Contacts of the strand formed by residues 593 - 602 (chain A) in PDB entry 4X7J
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 PHE 593 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A ARG* 5.0 4.3 - - - -
589A TYR* 3.2 37.2 + + + +
590A LEU* 3.5 17.3 - - - +
591A THR 3.6 0.4 - - - -
592A ASP* 1.3 94.0 - - + +
594A GLU* 1.3 60.4 + - - +
595A PRO* 3.8 7.0 - - - +
610A ALA* 4.0 22.4 - - + -
611A LYS 3.1 16.4 - - - +
612A ASN* 3.7 30.3 - - + -
613A LYS* 3.8 8.8 + - - -
619A TYR* 4.1 11.7 - + - -
621A ILE* 3.7 17.0 - - + -
658A TRP* 3.8 21.5 - + - -
887A GLN* 3.5 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A PHE* 1.3 73.4 - - - +
595A PRO* 1.3 71.5 - - + +
596A ILE* 3.6 6.6 + - + +
610A ALA* 4.2 1.1 - - - -
611A LYS* 2.8 71.6 + - + +
613A LYS* 4.3 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A TYR* 4.0 27.1 - - + +
590A LEU* 5.2 10.8 - - + -
593A PHE 3.8 7.4 - - - +
594A GLU* 1.3 88.6 - - + +
596A ILE* 1.3 62.0 + - - +
597A GLN 5.2 1.1 - - - +
608A PHE* 5.7 5.4 - - + -
609A GLU 3.9 5.6 - - - +
610A ALA* 4.0 5.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
594A GLU* 3.9 7.4 - - - +
595A PRO* 1.3 78.6 - - - +
597A GLN* 1.3 68.5 + - + +
609A GLU* 2.8 35.9 + - + +
610A ALA* 3.8 4.9 - - - -
611A LYS* 3.4 34.8 - - + +
618A ASN* 3.0 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A PRO* 4.0 1.5 - - - +
596A ILE* 1.3 86.8 - - + +
598A CYS* 1.3 66.7 + - - +
599A LEU* 4.1 10.3 - - + +
608A PHE* 3.4 8.4 - - - +
609A GLU* 2.8 60.5 + - + +
893A LYS* 3.6 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A GLN* 1.3 82.9 - - - +
599A LEU* 1.3 64.4 + - - +
600A GLY* 3.6 22.9 - - - -
601A ARG* 3.3 30.1 - - - +
606A VAL* 3.9 8.5 - - - -
607A VAL 3.7 6.7 - - - -
608A PHE* 4.0 14.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A GLN* 4.1 10.1 - - + +
598A CYS* 1.3 74.1 - - - +
600A GLY* 1.3 57.4 + - - +
607A VAL* 2.8 27.0 + - + +
608A PHE 3.9 7.6 - - - +
609A GLU* 3.7 36.8 - - + +
620A ALA* 4.3 2.2 - - + -
890A LEU* 3.9 24.5 - - + -
893A LYS* 3.8 36.4 - - + +
958A LEU* 3.9 16.8 - - + +
1101A 3Z1 4.0 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A CYS* 3.4 11.3 - - - -
599A LEU* 1.3 80.8 - - - +
601A ARG* 1.3 64.2 + - - +
606A VAL* 3.6 5.0 - - - +
607A VAL 2.9 25.0 + - - +
958A LEU* 3.8 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A CYS* 3.3 28.1 - - - +
600A GLY* 1.3 74.9 - - - +
602A GLY* 1.3 58.5 + - - +
605A GLY 3.4 15.3 - - - +
606A VAL* 4.1 24.8 - - + +
607A VAL* 4.7 0.7 - - - +
608A PHE* 5.9 0.4 - - - -
957A GLY 3.2 8.3 - - - -
958A LEU* 4.2 2.4 - - - +
959A VAL* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A ARG* 1.3 79.3 - - - +
603A GLY* 1.3 65.9 + - - -
604A PHE 3.4 0.5 + - - -
605A GLY* 3.1 19.0 + - - +
622A LYS* 5.9 1.0 - - - +
957A GLY* 3.3 16.3 + - - +
959A VAL* 3.8 18.2 - - - -
----------------------------------------------------------
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