Contacts of the strand formed by residues 946 - 958 (chain A) in PDB entry 5ES4
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 LEU 946 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905A VAL* 3.5 29.8 - - + -
907A THR* 4.2 12.8 - - + -
940A ASN* 3.8 13.2 - - - +
944A ARG 2.8 21.0 + - - +
945A ASP* 1.3 75.4 - - - +
947A PRO* 1.3 82.5 - - + +
948A VAL* 3.8 8.3 - - + -
1017A SER 4.8 0.2 - - - -
1018A PHE* 3.1 27.6 + - + +
1055A PHE* 3.7 30.1 - - + -
1060A TYR* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 947 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945A ASP 3.8 6.1 - - - +
946A LEU* 1.3 98.5 - - + +
948A VAL* 1.3 65.7 + - - +
1015A VAL 3.5 14.8 - - - +
1016A PRO* 3.9 15.3 - - + +
1017A SER* 5.3 1.3 - - - -
1018A PHE 4.2 4.5 - - - +
1055A PHE* 3.4 8.4 - - - +
1056A ASP* 4.9 4.1 + - + +
1060A TYR* 4.0 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 948 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907A THR* 4.4 3.8 - - + -
946A LEU* 3.8 21.8 - - + -
947A PRO* 1.3 79.6 - - - +
949A SER* 1.3 63.7 + - - +
950A ILE* 4.4 11.9 - - + -
1014A ASP* 3.8 2.1 - - - +
1015A VAL* 2.9 52.2 + - + +
1018A PHE* 3.7 29.2 - - + -
1053A ILE* 4.1 17.0 - - + -
1054A THR 3.2 12.8 - - - +
1055A PHE* 4.1 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 949 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A VAL* 1.3 75.7 - - - +
950A ILE* 1.3 61.7 + - - +
951A ASN* 3.4 4.0 + - - -
1012A ARG* 3.0 31.0 + - - +
1013A CYS 3.6 4.9 + - - -
1014A ASP* 2.4 28.2 + - - -
1053A ILE* 3.7 1.2 - - - -
1054A THR* 2.6 56.5 + - - -
1055A PHE* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 950 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A VAL* 5.5 6.3 - - + -
938A VAL* 4.1 17.9 - - + -
948A VAL* 4.4 6.1 - - + -
949A SER* 1.3 74.8 - - - +
951A ASN* 1.3 63.4 + - - +
952A PHE* 3.4 34.1 - - + -
1011A PHE 3.5 1.2 - - - +
1012A ARG* 3.4 3.8 - - - -
1013A CYS* 2.8 45.5 + - + +
1015A VAL* 4.3 12.1 - - + -
1024A LEU* 6.1 0.2 - - + -
1026A PHE* 4.0 24.7 - - + -
1051A ALA* 5.4 1.8 - - + -
1052A GLU 3.8 4.9 - - - +
1053A ILE* 3.8 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 951 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949A SER* 3.4 10.3 + - - -
950A ILE* 1.3 76.3 - - - +
952A PHE* 1.3 65.0 - - - +
953A TRP* 3.8 25.3 - - + -
1010A ARG* 5.0 7.4 - - + +
1011A PHE 3.1 12.1 - - - +
1012A ARG* 3.6 19.9 - - - +
1050A VAL 3.8 0.2 - - - +
1051A ALA* 3.1 6.8 - - - +
1052A GLU 2.9 35.1 + - - +
1054A THR* 3.2 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 952 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A VAL* 5.8 0.4 - - + -
936A TYR* 3.7 24.9 - + + -
950A ILE* 3.4 28.3 - - + -
951A ASN* 1.3 79.6 - - - +
953A TRP* 1.3 65.3 + - - +
954A VAL* 4.9 0.4 - - + -
969A VAL* 4.2 7.0 - - + -
1009A LEU 3.5 1.0 - - - +
1010A ARG* 3.2 7.8 - - - +
1011A PHE* 2.9 52.4 + - + -
1013A CYS* 4.4 15.0 - - - -
