Contacts of the helix formed by residues 745 - 753 (chain B) in PDB entry 5MJ6
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 PRO 745 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739B ALA* 4.3 0.2 - - - -
744B VAL* 1.3 92.2 - - + +
746B LEU* 1.3 64.1 + - - +
747B LYS* 3.6 45.3 - - + +
748B ARG* 2.9 43.8 + - + +
749B ALA 3.8 1.9 + - - -
1016B LYS* 5.8 5.4 - - - +
1017B ASN* 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 746 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B PHE* 4.8 10.3 - - + +
739B ALA* 3.7 21.8 - - + -
744B VAL 3.5 2.6 + - - -
745B PRO* 1.3 68.8 - - - +
747B LYS* 1.3 66.2 + - - +
749B ALA* 3.0 19.2 + - + +
750B PHE* 3.3 42.2 + - + -
775B ILE* 5.2 0.9 - - + -
1013B TRP* 4.2 23.6 - - + +
1017B ASN* 3.3 35.9 + - + +
1020B SER* 4.0 11.7 + - - +
1021B LEU* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 747 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B PRO* 3.6 32.0 - - + +
746B LEU* 1.3 72.2 - - - +
748B ARG* 1.3 58.7 + - + +
750B PHE* 3.0 23.3 + - - +
751B ASP* 3.1 26.2 + - - +
1020B SER* 4.9 6.8 + - - -
1024B TRP* 5.7 6.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 748 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B HIS* 4.6 1.6 - - - -
704B TYR 4.0 3.2 + - - -
706B ASP* 2.8 40.5 + - - +
709B TRP* 3.2 41.4 - - + +
713B ILE* 5.3 0.3 - - - +
735B ILE* 4.0 22.5 - - + +
744B VAL* 4.1 17.0 - - + +
745B PRO* 2.9 35.4 + - + +
747B LYS* 1.3 77.8 - - + +
749B ALA* 1.3 65.9 + - - +
751B ASP* 3.4 15.6 + - + +
752B LEU* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 749 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B ILE* 3.7 35.7 - - + +
736B PHE* 3.9 36.4 - - + -
739B ALA* 4.1 11.0 - - + +
745B PRO 3.8 1.2 + - - -
746B LEU* 3.0 14.5 + - + +
748B ARG* 1.3 78.2 - - - +
750B PHE* 1.3 61.3 + - + +
752B LEU* 3.4 11.3 + - - +
753B ILE* 3.5 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 750 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B PHE* 4.2 17.7 - + - -
746B LEU* 3.3 49.6 + - + -
747B LYS* 3.0 9.6 + - - +
749B ALA* 1.3 78.7 - - - +
751B ASP* 1.3 63.5 + - - +
752B LEU 3.2 1.5 + - - -
753B ILE* 3.7 26.0 - - + +
754B ASN* 3.7 20.3 + - - +
772B THR* 6.0 1.6 - - - -
775B ILE* 4.7 8.7 - - + -
791B LEU* 4.2 15.5 - - + -
795B VAL* 5.8 2.5 - - + -
1021B LEU* 3.6 17.5 - - + -
1024B TRP* 3.4 63.5 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 751 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B ILE* 3.4 17.8 - - + +
717B LYS* 3.2 15.4 + - - +
747B LYS* 3.1 28.2 + - - +
748B ARG* 3.6 16.8 - - + +
750B PHE* 1.3 77.3 - - - +
752B LEU* 1.3 62.4 + - - +
754B ASN* 3.2 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 752 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B TRP* 4.8 15.5 - - + -
712B LEU* 5.9 0.2 - - + -
713B ILE* 4.1 24.8 - - + +
716B LEU* 3.5 30.7 - - + +
717B LYS* 5.3 0.2 - - - -
731B LEU* 3.7 10.5 - - + +
732B ILE* 3.6 42.6 - - + +
735B ILE* 3.7 19.3 - - + -
748B ARG 3.2 10.6 + - - +
749B ALA 3.4 8.7 + - - +
750B PHE 3.2 0.8 - - - -
751B ASP* 1.3 76.4 - - - +
753B ILE* 1.3 58.5 + - + +
754B ASN 3.0 9.7 + - - -
755B TYR* 3.2 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 753 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B ILE* 4.1 24.9 - - + -
736B PHE* 3.7 29.4 - - + -
749B ALA 3.5 5.6 + - - +
750B PHE* 3.7 38.8 - - + +
752B LEU* 1.3 75.2 - - + +
754B ASN* 1.3 56.1 + - - +
755B TYR* 3.0 7.6 - - - -
756B LEU* 3.1 34.2 + - + +
768B ALA* 4.8 6.1 - - + -
772B THR* 5.3 4.0 - - - +
795B VAL* 4.9 13.0 - - + -
798B LEU* 3.2 30.7 - - + +
1024B TRP* 5.3 3.1 - - + -
----------------------------------------------------------
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