Contacts of the strand formed by residues 954 - 963 (chain B) in PDB entry 3U44
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 954 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950B GLU* 2.8 24.2 - - - +
951B SER* 3.0 25.9 + - - -
952B SER 3.1 3.2 + - - -
953B LYS* 1.3 79.3 - - - +
955B LEU* 1.3 63.2 + - - -
956B LEU* 4.1 0.2 - - - +
999B MET* 4.0 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 955 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948B LYS* 3.3 37.7 - - + +
949B ALA 4.5 3.4 - - - +
950B GLU* 3.3 12.4 + - + +
953B LYS 4.8 0.2 - - - +
954B GLY* 1.3 73.3 - - - -
956B LEU* 1.3 63.4 + - - +
957B LEU* 4.4 4.7 - - + -
993B SER* 4.1 9.2 - - - +
997B LEU* 3.2 44.6 - - + -
999B MET* 3.5 30.9 - - + +
1000B ARG 4.1 5.1 + - - +
1001B ALA* 3.6 8.4 - - + -
1002B THR* 3.2 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 956 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909B PHE* 3.8 18.3 - - + -
947B ASP 3.6 0.2 - - - +
948B LYS* 3.1 8.0 - - - +
949B ALA 2.9 37.8 + - - +
951B SER* 3.4 27.4 - - - +
953B LYS* 5.6 2.2 - - + -
954B GLY 4.1 0.2 - - - +
955B LEU* 1.3 75.5 - - - +
957B LEU* 1.3 63.6 + - - +
1002B THR* 3.3 34.8 - - + +
1004B ALA* 4.5 7.0 - - + -
1042B LEU* 4.9 2.0 - - + -
1047B VAL* 3.9 31.9 - - + -
1050B LEU* 3.6 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 957 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912B ILE* 3.7 20.2 - - + -
946B VAL* 6.2 1.1 - - + -
947B ASP 3.2 4.9 - - - +
948B LYS* 3.5 24.9 - - + -
955B LEU* 4.3 8.3 - - + -
956B LEU* 1.3 85.0 - - - +
958B ARG* 1.3 61.1 + - - +
986B LEU* 4.1 6.5 - - + +
989B SER* 3.5 41.1 - - - +
990B ILE* 4.4 7.4 - - + -
993B SER* 4.0 7.2 - - - +
996B TRP* 5.2 2.5 - - + -
997B LEU* 4.9 6.7 - - + -
1001B ALA* 3.6 24.8 - - + +
1002B THR 3.4 6.3 + - - -
1003B PRO* 3.7 6.2 - - - +
1004B ALA* 2.9 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 958 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B SER* 3.7 17.8 + - - -
909B PHE* 4.0 24.6 + - + +
945B ARG* 4.1 11.9 - - - +
946B VAL* 3.4 4.2 - - - +
947B ASP* 2.8 64.2 + - + +
957B LEU* 1.3 75.7 - - - +
959B ILE* 1.3 68.1 + - - +
960B VAL* 3.9 4.3 - - + +
986B LEU* 4.7 0.9 - - - -
1004B ALA* 3.7 13.2 - - + -
1005B GLY* 3.4 17.3 - - - +
1007B LEU* 3.4 24.3 - - - +
1037B MET* 4.9 6.7 - - - +
1051B MET* 3.1 48.0 + - - +
1062B ILE* 6.2 1.4 - - - +
1063B ILE* 4.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 959 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943B ILE* 4.1 11.7 - - + -
944B ASP 5.4 0.7 - - - +
945B ARG 3.0 15.3 - - - +
946B VAL* 3.5 15.7 - - + -
958B ARG* 1.3 78.8 - - - +
960B VAL* 1.3 69.2 + - - +
961B ALA* 5.6 0.4 - - + -
982B MET* 3.5 22.8 - - + +
985B TYR* 3.3 48.5 - - + +
986B LEU* 3.4 14.8 - - + +
989B SER* 3.4 15.5 - - - +
1005B GLY 3.3 7.1 + - - +
1006B VAL* 3.6 3.3 - - + -
1007B LEU* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 960 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944B ASP* 3.1 2.8 - - - +
945B ARG* 2.9 74.2 + - + +
947B ASP* 3.6 14.8 - - - +
958B ARG* 3.9 15.7 - - - +
959B ILE* 1.3 82.3 - - - +
961B ALA* 1.3 65.3 + - - +
962B TYR* 4.3 6.2 - - + +
1007B LEU* 3.4 20.4 - - + +
1009B PHE* 4.2 24.2 - - + +
1037B MET* 4.5 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 961 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944B ASP* 3.4 23.3 - - - +
959B ILE* 5.6 0.7 - - + -
960B VAL* 1.3 77.7 - - - +
962B TYR* 1.3 66.7 + - - +
963B LYS* 4.1 2.6 - - - +
981B GLN* 5.0 9.0 - - - +
982B MET* 3.9 24.9 - - + -
985B TYR* 5.8 1.6 - - + -
1007B LEU 3.1 8.1 + - - +
1008B TYR* 3.6 11.8 - - + +
1009B PHE 3.1 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 962 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831B HIS* 4.1 30.3 - + + -
834B LEU* 3.5 36.5 - - + +
848B TRP* 6.0 0.7 - - - -
896B VAL* 5.6 0.4 - - + -
900B LEU* 4.7 21.0 - - + +
914B LEU* 5.0 6.5 - - + +
915B GLU* 5.1 3.6 - - - -
944B ASP* 3.4 29.4 + - + +
945B ARG* 3.6 37.9 + - + -
960B VAL* 5.3 3.8 - - + -
961B ALA* 1.3 75.1 - - - +
963B LYS* 1.3 61.1 + - - +
1009B PHE* 3.6 27.6 - + + -
1011B ILE* 3.5 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 963 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830B PHE* 6.3 0.4 - - - -
961B ALA* 4.1 5.4 - - + +
962B TYR* 1.3 78.2 - - - +
964B SER* 1.3 64.7 + - - +
965B SER* 3.5 39.8 - - - +
966B ASP 5.1 4.0 - - - +
967B LYS 5.1 4.3 - - - +
1008B TYR* 4.3 26.5 - - + -
1009B PHE 2.7 19.1 + - - +
1010B HIS* 3.3 3.7 - - - -
1011B ILE* 2.7 37.5 + - - +
----------------------------------------------------------
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