Contacts of the strand formed by residues 599 - 606 (chain A) in PDB entry 1ZYC
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 599 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A ARG* 4.9 5.2 - - + -
595A TYR* 3.1 52.0 + + + +
596A ALA* 4.3 8.6 + - - +
597A SER 3.9 0.4 - - - -
598A ASP* 1.3 91.6 - - + +
600A GLU* 1.3 61.7 + - - +
601A GLU* 3.5 2.4 + - - +
616A ALA* 4.1 7.9 - - + -
617A ARG 3.2 16.6 - - - +
618A ASN* 3.0 34.1 - - + -
619A ALA 4.9 0.2 - - - +
625A TYR* 4.2 4.5 - + - -
627A ILE* 4.1 22.2 - - + -
662A TRP* 3.8 23.3 - + - -
787A GLN* 3.9 28.3 - - + -
899C THR* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A PHE* 1.3 71.4 - - - +
601A GLU* 1.3 79.5 + - - +
602A ILE* 4.0 4.8 - - + +
616A ALA* 3.3 1.1 - - - +
617A ARG* 2.9 33.7 + - + +
897C ASP* 4.1 13.5 - - + +
898C GLY* 2.9 51.4 - - - +
899C THR* 4.6 3.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A TYR* 2.4 30.8 + - + +
599A PHE 3.5 4.0 + - - -
600A GLU* 1.3 94.2 + - - +
602A ILE* 1.3 66.6 + - - +
603A ALA* 4.7 4.9 - - - +
604A VAL* 5.9 3.4 - - + +
614A VAL* 3.5 21.6 - - + +
615A LYS 4.4 0.2 - - - +
616A ALA* 3.7 7.4 - - - -
629A LYS* 2.6 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A GLU* 4.4 7.0 - - + +
601A GLU* 1.3 82.8 - - - +
603A ALA* 1.3 67.9 + - + +
615A LYS* 2.9 34.8 + - + +
616A ALA* 4.1 1.3 - - - -
617A ARG* 4.0 26.0 - - + +
624A TYR* 4.0 21.5 - - + +
897C ASP 4.2 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A GLU* 4.7 3.2 - - - +
602A ILE* 1.3 88.2 - - + +
604A VAL* 1.3 71.1 + - - +
605A LEU* 5.7 2.5 - - + -
614A VAL* 3.0 22.9 - - - +
615A LYS* 3.1 18.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
601A GLU* 5.9 3.6 - - + +
603A ALA* 1.3 83.3 - - - +
605A LEU* 1.3 66.7 + - - +
606A GLY* 3.7 12.3 - - - +
607A GLN* 4.5 8.1 - - - +
612A GLN* 3.8 38.8 - - + +
613A VAL 3.8 7.6 - - - +
614A VAL* 4.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A ALA* 5.6 2.7 - - + -
604A VAL* 1.3 79.2 - - - +
606A GLY* 1.3 58.0 + - - +
613A VAL* 2.8 21.1 + - + +
614A VAL 4.3 1.3 - - - -
615A LYS* 3.7 40.4 - - + +
626A ALA* 4.2 22.9 - - + -
790A TYR* 4.3 18.6 - - + +
791A CYS 5.6 2.0 - - - +
793A ASN* 6.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A VAL* 3.6 5.7 - - - +
605A LEU* 1.3 80.7 - - - +
607A GLN* 1.3 71.3 + - - +
612A GLN* 3.4 3.2 - - - -
613A VAL* 2.7 42.7 + - - +
----------------------------------------------------------
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