Contacts of the helix formed by residues 756 - 768 (chain N) 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 HIS 756 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254N GLU 4.4 13.7 - - - +
255N SER 4.6 1.8 - - - +
256N ALA 5.1 4.3 - - - +
257N SER* 5.0 2.2 - - - +
258N GLN* 6.3 0.2 - - - +
747N SER 3.5 15.4 + - - -
748N LEU 3.1 21.5 + - - +
749N GLN 3.8 7.4 - - - -
750N SER* 3.4 21.4 + - - +
751N ARG* 5.4 5.2 - - - -
754N HIS* 3.2 14.2 + - - +
755N THR* 1.3 72.2 - - - +
757N MET* 1.3 64.5 + - - +
758N PRO* 3.5 12.8 - - + -
759N SER* 3.3 29.9 + - - -
760N VAL* 3.4 12.4 + - - +
781N LEU 5.1 2.7 + - - -
782N ALA* 5.6 0.8 + - - -
784N THR* 5.8 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 757 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257N SER* 3.6 28.6 + - - +
258N GLN* 5.5 2.2 - - - +
486N MET* 4.6 2.2 - - + -
521N LEU* 3.9 24.5 - - + -
522N GLY* 6.1 1.8 - - - -
557N TYR* 3.2 45.3 - - + +
754N HIS* 4.0 8.1 - - + +
755N THR* 3.2 23.8 - - + +
756N HIS* 1.3 68.4 - - - +
758N PRO* 1.3 75.0 - - + +
759N SER 3.0 2.7 + - - -
760N VAL* 3.1 3.4 + - - +
761N VAL* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 758 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257N SER* 6.3 0.7 - - - -
258N GLN* 3.9 32.5 - - - +
452N ASN* 3.9 19.5 - - - +
486N MET* 4.1 11.7 - - + -
756N HIS* 3.5 15.3 - - + -
757N MET* 1.3 95.2 - - + +
759N SER* 1.3 56.0 + - - +
761N VAL* 3.9 1.4 + - - +
762N GLY 2.9 18.4 + - - -
781N LEU* 3.2 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 759 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747N SER 3.5 15.2 + - - -
748N LEU* 3.5 20.0 - - - +
756N HIS* 3.3 29.3 + - - -
757N MET 3.1 0.8 - - - -
758N PRO* 1.3 78.9 - - - +
760N VAL* 1.3 58.9 + - - +
762N GLY* 2.7 18.4 + - - -
763N VAL* 3.0 15.1 + - - +
781N LEU 3.5 6.4 + - - -
782N ALA* 2.9 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 760 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554N LEU* 6.4 0.7 - - + -
557N TYR* 3.4 32.5 - - + +
588N MET* 4.4 15.5 - - + -
591N CYS* 6.3 2.0 - - - -
624N PHE* 4.0 22.9 - - + -
748N LEU* 4.6 17.3 - - + +
755N THR* 3.4 26.2 - - - +
756N HIS 3.4 14.6 - - - +
757N MET* 3.1 2.8 + - - +
759N SER* 1.3 76.4 - - - +
761N VAL* 1.3 62.6 + - + +
763N VAL* 3.5 3.8 + - - +
764N LEU* 3.0 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 761 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483N LEU* 6.3 0.2 - - + -
486N MET* 4.1 14.4 - - + -
518N LEU* 4.1 20.6 - - + -
521N LEU* 3.6 28.0 - - + -
554N LEU* 3.9 17.0 - - + -
557N TYR* 4.1 9.2 - - - +
757N MET 3.0 15.3 + - - +
758N PRO 4.3 1.3 - - - +
760N VAL* 1.3 75.8 - - + +
762N GLY* 1.3 63.3 + - - +
764N LEU* 4.1 6.3 - - - -
765N VAL* 2.9 48.8 + - + +
778N PHE* 4.9 6.3 - - + -
781N LEU* 5.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 762 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758N PRO 2.9 15.9 + - - -
759N SER 2.7 16.7 + - - -
761N VAL* 1.3 73.5 - - - +
