Contacts of the helix formed by residues 742 - 754 (chain Z) in PDB entry 5L4K
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 742 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704Z LEU* 3.4 35.9 - - + +
705Z ASN* 3.7 15.0 - - - +
738Z ASN* 3.1 16.9 + - - +
741Z LEU* 1.3 75.6 - - + +
743Z ALA* 1.3 61.8 + - - +
744Z MET 3.3 2.6 + - - -
745Z LEU* 3.7 13.9 + - + +
746Z ARG* 3.0 24.6 + - - +
789Z SER* 4.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 743 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733Z GLY* 5.1 2.0 - - - +
737Z ASN* 3.7 21.5 - - - +
738Z ASN* 3.3 9.4 - - - +
739Z ALA 4.3 0.2 - - - +
740Z ARG* 4.0 16.1 - - + -
741Z LEU 3.6 0.4 - - - -
742Z ALA* 1.3 78.3 - - - +
744Z MET* 1.3 59.3 + - - +
745Z LEU 3.5 0.2 - - - -
746Z ARG* 3.3 25.9 + - - +
747Z GLN* 3.8 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 744 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369Z ARG* 3.6 40.2 - - + +
370Z MET* 5.1 1.8 - - - +
372Z LEU* 3.9 34.1 - - + -
373Z ALA* 3.7 22.2 - - + +
376Z PHE* 5.8 2.7 - - + -
740Z ARG* 3.0 26.2 + - + +
741Z LEU 3.7 6.5 - - - +
743Z ALA* 1.3 78.0 - - - +
745Z LEU* 1.3 83.5 + - - +
747Z GLN* 3.4 8.6 - - - +
748Z LEU* 3.0 32.0 + - + +
794Z ALA* 4.8 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 745 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369Z ARG* 5.6 2.0 - - - +
704Z LEU 5.1 0.2 - - - +
705Z ASN* 3.1 48.7 - - + +
708Z ASP* 3.2 37.6 - - + +
741Z LEU 3.9 14.4 - - - +
742Z ALA* 3.7 9.1 + - + +
743Z ALA 3.5 0.4 - - - -
744Z MET* 1.3 94.2 - - - +
746Z ARG* 1.3 60.2 + - + +
748Z LEU* 3.2 17.1 + - + +
749Z ALA 2.8 26.3 + - - -
787Z LEU* 5.0 9.0 - - + -
788Z MET 6.5 0.4 - - - -
789Z SER* 4.3 2.0 - - - +
794Z ALA* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 746 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699Z VAL 5.9 1.6 + - - -
704Z LEU* 4.9 15.1 + - - +
707Z LEU* 4.5 18.7 - - + +
708Z ASP* 4.8 5.6 - - - +
726Z ILE* 3.8 19.0 - - - +
729Z MET* 3.5 51.1 + - + +
732Z VAL* 4.2 10.5 + - - +
733Z GLY* 3.4 34.9 + - - +
736Z THR 5.0 1.2 + - - -
738Z ASN* 3.5 21.0 - - - +
742Z ALA* 3.0 16.3 + - - +
743Z ALA* 3.3 30.7 - - - +
744Z MET 3.4 0.4 - - - -
745Z LEU* 1.3 77.6 - - + +
747Z GLN* 1.3 63.7 + - - +
749Z ALA* 3.6 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 747 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363Z SER* 4.5 9.9 + - - -
370Z MET* 5.8 7.7 - - + +
373Z ALA* 4.0 18.2 - - + -
374Z SER* 6.2 0.4 - - - +
377Z VAL* 4.1 10.9 - - + +
726Z ILE* 5.7 0.4 - - - -
743Z ALA 3.8 11.6 + - - +
744Z MET* 3.4 12.0 + - - +
746Z ARG* 1.3 77.3 - - - +
748Z LEU* 1.3 70.1 + - - +
750Z GLN* 3.0 22.8 + - - +
751Z TYR* 4.1 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 748 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373Z ALA* 4.6 7.9 - - + +
376Z PHE* 4.0 38.4 - - + -
377Z VAL* 4.7 9.0 - - - -
