Contacts of the helix formed by residues 743 - 755 (chain B) in PDB entry 3E0D
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 TYR 743 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B GLU 4.5 1.4 + - - -
691B ILE* 3.9 10.5 - - + +
692B ALA* 3.5 27.1 + - + +
695B SER* 3.2 26.9 - - - -
736B GLU* 4.3 20.1 + - - -
737B THR* 4.9 8.1 - - - -
742B VAL* 1.3 85.8 + - + +
744B GLN* 1.3 60.5 + - - +
745B GLU* 3.8 10.1 - - + +
746B GLN* 3.0 51.8 + - + +
747B ILE* 3.4 9.5 + - - +
813B PHE* 2.1 34.1 - - + +
815B LYS* 4.0 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 744 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B ARG* 2.7 38.5 + - - +
743B TYR 1.3 65.4 - - - -
745B GLU* 1.3 61.3 + - - +
747B ILE* 3.0 13.7 + - + +
748B MET* 3.0 25.8 + - - +
766B ARG* 3.6 25.2 - - - +
809B ALA 6.0 0.4 - - - +
812B GLY* 3.2 20.7 + - - +
813B PHE* 2.0 40.0 + - - +
814B ASN* 2.9 27.9 - - - +
1222B DTP 5.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 745 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B GLY 4.6 9.2 - - - +
449B LEU* 3.7 40.2 + - + +
452B ARG* 3.9 12.4 - - + +
743B TYR* 3.1 4.9 - - + +
744B GLN* 1.3 73.8 - - - +
746B GLN* 1.3 61.2 + - + +
748B MET* 3.4 9.4 + - - +
749B GLN* 3.0 34.4 + - - +
813B PHE 2.5 30.8 - - - +
814B ASN* 2.2 35.9 + - - -
815B LYS* 2.8 18.3 + - + +
816B SER* 3.7 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 746 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B ILE* 3.2 35.6 - - + +
734B LEU* 3.6 12.2 - - + +
736B GLU* 5.0 2.4 - - - +
737B THR* 2.9 27.4 - - - +
740B ILE 3.4 5.5 + - - -
741B PRO* 4.8 3.1 - - + -
742B VAL* 2.8 33.9 - - - +
743B TYR* 3.0 40.7 + - + +
745B GLU* 1.3 79.7 - - + +
747B ILE* 1.3 62.1 + - - +
749B GLN* 4.2 3.8 - - - +
750B ILE* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 747 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B PRO* 4.5 14.6 - - + +
743B TYR 3.4 12.5 + - - +
744B GLN* 3.0 14.6 + - + +
746B GLN* 1.3 74.7 - - - +
748B MET* 1.3 68.3 + - - +
750B ILE* 3.0 9.7 + - - +
751B ALA* 2.9 24.7 + - + +
762B ALA 5.9 1.1 - - - +
765B LEU* 6.0 2.9 - - + -
766B ARG* 5.3 14.8 - - + +
769B MET* 5.5 4.5 - - + -
805B LEU* 4.2 33.9 - - + +
808B PHE* 3.8 15.0 - - + +
809B ALA* 3.7 37.0 - - + +
812B GLY* 4.7 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 748 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LEU* 5.4 4.9 - - + -
451B GLU* 4.6 1.8 - - + +
452B ARG* 3.1 48.7 - - + +
744B GLN 3.0 17.0 + - - +
745B GLU* 3.4 13.0 + - - +
747B ILE* 1.3 76.5 - - - +
749B GLN* 1.3 58.5 + - + +
751B ALA* 4.8 0.4 - - - -
752B SER* 2.8 31.0 + - - -
759B LEU* 3.3 37.7 - - + +
762B ALA* 3.2 30.1 - - + +
763B ASP* 3.8 20.6 - - + +
766B ARG* 4.0 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 749 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LEU* 4.4 26.3 - - + +
733B ILE* 3.7 33.7 - - + +
745B GLU* 3.0 25.2 + - - +
746B GLN* 3.8 4.3 - - - +
748B MET* 1.3 74.0 - - - +
750B ILE* 1.3 66.0 + - - +
752B SER* 3.1 1.1 + - - -
753B GLN* 2.8 38.8 + - - +
759B LEU* 4.1 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 750 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B TYR* 5.9 0.9 - - - -
730B LEU* 3.8 33.9 - - + -
733B ILE* 3.8 18.8 - - + -
734B LEU* 3.8 26.0 - - + -
741B PRO* 5.2 2.5 - - + -
746B GLN 3.1 21.3 + - - +
747B ILE* 3.0 9.5 + - - +
749B GLN* 1.3 75.5 - - - +
751B ALA* 1.3 60.2 + - - +
753B GLN* 3.9 1.5 - - - +
754B VAL* 2.9 40.0 + - + +
784B PHE* 5.5 0.7 - - + -
801B LEU* 4.6 8.1 - - + -
804B MET* 4.3 7.4 - - + -
805B LEU* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 751 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B ILE* 2.9 16.4 + - + +
748B MET* 3.8 3.4 - - - +
750B ILE* 1.3 76.2 - - - +
752B SER* 1.3 60.1 + - - +
755B ALA* 3.2 25.8 + - - +
757B TYR* 3.3 12.5 - - + +
762B ALA* 4.3 6.1 - - + +
765B LEU* 3.7 29.8 - - + -
784B PHE* 4.1 13.0 - - + -
805B LEU* 4.1 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 752 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748B MET 2.8 18.0 + - - -
749B GLN* 3.1 3.5 + - - -
751B ALA* 1.3 77.2 - - - +
753B GLN* 1.3 62.0 + - - +
756B GLY* 3.4 8.7 + - - -
757B TYR* 2.7 43.2 + - - +
759B LEU* 3.4 36.1 + - - +
762B ALA* 4.4 1.5 - - - +
791B ARG* 5.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 753 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B TYR* 3.7 35.8 - - + +
732B PRO* 6.0 3.5 - - - +
733B ILE* 3.5 29.0 - - - +
749B GLN* 2.8 26.7 + - - +
750B ILE* 4.1 1.8 - - - +
752B SER* 1.3 82.1 - - - +
754B VAL* 1.3 65.1 + - - +
756B GLY 3.9 1.6 + - - -
791B ARG* 3.1 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 754 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B ALA* 4.4 9.2 - - + -
729B TYR* 3.9 34.5 - - + -
730B LEU* 5.1 1.6 - - + -
750B ILE* 2.9 28.0 + - + +
753B GLN* 1.3 72.1 - - - +
755B ALA* 1.3 58.8 + - - +
784B PHE* 3.8 14.6 - - + -
787B GLY 3.4 4.2 - - - +
788B ALA* 3.5 8.0 - - + +
791B ARG* 3.4 23.4 - - - +
793B VAL* 4.1 20.0 - - + -
801B LEU* 3.7 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 755 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751B ALA 3.2 18.4 + - - +
754B VAL* 1.3 78.7 - - - +
756B GLY* 1.3 59.7 + - - +
757B TYR* 3.2 16.8 + - + -
783B ARG 5.0 1.7 - - - +
784B PHE* 3.5 38.6 - - + +
787B GLY* 3.2 31.0 - - - -
788B ALA 4.0 1.3 - - - +
----------------------------------------------------------
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