763N VAL* 1.3 59.3 + - - -
766N PHE* 3.7 11.4 + - - +
778N PHE* 2.8 37.5 - - - +
779N LEU* 3.7 3.4 - - - +
781N LEU* 4.2 2.7 - - - -
782N ALA* 4.1 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 763 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624N PHE* 4.7 3.6 - - + -
658N ILE* 3.8 37.4 - - + +
693N LEU* 4.9 10.3 - - + -
746N ILE* 4.1 24.9 - - + -
748N LEU* 3.9 16.2 - - + -
759N SER 3.0 11.9 + - - +
760N VAL 3.9 4.0 - - - +
762N GLY* 1.3 74.0 - - - +
764N LEU* 1.3 63.3 + - - +
765N VAL 3.6 0.2 - - - -
766N PHE* 4.1 3.6 - - + -
767N THR* 3.4 24.5 + - - +
779N LEU* 3.5 24.9 - - + -
782N ALA* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 764 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550N VAL* 5.4 2.2 - - + -
553N ALA* 6.3 2.0 - - + -
554N LEU* 3.9 27.1 - - + -
584N TYR* 4.0 21.1 - - + +
588N MET* 3.5 31.6 - - + -
620N GLU* 4.2 8.1 - - - +
624N PHE* 3.6 17.9 - - + -
658N ILE* 6.0 0.2 - - + -
760N VAL* 3.0 20.7 + - + +
761N VAL* 3.1 7.6 + - - +
763N VAL* 1.3 80.7 - - - +
765N VAL* 1.3 66.1 + - + +
766N PHE 3.7 0.3 + - - -
767N THR* 4.6 1.8 - - - -
768N GLN* 3.4 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 765 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514N LEU* 4.3 29.6 - - + -
550N VAL* 4.5 13.9 - - + -
554N LEU* 4.6 5.8 - - + -
761N VAL* 2.9 34.5 + - + +
764N LEU* 1.3 83.5 - - + +
766N PHE* 1.3 60.2 + - - +
768N GLN* 3.8 12.2 - - + +
775N LEU* 2.9 30.6 - - + +
778N PHE* 3.3 36.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 766 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375N PHE* 4.6 6.7 - + - -
654N MET* 5.1 2.2 - - + -
689N ILE* 3.8 36.8 - - + -
693N LEU* 4.3 14.1 - - + -
732N LEU* 4.0 21.5 - - + -
736N ILE* 5.1 0.9 - - + -
762N GLY 3.7 19.3 + - - +
763N VAL* 4.5 2.7 - - + -
764N LEU 3.4 0.4 - - - -
765N VAL* 1.3 75.7 - - - +
767N THR* 1.3 90.3 + - - +
768N GLN 3.0 7.0 + - - +
769N PHE* 3.4 32.4 - + - -
775N LEU 3.4 6.7 - - - +
776N SER* 4.2 18.4 - - - -
778N PHE* 4.3 0.9 - - - +
779N LEU* 3.8 48.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 767 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620N GLU* 4.1 20.2 - - + +
650N TYR* 3.8 10.9 + - - +
654N MET* 2.9 54.0 - - + +
658N ILE* 4.1 8.9 - - + +
693N LEU* 5.0 1.0 - - - +
763N VAL* 3.4 18.2 + - - +
764N LEU* 4.6 2.9 - - - -
766N PHE* 1.3 88.5 - - - +
768N GLN* 1.3 58.1 + - - +
769N PHE* 3.0 22.2 + - - -
770N TRP* 4.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 768 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514N LEU* 5.6 0.3 - - - +
546N ARG* 4.3 7.3 + - - +
550N VAL* 3.4 32.4 - - - +
584N TYR* 3.1 27.1 + - - +
620N GLU* 4.9 2.2 - - - +
764N LEU* 3.4 28.9 + - - +
765N VAL* 3.8 12.5 - - - +
766N PHE 3.0 9.4 - - - +
767N THR* 1.3 76.7 - - - +
769N PHE* 1.3 62.5 + - - +
770N TRP* 3.1 46.9 - - + +
775N LEU* 3.4 25.8 - - + +
----------------------------------------------------------
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