Contacts of the strand formed by residues 740 - 744 (chain A) in PDB entry 5TKD
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 ILE 740 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A PRO* 3.4 2.8 - - - +
695A LEU* 2.7 57.5 + - + +
714A VAL* 4.8 1.8 - - + -
718A LEU* 3.8 22.4 - - + -
735A VAL* 5.3 0.2 - - + -
736A CYS 3.5 12.6 - - - +
737A GLY 3.2 7.5 + - - +
739A ASN* 1.3 79.9 - - - +
741A LEU* 1.3 57.4 + - - +
755A ILE* 3.7 41.1 - - + -
756A LYS 3.8 2.5 - - - -
757A LEU* 4.3 13.5 - - + -
803A THR* 3.5 32.1 - - + -
807A ILE* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 741 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ALA* 4.4 7.2 - - + -
688A GLU 4.9 0.4 - - - +
690A VAL* 3.7 34.3 - - + -
693A GLY 3.5 3.8 - - - +
694A PRO* 3.9 24.0 - - + -
738A ARG 4.6 4.3 - - - +
739A ASN 4.6 0.2 - - - +
740A ILE* 1.3 75.7 - - - +
742A LEU* 1.3 63.1 + - - +
743A ALA 3.7 0.4 + - - -
755A ILE* 3.2 7.6 - - - +
756A LYS 2.8 38.3 + - - +
758A SER* 3.7 24.2 - - - -
901A 7GL 3.5 52.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 742 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A VAL* 3.5 5.0 - - - +
692A HIS* 2.8 43.8 + - + +
693A GLY 2.9 16.0 + - - +
695A LEU* 4.0 20.2 - - + -
698A TRP* 3.7 44.2 - - + -
710A TRP* 4.0 23.6 - - + -
741A LEU* 1.3 71.9 - - - +
743A ALA* 1.4 57.4 + - - +
744A ARG 4.0 15.0 - - - +
745A LEU* 3.8 13.7 - - + -
753A PRO* 4.7 1.6 - - + -
754A PHE 3.8 0.4 - - - -
755A ILE* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A VAL* 3.4 19.0 - - + +
691A GLU* 3.7 10.0 - - - +
692A HIS* 3.7 11.4 + - - -
741A LEU 3.7 1.0 + - - -
742A LEU* 1.4 72.0 - - - +
744A ARG* 1.3 88.2 + - + +
754A PHE* 2.9 32.7 + - + +
756A LYS* 4.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A GLU* 5.0 6.3 - - - +
692A HIS* 4.3 3.6 - - - -
742A LEU* 4.0 7.2 - - - +
743A ALA* 1.3 104.2 + - + +
745A LEU* 1.3 64.2 + - - +
752A SER 4.1 10.3 - - - +
753A PRO* 3.3 4.0 - - - +
754A PHE* 3.0 49.0 + - + +
691B GLU* 4.3 8.7 - - - +
692B HIS* 3.4 27.9 + - - -
745B LEU* 3.8 15.9 - - - +
747B LEU* 4.5 4.6 - - - +
748B ALA* 3.7 16.2 - - + +
902B SO4 2.8 42.0 + - - +
----------------------------------------------------------
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