Contacts of the strand formed by residues 600 - 603 (chain C) in PDB entry 3WF4
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 THR 600 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570C PHE* 4.0 13.0 - - + -
571C ILE 3.1 10.8 - - - +
572C GLN* 3.8 28.5 - - + +
598C GLN* 2.8 29.3 + - - +
599C LEU* 1.3 77.9 - - - +
601C LEU* 1.4 57.3 + - - +
639C VAL* 4.2 17.7 - - + -
641C ARG 4.3 1.3 - - - +
642C PRO* 3.5 9.0 - - - +
643C VAL* 2.8 36.6 + - + +
644C ILE* 4.6 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 601 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C TRP* 5.6 0.2 - - + -
329C THR* 4.0 6.5 - - + -
570C PHE* 3.3 7.1 - - - -
571C ILE* 2.7 54.2 + - + +
573C PHE* 4.4 3.8 - - + -
581C VAL* 3.9 17.7 - - + -
588C LEU* 3.6 24.9 - - + +
589C GLY 3.8 12.3 - - - -
590C ARG 3.7 26.2 - - - +
591C TYR* 4.2 15.9 - - + +
598C GLN* 3.6 20.9 - - + +
599C LEU 4.6 2.0 - - - +
600C THR* 1.4 80.5 - - - +
602C PHE* 1.3 66.4 + - - +
603C VAL 3.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 602 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PRO* 4.9 6.1 - - + -
64C TYR* 4.5 1.3 - + - -
68C ARG* 4.2 15.0 - - - -
312C THR* 3.6 21.9 - - + +
314C PHE* 4.5 14.5 - + - -
329C THR* 6.3 0.4 - - - +
339C GLU* 3.7 39.9 + - + +
340C ALA* 3.7 25.1 - - + -
568C ASP* 3.9 19.7 - - + -
569C THR 4.2 1.6 - - - -
570C PHE* 3.7 28.2 - + + -
588C LEU* 4.2 12.6 - - - +
598C GLN* 5.0 0.4 - - - +
600C THR 4.5 0.2 + - - -
601C LEU* 1.3 72.0 - - - +
603C VAL* 1.3 74.8 + - - +
604C PRO* 3.7 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 603 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C ASP* 3.4 4.9 - - - +
569C THR* 2.9 54.0 + - + +
571C ILE* 4.0 16.6 - - + +
583C ILE* 3.9 24.0 - - + -
588C LEU* 3.7 19.7 - - + -
601C LEU 3.9 9.9 - - - +
602C PHE* 1.3 79.4 - - - +
604C PRO* 1.4 73.8 - - + +
605C GLN* 4.6 0.2 - - - -
607C ILE* 4.3 10.8 - - + -
608C LEU* 4.4 12.6 - - + -
638C PHE* 4.5 0.4 - - + -
----------------------------------------------------------
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