Contacts of the helix formed by residues 740 - 755 (chain D) in PDB entry 3RMD
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 740 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738D PRO* 3.1 1.3 - - + -
739D LYS* 1.3 80.9 - - - +
741D VAL* 1.3 63.0 + - + +
743D LYS* 3.1 10.0 + - - +
744D ALA* 2.9 23.2 + - - +
767D PHE* 4.2 13.5 - - + -
771D PHE* 5.4 3.6 - - + -
774D LEU* 4.1 25.6 - - + -
778D SER* 3.7 24.3 + - - +
779D ILE* 5.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 741 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737D THR* 4.8 4.5 - - - -
738D PRO* 3.3 30.9 + - + +
740D ALA* 1.3 72.6 - - + +
742D GLN* 1.3 54.5 + - - +
743D LYS 2.6 6.5 + - - -
744D ALA* 2.5 28.7 + - - -
745D LEU* 2.7 26.9 + - + +
767D PHE* 4.4 3.6 - - + -
771D PHE* 4.7 14.6 - - + -
875D THR* 3.0 38.4 - - - +
876D PHE* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 742 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D TYR* 5.4 3.6 - - - -
732D THR* 4.5 15.5 - - - +
733D GLN* 2.8 43.9 + - - +
734D LYS 3.7 16.8 + - - -
735D SER* 5.5 0.6 + - - +
737D THR* 3.7 18.4 + - - +
738D PRO 3.0 13.3 + - - +
739D LYS* 3.5 34.9 - - + +
740D ALA 3.3 0.2 - - - -
741D VAL* 1.3 74.0 - - - +
743D LYS* 1.3 58.0 + - + +
745D LEU* 4.6 4.7 - - - +
746D LYS* 4.1 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 743 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739D LYS* 2.8 62.6 - - + +
740D ALA* 3.1 8.7 + - - +
741D VAL 2.6 1.4 + - - -
742D GLN* 1.3 78.1 - - + +
744D ALA* 1.3 65.6 + - - +
745D LEU 3.5 0.7 - - - -
746D LYS* 3.8 8.8 + - - +
747D GLU* 3.2 22.2 + - - +
763D TYR* 4.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 744 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740D ALA 2.9 5.6 + - - +
741D VAL* 2.5 17.9 + - - +
743D LYS* 1.3 70.2 - - - +
745D LEU* 1.3 53.7 + - - +
747D GLU* 3.0 6.1 + - - +
748D CYS* 2.8 31.0 + - - -
763D TYR* 3.6 19.5 - - + +
767D PHE* 3.6 36.1 - - + -
876D PHE* 3.7 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 745 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731D GLU* 6.2 0.4 - - + -
732D THR* 4.1 39.5 - - + +
737D THR* 5.8 4.5 - - + +
741D VAL* 2.7 33.4 + - + +
742D GLN 5.2 2.5 - - - +
744D ALA* 1.3 70.9 - - - +
746D LYS* 1.3 66.5 + - - +
748D CYS* 2.9 17.8 + - - +
749D ILE* 2.9 18.7 + - - +
875D THR 4.4 1.6 - - - +
876D PHE* 3.5 40.4 - - + +
879D PRO* 4.2 21.8 - - + -
880D LEU* 4.5 11.2 - - + +
883D PHE* 4.9 9.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 746 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725D LEU* 3.8 32.9 - - + +
727D ILE* 5.2 9.0 - - + -
732D THR* 4.8 5.7 - - + +
742D GLN 4.1 14.4 + - - +
743D LYS* 3.8 11.1 + - - +
744D ALA 3.3 0.2 - - - -
745D LEU* 1.3 77.5 - - - +
747D GLU* 1.3 58.7 + - - +
749D ILE* 3.1 13.2 + - - +
750D ARG* 2.8 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 747 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743D LYS 3.2 12.9 + - - +
744D ALA 3.0 11.2 + - - +
745D LEU 3.0 0.2 - - - -
746D LYS* 1.3 78.4 - - - +
748D CYS* 1.3 63.3 + - - +
750D ARG* 2.5 53.2 + - - +
751D ARG* 3.1 42.8 + - - +
763D TYR* 3.3 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 748 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744D ALA 2.8 15.8 + - - -
745D LEU* 2.9 11.2 + - - +
