.7 21.7 - - + +
591A ALA* 3.7 7.4 - - + -
592A LYS* 1.3 75.7 - - - +
594A ILE* 1.3 63.1 + - - +
595A VAL* 3.8 15.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
463A ALA* 4.0 12.3 - - + +
466A ALA* 3.7 22.2 - - + -
467A ILE* 3.6 34.1 - - + +
471A SER 4.9 3.8 - - - +
473A THR* 3.4 26.0 - - + +
475A ILE* 4.5 10.1 - - + -
560A THR* 6.1 2.0 - - - -
561A ILE 2.9 12.6 + - - +
562A VAL* 3.4 15.6 - - + +
563A VAL 3.0 27.8 + - - +
592A LYS 5.7 0.2 - - - -
593A LEU* 1.3 77.7 - - - +
595A VAL* 1.3 62.9 + - - +
596A ILE* 3.6 19.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A THR 3.3 6.5 + - - -
474A THR* 3.3 11.8 - - + +
475A ILE 2.8 28.3 + - - +
563A VAL* 3.5 21.1 - - + +
565A LEU* 3.7 32.5 - - + -
582A PHE* 3.5 27.6 - - + +
583A PHE* 3.9 17.9 - - + -
586A THR* 3.7 9.9 - - + -
593A LEU* 3.8 8.7 - - + -
594A ILE* 1.3 71.1 - - - +
596A ILE* 1.3 60.7 + - - +
597A ALA* 4.1 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ILE* 4.4 15.0 - - + -
463A ALA* 5.4 4.0 - - + -
475A ILE* 3.4 24.7 - - + +
477A VAL* 4.3 10.3 - - + -
489A VAL* 3.7 41.5 - - + -
492A VAL* 5.3 1.8 - - + -
493A VAL* 4.3 11.2 - - + -
562A VAL* 4.1 21.5 - - + -
563A VAL 3.0 9.9 + - - +
564A LEU* 3.3 18.4 - - + +
565A LEU 3.0 23.2 + - - -
594A ILE* 4.3 13.5 - - + -
595A VAL* 1.3 72.6 - - - +
597A ALA* 1.3 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A THR* 4.9 0.7 - - + -
475A ILE 2.8 12.3 + - - +
476A TYR* 3.4 12.7 - - + -
477A VAL* 3.1 25.2 + - - +
565A LEU* 3.8 10.1 - - + +
568A LEU* 3.7 24.9 - - + -
583A PHE* 3.8 25.6 - - + -
595A VAL* 3.6 6.5 + - + +
596A ILE* 1.3 70.9 - - - +
598A VAL* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A VAL* 3.2 18.4 - - + +
485A LYS* 3.7 42.2 - - + +
486A THR* 4.7 6.5 - - - +
489A VAL* 5.4 3.8 - - + -
564A LEU* 3.7 21.3 - - + -
565A LEU 3.3 3.8 + - - +
566A ASP* 3.3 35.0 - - - +
567A GLU* 3.1 27.2 + - - -
568A LEU* 3.4 5.8 + - - -
597A ALA* 1.3 72.8 - - - +
599A ALA* 1.3 61.6 + - - +
2001A AGS 5.4 1.8 - - - +
----------------------------------------------------------
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