Contacts of the helix formed by residues 783 - 794 (chain N) in PDB entry 5D4D
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 ARG 783 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684M PHE* 3.5 17.5 - - + -
685M GLU* 3.3 36.5 + - + +
874M LEU* 3.6 12.8 - - + -
1201M CTP 4.3 11.9 + - - -
782N SER* 1.3 80.1 - - - +
784N ASP* 1.3 73.6 + - - +
785N ILE 3.2 0.5 + - - -
786N ILE* 3.3 9.0 + - - +
787N LEU* 2.9 27.2 + - - +
1027N GLY 4.4 6.1 + - - -
1028N ALA* 2.7 46.6 + - - +
1029N ARG* 3.6 41.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 784 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678M PRO* 3.7 14.1 - - - +
681M GLY* 5.2 1.6 + - - -
683M ASN* 3.8 4.9 - - - +
684M PHE* 3.4 23.4 - - - -
685M GLU 4.4 1.0 + - - -
872M ASN* 2.3 33.1 + - - -
874M LEU* 3.1 16.9 - - - +
782N SER 3.1 0.8 + - - -
783N ARG* 1.3 80.8 - - - +
785N ILE* 1.3 57.4 + - - +
787N LEU* 3.2 6.6 + - - +
788N GLY 2.9 24.6 + - - -
938N GLY 3.7 0.9 - - - +
939N PHE* 3.5 24.6 - - + -
942N SER* 3.5 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 785 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684M PHE* 5.2 1.6 - - + -
730N PRO* 5.1 3.4 - - + -
731N LEU* 3.7 30.1 - - + -
781N PRO* 3.9 13.9 - - + -
782N SER* 3.1 17.2 + - - +
784N ASP* 1.3 72.9 - - - +
786N ILE* 1.3 66.0 + - - +
788N GLY 3.2 1.6 + - - -
789N LEU* 3.0 32.9 + - + +
934N LEU 3.3 29.6 - - - +
935N LYS* 3.7 25.8 - - + +
938N GLY* 3.6 8.6 - - - -
939N PHE* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 786 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781N PRO* 3.6 24.0 - - + +
782N SER* 3.6 24.6 + - - +
783N ARG 3.3 7.3 + - - +
785N ILE* 1.3 75.5 - - - +
787N LEU* 1.3 65.6 + - - +
789N LEU* 3.2 0.3 + - - +
790N TYR* 2.8 23.9 + - - +
906N GLN 4.5 0.2 - - - +
907N GLU* 4.3 6.5 - - - -
908N LYS* 3.7 35.2 - - + +
911N LEU* 4.2 13.2 - - + -
1026N SER* 3.3 36.8 - - - +
1027N GLY 3.9 13.7 - - - +
1028N ALA* 4.1 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 787 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678M PRO* 4.3 15.3 - - + -
874M LEU* 4.1 24.2 - - + -
783N ARG 2.9 15.4 + - - +
784N ASP* 3.3 10.1 - - - +
785N ILE 3.1 0.2 - - - -
786N ILE* 1.3 76.9 - - - +
788N GLY* 1.3 57.5 + - - +
790N TYR* 3.8 3.6 - - - +
791N TYR* 2.9 31.0 + - + +
942N SER* 4.6 5.4 - - - -
947N ILE* 3.8 38.8 - - + -
1022N VAL* 3.7 29.2 - - + -
1023N MET* 4.0 17.3 - - + -
1026N SER* 4.6 1.1 - - - +
1028N ALA* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 788 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784N ASP 2.9 10.7 + - - -
785N ILE 3.2 0.2 + - - -
787N LEU* 1.3 75.0 - - - +
789N LEU* 1.3 63.7 + - - +
791N TYR* 3.2 3.9 + - - +
792N ILE* 3.0 28.4 + - - +
938N GLY* 3.4 21.5 - - - -
941N PHE* 3.9 6.7 - - - +
942N SER* 3.6 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 789 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781N PRO* 5.1 0.2 - - + -
