Contacts of the strand formed by residues 930 - 936 (chain E) in PDB entry 3EI4
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 VAL 930 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922E LEU* 3.9 11.4 - - + -
923E VAL 3.2 9.4 - - - +
924E GLY* 4.5 1.8 - - - -
929E SER* 1.3 84.9 - - - +
931E LEU* 1.3 62.5 + - - +
947E ARG* 3.9 1.7 - - - +
948E ASP* 2.9 32.2 + - + +
954E MET* 4.3 10.5 - - + -
957E VAL* 3.5 30.3 - - + -
965E PHE* 5.3 2.9 - - + -
966E LEU 5.9 0.4 - - - -
967E GLY 5.9 0.2 - - - +
975E PHE* 4.1 18.2 - - + -
977E CYS* 3.5 33.7 - - + -
992E LEU* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 931 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905E HIS* 4.4 4.5 - - + +
907E ASN 4.3 7.0 - - - +
908E ASN* 3.1 27.6 - - - +
921E ILE 3.6 0.7 - - - +
922E LEU* 3.5 6.3 - - - +
923E VAL* 2.9 45.7 + - + +
925E ASP* 5.0 8.7 - - + +
928E ARG* 6.2 2.7 - - + +
929E SER 4.9 1.3 - - - +
930E VAL* 1.3 77.7 - - - +
932E LEU* 1.3 63.1 + - - +
933E LEU* 3.5 39.5 - - + -
944E GLU* 4.7 7.9 - - - +
946E ALA 3.4 10.8 - - - +
947E ARG* 3.9 20.9 - - + -
992E LEU* 4.0 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 932 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920E PHE* 4.1 20.6 - - + -
921E ILE 3.7 19.5 - - - +
922E LEU* 4.4 3.4 - - + +
931E LEU* 1.3 79.0 - - - +
933E LEU* 1.3 64.5 + - - +
944E GLU* 3.9 0.9 - - - -
945E ILE* 2.9 41.1 + - + -
946E ALA* 2.7 21.2 + - + +
959E ILE* 6.0 0.4 - - + -
962E ASP 5.0 0.2 - - - +
965E PHE* 3.7 42.4 - - + -
979E LYS* 4.1 28.5 - - + -
992E LEU* 3.9 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 933 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888E VAL* 4.5 11.2 - - + -
905E HIS* 3.5 53.8 - - + +
920E PHE* 3.5 6.1 - - - -
921E ILE* 2.7 47.8 + - + +
923E VAL* 4.1 18.6 - - + -
931E LEU* 3.5 13.2 - - + -
932E LEU* 1.3 74.7 - - - +
934E ALA* 1.3 61.5 + - - +
942E PHE* 4.7 10.8 - - + -
943E GLU 3.7 5.4 - - - +
944E GLU* 3.6 29.8 - - + +
945E ILE* 3.8 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 934 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919E ASP* 3.6 5.6 - - + +
920E PHE* 4.0 11.7 - - + -
933E LEU* 1.3 73.5 - - - +
935E TYR* 1.3 69.4 + - - +
936E LYS* 3.7 11.9 + - + -
941E ASN 3.7 0.7 - - - +
942E PHE* 3.4 9.9 - - - -
943E GLU* 3.0 37.4 + - + +
945E ILE* 3.1 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 935 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876E PHE* 3.8 31.2 - + + -
890E LEU* 4.2 16.4 - - + -
892E GLU* 5.1 1.4 + - - -
902E GLU* 2.6 36.5 + - - -
903E CYS* 3.9 20.4 - - - -
919E ASP* 3.0 31.3 + - + +
921E ILE* 4.7 1.8 - - - +
934E ALA* 1.3 74.0 - - - +
936E LYS* 1.3 77.9 + - - +
937E PRO* 3.5 25.1 - - + +
940E GLY* 3.6 13.5 - - - -
941E ASN 3.7 7.0 - - - -
942E PHE* 4.6 8.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 936 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934E ALA* 3.7 12.5 - - + +
935E TYR* 1.3 82.4 - - - +
937E PRO* 1.3 65.4 - - + +
939E GLU* 3.1 27.0 + - + +
940E GLY 2.9 22.9 + - - -
941E ASN* 3.2 24.8 + - - +
943E GLU* 3.4 48.7 + - - +
----------------------------------------------------------
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