Contacts of the helix formed by residues 712 - 733 (chain B) in PDB entry 1MQB
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 712 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B PHE* 1.3 75.9 - - - +
713B VAL* 1.3 62.5 + - - +
714B LEU* 3.2 11.1 + - - +
715B GLN* 2.9 44.4 + - - +
716B LEU* 3.1 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 713 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B PHE 4.1 0.2 + - - -
712B SER* 1.3 73.0 - - - +
714B LEU* 1.3 57.3 + - - +
716B LEU* 3.2 13.2 + - + +
717B VAL* 2.9 45.5 + - + +
811B MET* 4.5 7.0 - - + -
841B ASP* 4.8 7.4 - - + +
843B PRO* 3.5 38.4 - - + -
881B LEU* 4.3 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 714 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712B SER* 3.1 8.9 - - - +
713B VAL* 1.3 77.4 - - - +
715B GLN* 1.3 61.3 + - + +
717B VAL* 3.2 4.8 + - - +
718B GLY* 2.7 29.3 + - - -
874B LEU 4.8 0.7 - - - +
875B ILE* 3.9 42.9 - - + +
878B PRO* 4.4 24.5 - - + -
881B LEU* 4.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 715 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B GLU 4.7 0.7 - - - +
711B PHE* 3.4 26.6 - - + +
712B SER* 2.9 39.3 + - - +
714B LEU* 1.3 79.4 - - + +
716B LEU* 1.3 62.0 + - - +
718B GLY* 3.3 2.4 + - - -
719B MET* 3.1 27.3 + - - +
751B LEU* 4.1 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 716 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B LEU* 4.1 10.8 - - + -
711B PHE* 4.4 6.7 - - + +
712B SER 3.1 17.4 + - - +
713B VAL* 3.5 11.0 - - + +
714B LEU 3.1 0.2 - - - -
715B GLN* 1.3 73.9 - - - +
717B VAL* 1.3 67.0 + - - +
719B MET* 3.1 36.9 + - + +
720B LEU* 3.1 19.3 + - - +
810B VAL* 3.7 22.1 - - + +
811B MET* 3.7 33.2 - - + +
813B TYR* 3.7 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 717 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B VAL* 2.9 35.9 + - + +
714B LEU* 3.7 5.2 - - - +
716B LEU* 1.3 72.5 - - - +
718B GLY* 1.3 65.3 + - - +
720B LEU* 3.0 11.1 + - - +
721B ARG* 2.8 22.2 + - - +
811B MET* 4.9 5.6 - - - -
846B ILE* 4.0 24.9 - - + -
871B LEU* 3.7 28.0 - - + +
874B LEU* 5.0 2.0 - - + -
875B ILE* 3.6 24.2 - - + -
881B LEU* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 718 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714B LEU 2.7 17.3 + - - -
715B GLN* 3.6 3.8 - - - -
716B LEU 3.2 0.2 - - - -
717B VAL* 1.3 76.6 - - - +
719B MET* 1.3 61.1 + - - +
721B ARG* 3.1 12.4 + - - +
722B GLY* 3.1 11.3 + - - -
751B LEU 5.6 0.4 - - - -
875B ILE* 3.9 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 719 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700B LEU* 4.2 17.3 - - + -
703B PHE* 5.2 1.3 - - - -
704B LEU* 3.7 19.5 - - + -
711B PHE* 5.2 4.0 - - + -
715B GLN 3.1 15.6 + - - +
716B LEU* 3.1 40.3 + - + +
718B GLY* 1.3 74.6 - - - +
720B LEU* 1.3 62.3 + - - +
722B GLY* 3.4 2.9 + - - -
723B ILE* 3.1 30.2 + - + +
747B VAL* 4.8 1.6 - - - -
751B LEU* 3.4 49.4 - - + +
753B CYS* 3.7 17.8 - - - +
810B VAL* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 720 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B LEU 3.1 14.8 + - - +
717B VAL* 3.0 13.1 + - + +
719B MET* 1.3 73.4 - - - +
721B ARG* 1.3 60.1 + - - +
723B ILE* 3.2 11.4 + - + +
724B ALA* 2.8 30.1 + - - +
803B PHE* 3.6 10.4 - - + -
806B VAL* 4.3 2.5 - - + -
807B MET* 3.6 52.0 - - + +
810B VAL* 3.7 24.0 - - + -
811B MET* 3.9 25.1 - - + -
846B ILE* 4.9 4.0 - - + -
871B LEU* 3.8 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 721 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B HIS* 6.3 0.4 - - - -
674B ASN* 4.8 5.7 - - - +
717B VAL 2.8 11.9 + - - +
718B GLY 3.1 10.3 + - - +
720B LEU* 1.3 76.1 - - - +
722B GLY* 1.3 60.1 + - - +
724B ALA* 3.3 5.1 + - - +
725B ALA* 2.9 42.0 + - - +
868B VAL* 3.8 22.0 - - + +
871B LEU* 3.7 20.8 - - + +
872B ASP* 2.8 42.1 + - - +
875B ILE* 3.8 18.2 - - + -
876B ARG* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 722 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B ASN* 3.0 36.4 - - - +
718B GLY 3.1 9.4 + - - -
719B MET 3.4 3.8 + - - -
721B ARG* 1.3 82.0 - - - +
723B ILE* 1.3 64.3 + - - +
725B ALA* 3.2 1.4 + - - -
726B GLY 3.0 18.0 + - - -