747D GLU* 1.3 75.3 - - - +
749D ILE* 1.3 61.7 + - + +
751D ARG* 3.6 3.6 + - - +
752D MET* 3.0 31.1 + - - +
760D LEU* 3.9 14.7 - - + +
763D TYR* 4.0 18.6 - - - -
764D PHE* 5.6 1.3 - - - -
876D PHE* 4.0 16.2 - - - -
880D LEU* 3.7 43.3 - - + -
883D PHE* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 749 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701D PHE* 4.4 8.1 - - + -
709D ALA* 4.4 9.2 - - + -
725D LEU* 4.5 4.5 - - + -
727D ILE* 3.5 34.1 - - + -
730D LEU* 3.7 15.7 - - + -
732D THR* 3.7 23.3 - - + -
745D LEU 2.9 10.9 + - - +
746D LYS* 3.4 7.2 - - - +
748D CYS* 1.3 72.3 - - - +
750D ARG* 1.3 69.0 + - - +
751D ARG 2.9 1.1 - - - -
752D MET* 2.8 20.8 + - - -
753D LEU* 3.0 34.0 + - + +
883D PHE* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 750 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725D LEU* 3.6 22.8 - - + +
746D LYS* 2.8 21.7 + - + +
747D GLU* 2.5 44.8 + - - +
749D ILE* 1.3 72.1 - - - +
751D ARG* 1.3 86.4 + - - +
753D LEU* 3.4 1.8 + - - -
754D GLN* 3.0 63.3 + - - +
755D GLU* 2.7 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 751 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747D GLU* 3.1 29.7 + - - +
748D CYS* 3.8 4.9 - - - +
749D ILE 2.8 1.6 + - - -
750D ARG* 1.3 100.5 - - - +
752D MET* 1.3 58.4 + - - +
753D LEU 2.9 5.2 - - - -
755D GLU* 2.8 33.4 + - - +
756D GLY 3.4 7.9 + - - -
759D SER* 2.9 39.3 + - - +
760D LEU* 4.5 7.0 - - - +
762D GLU* 2.8 29.6 + - - -
763D TYR* 2.8 46.1 - - - +
766D GLU* 5.6 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 752 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696D LYS 4.7 0.3 - - - +
697D GLY* 3.5 2.7 - - - -
698D ILE* 2.7 49.2 + - + +
701D PHE* 4.7 10.8 - - + -
748D CYS 3.0 19.3 + - - +
749D ILE* 2.8 12.8 + - - +
751D ARG* 1.3 72.5 - - - +
753D LEU* 1.3 53.0 + - + +
756D GLY* 4.8 5.2 + - - +
760D LEU* 3.4 36.3 - - + +
880D LEU* 4.9 2.2 - - - -
883D PHE* 4.5 15.7 - - - -
884D THR* 3.6 29.6 - - + -
887D ALA* 4.2 7.6 - - + -
889D LEU* 3.2 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 753 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D PRO* 3.5 13.9 - - - +
692D PRO* 3.5 0.5 - - - +
697D GLY* 3.3 13.7 - - - -
698D ILE* 3.6 16.8 - - + -
699D GLY* 3.5 13.5 + - - +
700D GLY* 3.4 27.6 - - - +
701D PHE* 4.0 12.3 - - + -
709D ALA* 4.4 1.3 - - + +
710D LEU* 3.7 12.3 - - - +
711D ASN* 3.5 42.1 + - + +
725D LEU* 5.0 9.0 - - + -
749D ILE* 3.0 30.2 + - + +
750D ARG* 3.9 3.6 - - - +
751D ARG 2.9 0.8 - - - -
752D MET* 1.3 80.3 - - - +
754D GLN* 1.3 60.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 754 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692D PRO* 3.4 20.1 - - + +
695D SER* 3.3 22.3 - - - -
711D ASN* 3.6 26.0 + - - +
723D PRO* 4.3 19.4 + - + +
725D LEU* 4.4 12.5 - - - +
750D ARG* 3.0 53.1 + - - +
753D LEU* 1.3 83.2 - - + +
755D GLU* 1.3 68.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 755 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695D SER* 4.5 1.1 - - - -
696D LYS* 2.9 25.5 + - - +
697D GLY* 3.5 2.6 - - - +
750D ARG* 2.7 42.7 + - - -
751D ARG* 2.8 20.8 + - - +
754D GLN* 1.3 82.1 - - - +
756D GLY* 1.3 59.0 + - - +
758D GLU* 3.8 12.7 - - - +
759D SER* 2.5 37.6 + - - -
----------------------------------------------------------
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