Contacts of the strand formed by residues 940 - 945 (chain B) in PDB entry 4E5W
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 TYR 940 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868B THR* 4.4 16.9 + - + -
926B ILE* 4.1 12.3 - - + +
929B LEU* 3.9 29.0 + - + +
930B ARG* 3.6 54.1 - - + +
932B LEU 5.8 1.9 + - - +
938B VAL 3.6 4.2 + - - -
939B LYS* 1.3 77.6 - - - +
941B LYS* 1.3 64.0 + - - +
942B GLY* 3.4 38.9 - - - -
943B ILE* 3.8 12.8 + - - +
954B LEU* 3.7 22.9 - - + -
955B ILE 4.0 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 941 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867B PRO 4.4 1.4 - - - +
868B THR* 3.6 23.0 - - - +
870B PHE* 3.7 13.2 - - + -
903B GLU* 3.2 41.1 + - - -
904B GLN 5.4 0.7 - - - +
905B VAL* 3.8 12.3 - - + -
939B LYS* 3.6 2.9 + - + +
940B TYR* 1.3 80.4 - - - +
942B GLY* 1.3 56.7 + - - +
955B ILE* 2.8 25.7 + - + +
956B MET 3.6 5.6 - - - +
957B GLU* 3.5 39.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 942 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868B THR 3.1 14.1 - - - -
870B PHE* 3.9 2.9 - - - -
940B TYR* 3.4 21.0 - - - -
941B LYS* 1.3 79.9 - - - +
943B ILE* 1.3 69.8 + - - +
954B LEU* 4.1 0.2 - - - -
955B ILE* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 943 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868B THR* 2.8 14.0 + - - +
869B HIS* 3.7 7.3 + - - +
870B PHE* 2.9 24.8 + - - -
926B ILE* 3.7 31.4 - - + -
940B TYR* 3.8 9.9 - - - +
942B GLY* 1.3 79.1 - - - +
944B CYS* 1.3 60.8 + - - +
945B THR* 3.7 25.9 + - + -
952B ILE* 3.9 18.6 - - + -
953B LYS 3.3 12.8 - - - +
955B ILE* 4.0 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 944 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870B PHE 3.3 21.1 - - - +
872B LYS* 3.6 40.8 - - - -
875B LEU* 4.2 12.3 - - + -
943B ILE* 1.3 73.9 - - - +
945B THR* 1.3 65.0 + - - +
946B GLU* 4.1 3.1 + - - +
952B ILE* 3.3 4.4 - - - -
953B LYS* 2.9 58.0 + - + +
955B ILE* 4.3 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 945 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869B HIS* 4.0 24.0 + - - +
870B PHE 4.5 1.0 + - - -
872B LYS* 5.6 2.4 + - - +
943B ILE* 3.7 29.5 + - + -
944B CYS* 1.3 79.6 - - - +
946B GLU* 1.3 64.6 + - - +
951B GLY 3.7 6.5 - - - +
952B ILE* 4.1 13.5 - - + -
----------------------------------------------------------
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