753B CYS* 4.4 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 723 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674B ASN* 5.2 0.4 - - - -
700B LEU* 3.9 28.3 - - + -
719B MET 3.1 21.7 + - - +
720B LEU* 3.2 13.0 + - + +
722B GLY* 1.3 75.5 - - - +
724B ALA* 1.3 63.4 + - - +
726B GLY* 3.2 2.8 + - - +
727B MET* 3.0 25.5 + - + +
740B LEU* 4.4 10.5 - - + -
745B ILE* 3.9 27.6 - - + -
753B CYS* 3.7 17.5 - - + -
755B VAL* 4.3 7.3 - - + +
803B PHE* 3.7 20.4 - - + -
806B VAL* 3.9 18.2 - - + -
810B VAL* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 724 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B LEU 2.8 16.7 + - - +
721B ARG* 3.5 8.3 - - - +
723B ILE* 1.3 77.1 - - - +
725B ALA* 1.3 50.3 + - - +
727B MET* 3.2 6.6 + - - +
728B LYS* 2.7 34.0 + - - +
803B PHE* 3.7 10.9 - - + -
864B PHE* 3.9 6.9 - - + -
867B ILE* 3.5 33.2 - - + -
868B VAL* 3.8 12.1 - - + +
871B LEU* 4.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 725 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B HIS* 3.5 9.5 + - + +
674B ASN* 3.6 19.7 - - - +
721B ARG* 2.9 33.0 + - - +
723B ILE 3.2 0.4 - - - -
724B ALA* 1.3 73.8 - - - +
726B GLY* 1.3 65.9 + - - +
728B LYS* 3.4 6.8 + - + +
729B TYR* 3.0 24.1 + - - +
868B VAL* 3.8 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 726 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B HIS* 3.8 8.5 - - - -
674B ASN* 3.6 29.4 - - - +
675B ILE* 3.5 17.8 - - - +
722B GLY 3.0 10.3 + - - -
723B ILE 3.7 2.9 - - - -
725B ALA* 1.3 75.8 - - - +
727B MET* 1.3 56.9 + - - +
729B TYR* 3.3 2.9 + - - +
730B LEU* 3.0 21.3 + - - +
755B VAL* 4.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 727 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B ILE* 3.0 24.5 + - + +
724B ALA 3.4 1.6 - - - +
726B GLY* 1.3 73.2 - - - +
728B LYS* 1.3 63.7 + - - +
729B TYR 3.1 1.1 - - - -
730B LEU* 3.1 16.8 + - + +
731B ALA* 3.0 24.8 + - - +
735B TYR 5.6 0.4 - - - +
737B HIS* 4.0 12.8 - - + +
740B LEU* 4.0 22.0 - - + -
755B VAL* 3.9 24.7 - - + -
799B ASP* 3.4 40.4 - - + +
864B PHE* 3.4 38.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 728 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B ALA 2.7 20.2 + - - +
725B ALA* 3.4 10.1 + - + +
727B MET* 1.3 70.9 - - - +
729B TYR* 1.3 58.9 + - - +
731B ALA* 3.4 4.3 + - - +
732B ASN* 2.9 50.9 + - - +
864B PHE* 3.6 15.8 - - + +
865B ALA* 4.1 28.7 - - + +
868B VAL* 4.2 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 729 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B GLN 4.0 1.7 + - - -
670B PHE* 3.2 31.4 - + + -
671B SER 3.0 30.4 + - - -
672B HIS* 3.5 41.7 - + + +
675B ILE* 3.9 10.3 - - + -
725B ALA 3.0 16.9 + - - +
726B GLY 3.6 2.2 - - - +
727B MET 3.1 0.2 - - - -
728B LYS* 1.3 77.6 - - - +
730B LEU* 1.3 62.7 + - + +
732B ASN* 3.4 9.4 + - + +
733B MET* 3.0 60.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 730 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B PHE* 3.4 43.5 - - + -
675B ILE* 3.4 28.7 - - + -
726B GLY 3.0 11.6 + - - +
727B MET* 3.1 23.7 + - + +
729B TYR* 1.3 77.6 - - + +
731B ALA* 1.3 64.4 + - - +
733B MET* 3.1 11.0 + - - +
734B ASN 3.1 0.2 + - - -
735B TYR* 3.0 42.2 + - + +
737B HIS* 4.4 6.1 - - + +
755B VAL* 4.1 11.9 - - + -
758B PHE* 3.5 20.0 - - + -
761B SER* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 731 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B MET* 3.0 12.1 + - - +
728B LYS* 3.6 10.5 - - - +
730B LEU* 1.3 75.8 - - - +
732B ASN* 1.3 58.7 + - - +
734B ASN* 2.6 29.8 + - - +
735B TYR 3.8 7.7 + - - +
764B LEU* 5.1 2.5 - - - +
796B SER* 3.2 29.6 - - - +
864B PHE* 4.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 732 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B LYS* 2.9 51.5 + - - +
729B TYR* 3.7 9.6 - - + +
731B ALA* 1.3 77.6 - - - +
733B MET* 1.3 60.8 + - + +
734B ASN* 3.1 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 733 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B GLN* 3.9 28.5 - - + +
670B PHE* 4.2 18.6 - - + -
729B TYR* 3.0 51.8 + - + +
730B LEU 3.1 9.6 + - - +
732B ASN* 1.3 75.9 - - + +
734B ASN* 1.3 70.0 + - - +
735B TYR* 3.5 12.1 - - + -
763B VAL* 5.7 0.2 - - - +
----------------------------------------------------------
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