380Z PHE* 4.1 11.2 - - + -
708Z ASP* 4.8 5.2 - - - +
712Z LYS* 5.2 4.3 - - + -
744Z MET* 3.0 15.0 + - - +
745Z LEU* 3.5 33.2 - - + +
747Z GLN* 1.3 82.7 - - - +
749Z ALA* 1.3 68.6 + - - +
750Z GLN 3.0 0.7 + - - -
751Z TYR* 3.2 2.4 + - - +
752Z HIS* 3.0 43.2 + - + -
800Z LEU* 5.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 749 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708Z ASP* 3.4 14.8 - - - +
711Z SER* 4.0 24.6 - - - +
712Z LYS* 4.4 8.8 - - + +
726Z ILE* 4.3 4.4 - - + +
745Z LEU 2.8 17.7 + - - +
746Z ARG* 3.6 11.7 - - - +
747Z GLN 3.0 0.4 + - - -
748Z LEU* 1.3 83.7 - - - +
750Z GLN* 1.3 57.2 + - - +
752Z HIS* 4.2 3.3 - - - +
753Z ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 750 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719Z PRO* 3.6 27.1 - - - +
722Z SER 3.9 5.4 + - - +
723Z TYR* 4.0 15.6 - - - +
726Z ILE* 3.1 41.0 - - + +
727Z PHE* 4.9 7.3 + - + -
746Z ARG 3.9 1.4 + - - -
747Z GLN* 3.0 14.7 + - - +
749Z ALA* 1.3 79.2 - - - +
751Z TYR* 1.3 80.2 + - + +
753Z ALA* 3.1 18.9 - - - +
754Z LYS* 3.3 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 751 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361Z SER* 5.9 2.9 - - - -
363Z SER* 5.0 3.9 + - - -
377Z VAL* 3.6 42.6 - - + -
380Z PHE* 3.5 26.7 - - + +
381Z VAL* 4.5 20.6 - - + +
747Z GLN* 4.1 17.3 + - - -
748Z LEU 3.2 2.1 + - - +
750Z GLN* 1.3 93.4 - - + +
752Z HIS* 1.3 62.2 + - - +
753Z ALA 3.0 0.9 - - - -
754Z LYS* 2.6 56.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 752 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380Z PHE* 3.3 39.8 - - + -
680Z ARG* 3.1 33.9 + - - -
712Z LYS* 3.7 34.2 + - + +
715Z HIS* 4.6 4.1 + + - -
748Z LEU* 3.0 27.4 + - + +
749Z ALA* 4.2 2.0 - - - +
751Z TYR* 1.3 75.8 - - - +
753Z ALA* 1.3 66.2 + - - +
754Z LYS 4.0 1.9 - - - +
755Z ASP* 4.8 3.5 - - - +
762Z VAL* 5.9 1.2 - - - +
800Z LEU* 3.6 40.1 + - + +
803Z PHE* 4.7 3.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 753 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711Z SER 4.5 2.9 - - - +
715Z HIS* 2.6 62.9 + - + -
717Z ALA* 3.3 9.0 - - - +
719Z PRO* 5.5 0.4 - - + -
722Z SER* 5.1 0.4 - - - +
726Z ILE* 5.1 3.8 - - + -
749Z ALA 2.9 23.2 + - - +
750Z GLN* 3.1 12.8 - - - +
751Z TYR 3.0 0.2 - - - -
752Z HIS* 1.3 80.5 - - - +
754Z LYS* 1.3 58.2 + - + +
755Z ASP* 4.5 2.4 - - - +
761Z MET* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 754 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380Z PHE 4.7 1.6 - - - +
381Z VAL* 5.8 0.6 - - - -
717Z ALA* 3.0 24.9 - - - +
718Z ASP* 4.0 2.9 - - + -
719Z PRO* 3.6 20.6 - - + +
723Z TYR* 3.7 27.3 + - - -
750Z GLN* 3.3 24.5 - - - +
751Z TYR* 2.6 55.9 + - + +
752Z HIS 4.0 0.7 - - - +
753Z ALA* 1.3 75.0 - - - +
755Z ASP* 1.3 80.0 + - - +
756Z PRO* 5.9 1.6 - - + -
----------------------------------------------------------
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