Contacts of the strand formed by residues 778 - 785 (chain A) in PDB entry 1IU1
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 778 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A ILE* 3.6 3.4 - - + +
736A GLN* 3.3 4.9 - - - -
737A ALA* 2.8 39.9 + - + +
748A PHE* 3.6 33.2 - - + -
765A PRO* 4.1 17.0 - - + -
766A SER* 3.6 4.9 - - - +
767A SER* 3.4 32.1 - - - +
768A SER 3.8 2.5 - - - -
769A ILE 3.3 39.5 - - - +
770A VAL* 3.6 9.9 - - + -
777A THR* 1.3 73.4 - - - +
779A THR* 1.3 64.4 + - - +
780A GLN* 4.2 4.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 779 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A THR* 3.7 27.6 - - + -
735A ILE 3.3 4.0 - - - +
736A GLN* 2.7 23.6 + - - +
764A SER 4.3 0.9 - - - +
765A PRO* 3.5 1.2 - - - +
766A SER* 2.8 40.5 + - - -
777A THR* 3.9 4.6 + - - -
778A ILE* 1.3 75.0 - - - +
780A GLN* 1.3 65.9 + - - +
781A VAL* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 780 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A THR 3.7 0.2 - - - -
735A ILE* 2.8 56.5 + - + +
748A PHE* 5.4 0.9 - - - -
750A PHE* 3.6 40.8 + - - +
762A LEU* 4.1 16.3 - - - +
763A LEU 2.9 29.9 + - - +
764A SER 4.5 2.0 - - - -
765A PRO* 3.7 32.7 - - + +
778A ILE* 5.1 2.9 - - + +
779A THR* 1.3 76.2 - - - +
781A VAL* 1.3 66.5 + - - +
782A ILE* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 781 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A VAL* 3.8 26.2 - - + -
733A ILE 3.4 2.5 - - - +
734A THR* 3.9 22.9 - - + +
763A LEU* 2.9 58.5 + - + +
764A SER 4.8 1.6 + - - -
779A THR* 5.3 3.4 - - + -
780A GLN* 1.3 78.0 - - - +
782A ILE* 1.3 70.9 + - - +
783A LYS* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 782 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A PHE* 5.7 0.4 - - + -
731A THR 4.0 0.2 - - - +
732A VAL* 3.7 1.0 - - - -
733A ILE* 2.7 40.8 + - + +
735A ILE* 3.7 23.6 - - + -
750A PHE* 3.0 40.4 - - + -
752A ALA* 5.2 1.1 - - + -
760A LEU* 2.8 40.2 - - + -
761A GLN 3.2 5.6 - - - +
762A LEU* 3.9 19.7 - - + -
780A GLN* 4.8 3.1 - - + +
781A VAL* 1.3 78.2 - - - +
783A LYS* 1.3 65.6 + - - +
784A VAL* 4.2 5.8 - - + -
794A MET* 4.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 783 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A VAL* 4.8 12.8 - - + -
731A THR 3.7 5.2 - - - +
732A VAL* 4.3 22.3 - - + +
759A GLN 3.8 0.5 - - - +
760A LEU* 3.5 5.5 - - - +
761A GLN* 2.8 62.9 + - + +
763A LEU* 4.3 15.7 - - + +
781A VAL* 4.2 19.5 - - + -
782A ILE* 1.3 79.4 - - - +
784A VAL* 1.3 61.4 + - - +
785A LEU 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 784 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A SER 3.4 1.7 - - - +
730A VAL* 3.4 7.0 - - - +
731A THR* 2.9 40.1 + - - +
733A ILE* 3.9 27.4 - - + -
754A VAL* 4.9 3.6 - - + -
758A PHE* 3.8 28.3 - - + -
759A GLN 3.6 5.4 - - - +
760A LEU* 3.6 22.2 - - + -
782A ILE* 4.2 1.6 - - + -
783A LYS* 1.3 74.1 - - - +
785A LEU* 1.3 63.3 + - - +
786A ASN* 4.6 3.3 - - + +
792A LEU* 3.8 17.5 - - + -
794A MET* 4.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 785 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ASN* 4.2 5.8 - - - +
729A SER* 3.3 19.1 - - - +
730A VAL* 3.5 27.8 - - + +
758A PHE* 3.4 8.0 - - - +
759A GLN* 2.9 69.6 + - + +
783A LYS 4.1 1.0 + - - -
784A VAL* 1.3 72.6 - - - +
786A ASN* 1.3 58.3 - - - +
787A PRO* 3.3 20.9 - - + +
----------------------------------------------------------
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