785N ILE* 3.0 28.5 + - + +
786N ILE 3.9 1.8 - - - +
788N GLY* 1.3 74.1 - - - +
790N TYR* 1.3 64.1 + - - +
792N ILE* 3.2 20.1 - - + +
793N THR* 2.9 28.6 + - - +
882N PHE* 3.8 23.6 - - + -
885N ILE* 4.6 9.9 - - + -
906N GLN* 4.3 8.3 - - + -
911N LEU* 4.2 22.7 - - + -
934N LEU* 3.7 40.6 - - + +
937N TYR* 4.8 2.5 - - + -
938N GLY* 4.0 14.1 - - - +
941N PHE* 5.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 790 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786N ILE 2.8 19.4 + - - +
787N LEU 3.8 2.5 - - - +
789N LEU* 1.3 72.4 - - - +
791N TYR* 1.3 69.2 + - - +
793N THR* 3.1 3.5 + - - -
794N GLN* 3.0 52.6 + - + +
905N PRO* 4.0 18.4 - - + -
906N GLN 3.2 31.4 + - - +
907N GLU* 4.2 5.4 - - + -
1016N PRO 5.3 3.5 + - - -
1017N PHE* 6.0 1.3 - + - -
1021N TYR* 5.5 3.1 - - - -
1022N VAL* 3.8 39.5 - - + +
1025N GLN* 4.0 26.0 + - + +
1026N SER* 3.5 31.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 791 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946M ARG* 3.3 13.5 + - - -
984M GLU* 2.5 31.1 + - - +
787N LEU 2.9 20.0 + - - +
788N GLY* 3.2 6.5 + - - +
790N TYR* 1.3 82.9 - - + +
792N ILE* 1.3 73.8 + - + +
794N GLN* 3.8 5.4 + - - +
860N LEU* 6.3 0.7 - - + -
861N GLN* 3.1 42.6 + - - +
941N PHE* 4.5 4.9 - - + -
944N THR* 5.9 0.2 - - - -
945N SER* 3.3 51.5 + - - -
947N ILE* 5.0 13.7 - - + -
1017N PHE* 5.2 16.7 - + - -
1022N VAL* 5.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 792 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788N GLY 3.0 14.9 + - - +
789N LEU* 3.2 25.6 - - + +
791N TYR* 1.3 88.7 - - + +
793N THR* 1.3 64.8 + - + +
794N GLN 3.5 2.2 + - - +
860N LEU* 4.1 24.3 - - + +
861N GLN* 3.9 6.5 - - - +
876N SER* 4.5 0.7 + - - -
878N GLY* 3.3 36.7 - - - +
881N LEU* 4.5 9.6 - - + -
882N PHE* 4.8 2.5 - - + -
885N ILE* 4.7 4.3 - - + -
941N PHE* 3.4 54.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 793 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789N LEU 2.9 22.3 + - - +
790N TYR* 3.1 4.0 + - - -
792N ILE* 1.3 84.7 - - + +
794N GLN* 1.3 59.3 + - - +
795N VAL* 5.1 0.4 - - - -
876N SER* 5.1 0.4 - - - -
878N GLY 4.3 3.8 - - - +
879N ARG* 2.9 43.9 + - + -
882N PHE* 3.8 26.5 - - + -
904N VAL 4.8 1.1 - - - -
905N PRO* 3.7 5.8 - - - +
906N GLN* 2.8 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 794 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790N TYR* 3.0 47.6 + - + +
791N TYR 3.8 2.6 + - - +
792N ILE 3.5 1.0 - - - +
793N THR* 1.3 79.7 - - - +
795N VAL* 1.3 94.9 + - - +
861N GLN* 3.1 31.0 - - - +
876N SER* 5.3 0.2 + - - -
879N ARG* 4.2 1.9 + - - -
905N PRO* 3.4 28.5 - - + +
1016N PRO* 5.8 2.9 - - + +
1017N PHE* 3.9 26.6 - - + -
----------------------------------------------------------
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