Contacts of the strand formed by residues 1019 - 1023 (chain A) in PDB entry 1DJL
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 THR1019 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A THR* 3.1 18.0 + - - +
990A TRP* 5.5 1.2 - - - +
994A GLN* 4.1 0.4 - - - -
995A VAL* 3.4 16.4 - - + +
997A VAL* 3.8 27.8 - - + -
1013A ILE* 2.8 36.7 + - + +
1014A PHE* 4.3 10.9 - - - +
1016A LYS* 3.0 22.5 + - - +
1017A PRO 3.2 3.7 - - - +
1018A ASN* 1.3 82.0 + - - +
1020A ALA* 1.3 66.9 + - - +
1021A MET* 4.3 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1020 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A THR* 3.8 9.4 - - - +
869A ILE* 3.7 37.2 - - + -
877A MET* 4.7 3.4 - - + -
994A GLN* 3.6 16.6 - - - +
995A VAL 2.8 7.1 + - - +
996A ILE* 3.2 5.5 - - + +
997A VAL* 2.8 31.5 + - - +
1019A THR* 1.3 77.6 - - - +
1021A MET* 1.3 57.6 + - - +
1022A LEU 3.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1021 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A HIS* 3.8 21.8 - - + -
867A THR 2.8 21.1 + - - +
868A GLU* 3.2 9.7 - - + +
869A ILE* 3.0 25.6 + - - +
997A VAL* 3.5 35.7 - - + -
999A LYS* 4.1 0.7 - - + -
1001A SER 3.9 21.1 - - - +
1002A LEU* 3.9 14.1 - - + -
1014A PHE* 3.8 38.1 - - + +
1019A THR* 4.3 6.1 - - + +
1020A ALA* 1.3 72.6 - - - +
1022A LEU* 1.3 59.8 + - - +
1023A LEU* 3.7 20.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1022 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A ILE* 3.5 26.0 - - + +
870A ASN* 4.1 17.0 - - - +
871A LEU* 4.1 12.8 - - + +
874A ALA* 3.9 21.8 - - + -
996A ILE* 3.9 19.5 - - + -
997A VAL 2.8 10.0 + - - +
998A MET* 3.5 33.4 - - + +
999A LYS 3.7 0.2 - - - +
1020A ALA 3.9 0.6 + - - -
1021A MET* 1.3 71.9 - - - +
1023A LEU* 1.3 65.4 + - - +
1024A GLY 3.7 1.4 + - - +
1029A THR* 3.5 30.7 + - + +
1033A LEU* 4.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1023 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A GLU* 3.7 35.4 - - + +
869A ILE 5.2 0.6 + - - -
997A VAL 5.0 0.2 - - - +
999A LYS* 3.3 13.7 - - + +
1000A ARG 3.9 10.5 - - - +
1001A SER* 4.0 24.0 - - - +
1002A LEU* 4.5 10.8 - - + -
1021A MET* 3.7 30.2 + - + -
1022A LEU* 1.3 78.0 - - - +
1024A GLY* 1.3 58.5 + - - +
1029A THR* 4.4 3.9 + - - -
----------------------------------------------------------
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