Contacts of the helix formed by residues 733 - 742 (chain B) in PDB entry 4PE5
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 ALA 733 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B GLU 5.5 0.2 - - - +
532B THR* 3.1 17.5 + - - +
533B GLY 2.5 23.6 + - - +
535B SER* 3.3 27.4 - - - +
732B ASP* 1.3 69.6 - - - +
734B ALA* 1.3 61.1 + - - +
736B LEU* 3.3 2.1 + - - +
737B ASN* 2.8 42.3 + - - +
756B VAL* 4.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 734 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B PHE* 3.7 25.6 - - + -
530B ILE* 4.2 12.8 - - + -
531B GLU 4.6 3.6 - - - +
532B THR* 3.1 14.5 + - - +
732B ASP* 3.0 9.6 + - - +
733B ALA* 1.3 78.3 - - - +
735B VAL* 1.3 57.4 - - - +
737B ASN* 3.2 9.2 + - - +
738B TYR* 2.9 31.1 + - - +
762B TYR* 4.5 1.6 - - + -
797B LEU* 5.6 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 735 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B GLU* 3.5 29.6 - - + +
414B ALA 4.4 8.5 - - - +
416B PHE* 4.1 13.9 - - + -
714B VAL* 4.5 11.2 - - + -
731B TYR* 3.6 30.7 - - + +
732B ASP* 3.2 5.3 + - + +
733B ALA 3.4 0.2 - - - -
734B ALA* 1.3 75.7 - - - +
736B LEU* 1.3 58.0 + - + +
738B TYR* 3.5 6.7 + - + +
739B MET* 2.9 34.7 + - + +
762B TYR* 3.3 24.0 - - - +
921B GLU* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 736 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B SER* 3.4 36.1 - - - +
536B VAL 3.9 1.3 - - - -
537B MET* 3.8 32.6 - - + +
714B VAL* 5.4 2.7 - - + -
729B PHE* 3.8 21.5 - - + +
731B TYR* 3.6 31.9 - - + +
732B ASP 3.2 15.0 + - - +
733B ALA* 3.7 4.3 - - - +
735B VAL* 1.3 77.1 - - + +
737B ASN* 1.3 63.7 + - - +
739B MET* 3.8 7.3 - - + +
740B ALA* 2.9 30.5 + - - +
750B THR* 5.4 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 737 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B SER* 5.5 1.2 + - - -
733B ALA* 2.8 33.2 + - - +
734B ALA* 3.2 8.1 + - - +
736B LEU* 1.3 76.2 - - - +
738B TYR* 1.3 59.4 + - - +
740B ALA* 3.3 6.6 + - - +
741B GLY* 2.9 24.9 + - - -
750B THR* 4.2 22.9 + - - +
754B GLY* 5.2 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 738 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A ASN* 6.1 1.4 - - - +
414B ALA* 4.6 10.1 - - + +
415B PRO* 3.5 46.1 - - + +
418B ILE* 5.5 3.1 - - - +
734B ALA 2.9 15.7 + - - +
735B VAL* 3.9 4.9 - - + +
737B ASN* 1.3 76.4 - - - +
739B MET* 1.3 69.9 + - - +
741B GLY* 3.1 1.8 + - - -
742B ARG* 2.6 54.4 + - + +
796B TRP 3.2 24.9 + - - -
797B LEU* 4.1 23.1 - - + -
798B THR 4.3 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 739 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ALA* 6.1 1.3 - - - +
714B VAL* 5.5 13.5 - - + -
715B ASP* 5.2 15.0 - - + -
718B LEU* 3.8 40.3 - - + +
735B VAL* 2.9 24.7 + - + +
736B LEU* 3.8 10.5 - - + +
737B ASN 3.3 0.2 - - - -
738B TYR* 1.3 92.3 - - - +
740B ALA* 1.3 60.6 + - - +
742B ARG 3.0 28.2 - - - +
743B ASP* 3.5 11.6 - - - +
748B LEU* 5.3 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 740 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B LEU 2.9 19.5 + - - +
737B ASN* 3.6 6.7 - - - +
738B TYR 3.2 0.2 - - - -
739B MET* 1.3 76.8 - - - +
741B GLY* 1.3 62.3 + - - +
743B ASP* 4.7 3.2 - - - +
746B CYS* 5.8 0.2 - - - -
748B LEU* 4.0 28.3 - - + +
749B VAL* 4.3 13.7 - - + -
750B THR* 4.5 8.3 - - + +
801B CYS* 3.4 20.4 - - - +
802B HIS* 5.7 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 741 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B ASN 2.9 14.5 + - - -
738B TYR* 3.5 2.9 - - - -
740B ALA* 1.3 78.9 - - - +
742B ARG* 1.3 58.0 + - - +
743B ASP 3.9 0.6 + - - -
799B GLY* 3.7 17.5 - - - -
800B ILE* 2.8 28.8 + - - +
801B CYS* 2.9 19.9 + - - +
802B HIS* 6.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 742 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A PRO* 6.2 2.7 - - + -
738B TYR* 2.6 44.3 + - + +
739B MET* 3.0 24.6 - - - +
741B GLY* 1.3 72.2 - - - +
743B ASP* 1.3 59.8 + - - +
798B THR 4.9 5.2 - - - +
799B GLY* 5.3 0.4 - - - -
800B ILE* 4.6 6.7 - - + +
----------------------------------------------------------
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