Contacts of the strand formed by residues 1047 - 1054 (chain C) in PDB entry 6VSB
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 TYR1047 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A TRP* 3.4 35.6 + + - -
887A THR* 4.3 13.4 - - - +
890A ALA* 3.8 22.2 - - + -
909C ILE* 4.1 41.1 - - + -
1046C GLY* 1.3 70.0 - - - -
1048C HIS* 1.3 66.6 + - - +
1049C LEU* 3.3 2.4 + - - +
1066C THR* 3.2 2.7 - - - -
1067C TYR* 2.9 56.9 + + - +
1069C PRO* 4.3 14.8 - - + -
1108C ASN* 4.2 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1048 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909C ILE* 3.6 6.5 - - - +
1032C CYS* 3.1 39.5 - - + +
1035C GLY 4.3 2.0 - - - -
1036C GLN* 3.5 23.7 + - - +
1037C SER* 3.2 40.7 + - - +
1038C LYS 6.0 0.2 - - - -
1039C ARG 5.7 4.0 - - - +
1043C CYS* 3.4 36.7 - - + +
1044C GLY 5.7 0.2 - - - +
1046C GLY 3.5 5.0 + - - +
1047C TYR* 1.3 70.8 - - - +
1049C LEU* 1.3 61.1 + - - +
1050C MET* 3.5 14.2 + - - -
1051C SER* 3.1 23.7 + - - -
1064C HIS* 4.8 0.4 - - + -
1065C VAL 4.4 2.5 - - - -
1066C THR* 3.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1049 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720C ILE* 4.7 7.4 - - + -
902C MET* 4.2 20.0 - - + -
905C ARG* 2.8 46.3 + - + +
906C PHE* 3.4 42.6 - - + -
909C ILE* 3.6 33.0 - - + -
1036C GLN* 4.0 4.0 - - - +
1047C TYR 3.3 0.4 + - - +
1048C HIS* 1.3 77.1 - - - +
1050C MET* 1.3 62.4 + - + +
1065C VAL* 3.0 15.7 + - + +
1066C THR* 4.0 4.5 - - - +
1067C TYR* 3.7 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1050 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881C THR* 5.0 5.2 - - - +
898C PHE* 3.7 28.5 - - + -
901C GLN* 4.4 13.7 - - - +
902C MET* 3.4 33.0 - - + +
905C ARG* 3.8 14.8 - - - +
927C PHE* 4.4 8.3 - - - -
1032C CYS 4.5 0.2 - - - -
1048C HIS* 3.5 8.4 + - - -
1049C LEU* 1.3 81.1 - - - +
1051C SER* 1.3 70.1 + - - +
1052C PHE* 3.3 33.9 - - + -
1065C VAL* 2.9 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1051 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881C THR* 4.3 6.8 + - - +
1032C CYS 3.6 18.8 + - - -
1033C VAL* 3.8 28.5 + - - +
1048C HIS* 3.1 6.0 + - - -
1050C MET* 1.3 82.2 + - - +
1052C PHE* 1.3 76.6 + - - +
1062C PHE* 4.9 1.1 - - - -
1063C LEU 3.1 9.4 - - - -
1064C HIS* 2.4 40.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1052 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722C VAL* 6.0 0.2 - - + -
802C PHE* 3.5 16.8 - + - -
805C ILE* 4.1 12.6 - - + -
878C LEU* 3.2 30.3 - - + -
881C THR* 3.8 10.3 - - + -
882C ILE* 3.9 20.2 - - + -
927C PHE* 4.1 12.6 - + - -
1050C MET* 3.3 46.2 - - + -
1051C SER* 1.3 81.2 - - - +
1053C PRO* 1.3 69.0 - - - +
1054C GLN* 5.4 0.9 - - - +
1062C PHE* 3.6 4.9 - - - -
1063C LEU* 3.0 53.8 + - + +
1065C VAL* 4.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1053 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874C THR* 4.1 19.6 - - + +
877C LEU* 4.0 35.0 - - + +
878C LEU* 4.8 3.3 - - - +
881C THR* 5.6 0.2 - - + -
1029C MET* 4.2 12.3 - - + -
1033C VAL* 3.7 23.6 - - + -
1052C PHE* 1.3 88.0 - - + +
1054C GLN* 1.3 78.6 + - - +
1060C VAL* 4.4 6.1 - - + -
1061C VAL 3.7 4.3 - - - +
1062C PHE* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1054 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805C ILE* 3.4 26.7 + - - +
816C SER* 3.1 19.9 + - - -
818C ILE* 3.6 20.3 - - + +
819C GLU* 3.1 21.9 + - + +
822C LEU* 4.3 11.7 - - + -
874C THR* 4.2 7.0 + - - -
878C LEU* 3.9 11.1 - - - +
1052C PHE* 5.4 0.4 - - - +
1053C PRO* 1.3 91.3 + - - +
1055C SER* 1.3 69.9 + - - +
1060C VAL* 3.7 7.4 - - - +
1061C VAL* 2.7 35.9 + - + +
1063C LEU* 3.4 28.9 - - + -
----------------------------------------------------------
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