1026A PHE* 3.5 33.7 - + + -
1028A LEU* 4.0 28.0 - - + -
1050A VAL 3.2 6.3 - - - +
1051A ALA* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 953 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951A ASN* 3.8 23.8 - - + -
952A PHE* 1.3 73.4 - - - +
954A VAL* 1.3 60.6 + - - +
955A PRO* 4.0 1.9 - - - +
984A ILE* 4.8 8.7 - - + +
1003A CYS* 3.5 28.6 - - + -
1008A CYS* 5.0 1.6 - - + -
1009A LEU 3.4 4.5 - - - -
1010A ARG* 3.6 39.9 - - + +
1048A VAL 4.3 0.2 - - - +
1049A SER* 3.2 28.1 - - - -
1050A VAL* 3.0 39.8 + - + +
1052A GLU* 3.2 46.9 - - + -
1054A THR* 6.4 0.2 - - + -
1071A ARG* 5.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 954 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952A PHE* 4.9 0.2 - - + -
953A TRP* 1.3 81.7 - - - +
955A PRO* 1.3 78.5 - - + +
956A VAL* 3.1 4.4 + - + +
964A TRP* 3.8 21.8 - - + -
967A VAL* 4.0 24.7 - - + -
1003A CYS* 4.1 1.2 - - - -
1008A CYS* 4.1 2.5 - - - -
1009A LEU* 3.0 39.5 + - + +
1011A PHE* 4.6 9.4 - - + -
1028A LEU* 3.7 38.4 - - + -
1049A SER* 4.2 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 955 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953A TRP 4.0 2.0 - - - +
954A VAL* 1.3 83.5 - - + +
956A VAL* 1.3 58.8 + - - +
957A GLU 3.9 0.2 - - - -
963A VAL* 3.9 7.0 - - + +
964A TRP* 3.2 29.9 + - + +
1001A LEU* 3.9 19.3 - - + +
1002A ASP* 3.9 25.6 - - - -
1003A CYS* 4.3 3.1 - - - +
1006A ALA* 3.5 23.8 - - + -
1008A CYS* 3.9 4.0 - - - -
1047A VAL* 4.6 8.5 - - + -
1048A VAL 3.3 27.8 - - - +
1049A SER* 4.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 956 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954A VAL* 3.1 24.0 + - + +
955A PRO* 1.3 74.5 - - - +
957A GLU* 1.3 61.0 + - + +
962A ALA* 3.6 4.2 - - - -
963A VAL* 2.8 29.8 + - - -
964A TRP 3.2 17.5 - - - +
965A MET* 5.3 2.5 - - - -
966A ASP 5.9 0.7 - - - +
967A VAL* 4.3 12.3 - - + -
983A LYS* 5.8 8.5 - - - -
1007A GLY 3.0 8.8 + - - +
1008A CYS 4.8 1.1 - - - -
1009A LEU* 3.7 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 957 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956A VAL* 1.3 83.6 - - + +
958A LEU* 1.3 61.0 + - - +
959A ASN 4.2 0.8 + - - +
960A GLN* 3.1 46.7 + - - +
961A GLU 3.4 5.6 - - - +
962A ALA* 4.9 1.1 - - - +
963A VAL* 4.2 1.6 - - - -
1006A ALA* 3.4 2.7 - - - -
1007A GLY* 2.6 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 958 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957A GLU* 1.3 71.9 - - - +
959A ASN* 1.3 93.5 + - - +
960A GLN 3.2 1.8 - - - -
961A GLU* 2.7 37.6 + - - +
963A VAL* 3.7 16.4 - - + +
991A PHE* 5.1 1.6 - - + -
995A ILE* 6.3 0.4 - - + -
1001A LEU* 3.5 31.4 - - + -
1005A ILE* 3.5 42.0 - - + +
1006A ALA* 4.3 1.6 - - + -
1007A GLY 4.8 0.2 - - - +
1036A TRP* 4.1 15.5 - - + -
1039A GLN* 4.6 2.2 - - - +
1040A ILE* 4.2 16.8 - - + -
----------------------------------------------------------
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