Contacts of the helix formed by residues 601 - 608 (chain B) in PDB entry 4Y5U
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 SER 601 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B TYR* 4.1 7.4 - - - -
597B LEU* 3.5 13.2 + - - -
598B SER 5.1 0.4 + - - -
600B ARG* 1.3 76.7 - - - +
602B LEU* 1.3 65.1 + - - +
603B GLY 3.6 0.9 + - - -
604B ASP* 3.4 24.4 + - - +
605B ARG* 3.0 22.9 + - - +
626B ARG* 3.5 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B LEU* 3.8 24.0 - - + -
532B TYR* 3.8 24.7 + - + -
538B ILE* 4.9 1.3 - - + -
561B LEU* 3.9 27.4 - - + -
571B ILE* 4.3 14.8 - - + -
573B ILE* 4.7 7.0 - - + -
592B PHE* 4.0 31.2 - - + -
597B LEU* 3.4 17.8 - - + +
601B SER* 1.3 72.8 - - - +
603B GLY* 1.3 63.7 + - - +
605B ARG* 3.2 6.9 + - + +
606B ILE* 3.1 39.9 + - + +
625B PHE* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 603 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B TYR* 3.0 16.0 + - - -
601B SER 3.3 0.2 - - - -
602B LEU* 1.3 78.4 - - - +
604B ASP* 1.3 60.3 + - - +
606B ILE* 3.5 4.2 + - - +
607B ARG* 3.2 29.7 + - - +
625B PHE* 4.3 16.3 - - - +
626B ARG* 3.4 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ARG* 3.6 41.6 + - + +
601B SER* 3.4 19.2 + - - +
602B LEU 3.3 0.2 - - - -
603B GLY* 1.3 72.3 - - - +
605B ARG* 1.3 62.0 + - - +
607B ARG* 3.4 18.3 + - - +
608B ASP* 3.0 34.3 + - - +
626B ARG* 4.0 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A ALA* 5.5 2.2 + - - +
645A THR 6.0 0.2 - - - -
646A ILE* 3.9 23.3 - - - +
573B ILE* 5.5 0.9 - - + -
592B PHE* 3.2 43.1 - - + -
596B ASP* 2.8 34.6 + - - +
597B LEU* 4.1 12.1 - - - +
599B ILE* 4.7 3.2 - - - +
600B ARG* 3.1 31.8 + - + +
601B SER 3.0 14.8 - - - +
602B LEU* 3.5 7.9 - - + +
604B ASP* 1.3 76.0 - - - +
606B ILE* 1.3 60.8 + - - +
608B ASP* 3.5 20.2 + - - +
609B LEU* 3.7 5.9 + - - +
648B MET* 3.7 41.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B PHE* 3.9 26.9 - - + -
561B LEU* 4.2 10.1 - - + -
573B ILE* 4.2 19.3 - - + -
602B LEU* 3.1 32.2 + - + +
603B GLY* 3.6 7.9 - - - +
604B ASP 3.2 0.2 - - - -
605B ARG* 1.3 76.8 - - - +
607B ARG* 1.3 60.1 + - + +
609B LEU* 3.4 8.8 + - - +
612B LEU* 3.9 12.8 - - + +
621B LYS* 3.2 27.1 + - + +
625B PHE* 3.7 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B GLY 3.2 16.4 + - - +
604B ASP* 3.8 14.6 + - - +
605B ARG 3.4 0.2 - - - -
606B ILE* 1.3 76.0 - - + +
608B ASP* 1.3 61.0 - - - +
609B LEU 2.9 7.8 + - - +
610B ALA* 5.2 0.5 - - - -
621B LYS* 3.8 20.7 + - + +
622B ASP* 3.8 23.8 - - - +
625B PHE* 3.9 16.5 + - + +
626B ARG* 2.5 69.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ARG* 2.5 47.3 + - - -
604B ASP 3.0 19.6 + - - +
605B ARG* 3.5 8.6 - - - +
606B ILE 3.4 0.4 - - - -
607B ARG* 1.3 76.1 - - - +
609B LEU* 1.3 61.9 + - - +
610B ALA* 3.7 3.3 + - - +
646B ILE 4.1 0.2 - - - +
647B LYS* 3.7 33.3 - - + +
648B MET* 2.9 34.7 + - + +
----------------------------------------------------------
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