Contacts of the strand formed by residues 861 - 868 (chain F) in PDB entry 3N1Q
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 GLY 861 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859F ILE* 3.2 10.9 - - - +
860F GLN* 1.3 75.1 - - - +
862F PHE* 1.3 60.6 + - - -
882F VAL 5.2 1.1 - - - -
883F GLU 2.3 28.7 - - - -
884F GLY* 3.8 2.9 - - - -
906F CYS* 3.4 1.7 - - - -
907F PHE* 2.8 39.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 862 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830F PRO* 4.2 8.1 - - + -
847F TRP* 3.7 26.0 - + + -
849F TYR* 4.5 18.6 - + + -
859F ILE* 4.6 7.4 - - + -
861F GLY* 1.3 74.6 - - - -
863F TYR* 1.3 59.7 + - - +
864F ILE* 3.9 8.9 - - + +
880F ASP 3.5 10.7 - - - +
881F VAL* 3.5 2.1 - - - -
882F VAL* 3.5 17.6 + - + +
883F GLU 3.2 14.0 + - - -
884F GLY* 3.7 26.7 - - - -
885F SER 5.0 0.7 - - - -
886F LYS 3.3 19.1 - - - -
887F GLN* 6.2 0.9 - - + -
904F MET* 3.6 28.3 - - + -
905F GLN 3.6 2.2 - - - -
906F CYS* 3.4 32.8 - - + -
907F PHE* 3.3 12.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 863 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862F PHE* 1.3 73.4 - - - +
864F ILE* 1.3 61.7 + - - +
865F TYR* 3.4 31.5 - - + -
879F ARG* 3.2 39.2 + - + -
880F ASP 3.7 0.7 - - - -
881F VAL* 3.8 16.6 - - + -
904F MET* 3.1 8.8 - - - +
905F GLN* 2.8 44.4 + - + +
907F PHE* 3.2 63.7 - + + -
912F GLU* 3.7 14.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 864 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845F LEU* 4.2 21.1 - - + -
847F TRP* 4.3 6.1 - - + -
862F PHE* 3.9 22.0 - - + +
863F TYR* 1.3 79.2 - - - +
865F TYR* 1.3 65.3 + - - +
866F TYR* 3.6 6.6 - - + -
878F LYS 3.6 0.3 - - - +
879F ARG* 3.4 3.4 - - - -
880F ASP* 3.0 42.8 + - + +
882F VAL* 4.2 17.9 - - + -
889F HIS* 4.1 16.6 - - + +
891F ILE* 3.5 32.1 - - + -
902F ILE* 4.6 2.0 - - + -
903F LYS 4.1 2.7 - - - +
904F MET* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 865 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863F TYR* 3.4 23.4 - - + +
864F ILE* 1.3 73.7 - - - +
866F TYR* 1.3 60.6 + - - +
877F TYR* 3.4 34.1 - + + -
878F LYS 3.0 19.3 - - - +
879F ARG* 3.1 43.6 + - + -
901F ASP 3.5 0.3 - - - +
902F ILE* 3.4 8.8 - - - +
903F LYS* 2.9 40.9 + - + +
905F GLN* 2.9 30.3 + - + -
915F PHE* 3.5 28.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 866 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864F ILE 3.6 13.7 - - - -
865F TYR* 1.3 74.7 - - - +
867F ARG* 1.3 61.6 + - - +
868F PRO* 4.9 0.3 - - - +
876F ASP 4.0 0.5 - - - +
877F TYR* 3.8 1.8 - - - -
878F LYS* 2.9 64.2 + - + +
880F ASP* 2.7 45.6 + - + -
891F ILE* 3.7 42.9 - - + +
892F GLY 5.1 3.2 + - - -
894F LEU* 4.1 18.6 - - + -
900F TYR* 4.9 12.1 - + + -
901F ASP 3.0 10.5 - - - +
902F ILE* 4.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 867 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E LYS* 3.4 4.8 - - - +
90E GLU* 3.1 22.6 - - - +
866F TYR* 1.3 75.7 - - - +
868F PRO* 1.3 77.9 - - + +
869F THR 3.2 0.2 + - - -
871F SER* 3.1 23.3 + - - -
872F ASP* 3.6 3.4 - - - +
873F ASN 2.6 55.7 + - - +
874F ASP* 3.1 12.3 + - - -
876F ASP* 3.2 20.9 - - + +
877F TYR* 3.0 36.1 + - + -
900F TYR* 3.3 8.8 - - - -
901F ASP* 2.6 63.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 868 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866F TYR 4.9 0.2 - - - +
867F ARG* 1.3 102.0 - - + +
869F THR* 1.3 57.6 + - - +
870F ASP* 2.8 15.0 - - + +
871F SER* 2.9 31.2 + - - +
876F ASP* 4.1 7.4 - - + +
898F THR* 5.6 4.0 - - + -
899F SER 3.8 7.0 - - - +
900F TYR* 4.4 12.5 - - + -
901F ASP* 3.7 0.9 - - - +
----------------------------------------------------------
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