Contacts of the strand formed by residues 973 - 978 (chain A) in PDB entry 1D0H
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 GLU 973 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971A THR 3.4 4.6 + - - +
972A ASN* 1.3 78.9 + - - +
974A TYR* 1.3 62.5 + - - +
994A SER* 2.7 29.6 + - - +
995A LEU 3.4 8.5 - - - +
996A LYS* 3.9 22.8 + - + +
1001A ILE* 3.9 22.0 - - - +
1003A THR* 4.5 4.3 - - - +
1013A GLN* 4.2 12.6 + - - -
1076A ARG* 4.1 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 974 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958A VAL* 4.9 2.3 - - - +
972A ASN* 3.7 14.8 - - - -
973A GLU* 1.3 76.1 - - - +
975A SER* 1.3 72.5 + - - +
976A ILE* 3.8 19.6 + - + +
994A SER* 3.1 15.7 - - - -
995A LEU* 2.9 55.8 + - + +
996A LYS* 4.9 1.3 - - - -
997A GLY 5.4 3.1 - - - -
1074A LEU* 4.3 6.5 - - + -
1075A ASP 3.4 14.1 - - - +
1076A ARG 3.9 0.7 - - - +
1077A CYS* 3.7 40.2 - - + +
1082A GLN* 3.0 43.0 + - + -
1084A VAL* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 975 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973A GLU* 5.4 0.2 - - - +
974A TYR* 1.3 75.2 - - - +
976A ILE* 1.3 65.7 + - - +
977A ILE 4.6 3.1 - - - -
978A SER* 4.4 10.6 - - - -
992A SER* 4.5 16.2 - - - -
993A VAL 3.6 11.0 - - - -
994A SER* 3.7 7.4 - - - -
1073A LYS 3.1 1.9 + - - +
1074A LEU* 3.5 1.2 - - - -
1075A ASP* 2.9 52.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 976 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925A LEU* 4.5 0.2 - - - +
954A PHE* 5.1 0.7 - - + -
956A LEU* 3.9 30.1 - - + -
974A TYR* 3.8 25.4 - - + +
975A SER* 1.3 80.8 - - - +
977A ILE* 1.3 76.8 + - + +
993A VAL* 2.9 31.5 + - + +
994A SER* 4.9 0.9 - - - -
995A LEU* 4.1 17.3 - - + -
1071A THR 4.3 0.7 - - - -
1072A LEU* 3.4 4.7 - - - +
1073A LYS 2.9 33.0 + - - -
1074A LEU* 4.3 9.0 - - + -
1084A VAL* 3.9 22.2 - - + -
1086A ILE* 4.3 7.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 977 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954A PHE* 4.0 32.5 - - + -
976A ILE* 1.3 91.9 - - + +
978A SER* 1.3 65.4 + - - +
991A TRP* 3.9 14.7 - - + -
992A SER* 3.2 2.4 - - - -
993A VAL* 2.7 38.9 + - + +
1070A ILE* 4.3 2.9 - - + -
1071A THR 3.4 7.6 - - - +
1072A LEU* 4.2 14.8 - - + -
1086A ILE* 3.8 25.4 - - + -
1089A PHE* 3.9 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 978 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975A SER* 4.4 13.0 - - - -
977A ILE* 1.3 79.5 - - - +
979A SER* 1.3 57.6 + - - +
980A MET* 2.9 36.0 + - - +
991A TRP* 3.6 9.6 - - - -
992A SER* 3.9 10.4 - - - +
1069A ASN 3.9 0.7 - - - +
1070A ILE* 3.6 1.7 - - - -
1071A THR* 2.8 44.6 + - - +
1075A ASP* 5.9 2.5 - - - -
----------------------------------------------------------
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