Contacts of the helix formed by residues 757 - 771 (chain A) in PDB entry 3U44
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 GLY 757 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A VAL* 3.7 8.5 - - - +
750A TYR* 2.9 22.7 + - - -
756A ARG* 1.3 76.0 - - - +
758A LEU* 1.3 63.6 + - - -
759A PHE* 3.4 3.1 - - - -
760A ARG 4.3 0.7 - - - -
761A PHE* 3.4 7.8 + - - +
385B GLU* 5.6 3.5 + - - -
405B ARG* 6.0 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A LEU* 3.6 38.1 - - + +
633A ILE* 4.2 14.6 - - + -
634A ASP* 3.6 29.2 - - + +
705A SER* 5.0 9.2 - - - +
710A VAL* 3.8 26.1 - - + +
713A LEU* 4.5 11.4 - - + -
757A GLY* 1.3 70.1 - - - -
759A PHE* 1.3 66.3 + - - +
761A PHE* 3.4 10.1 + - + +
762A LEU* 3.0 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 759 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ASP* 3.3 32.6 + - - +
757A GLY* 3.4 1.3 - - - -
758A LEU* 1.3 79.5 - - - +
760A ARG* 1.3 67.5 + - + +
762A LEU* 3.1 16.1 + - + +
763A ARG* 3.1 63.7 + - + +
400B TYR* 4.5 4.5 - + - -
401B GLU* 4.0 18.6 - - + -
408B LYS* 5.4 1.1 - - - +
430B GLU* 3.4 24.5 - - - -
434B ILE* 3.9 22.2 - - + -
816B ARG* 4.2 7.4 - - - -
818B PHE* 6.6 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 6.0 2.4 - - - +
144A GLU* 5.9 0.4 + - - -
750A TYR* 3.0 20.4 - - + +
755A PHE* 4.3 31.4 - - + -
756A ARG 3.5 15.3 - - - +
757A GLY* 4.0 1.4 + - - -
758A LEU 3.4 0.2 - - - -
759A PHE* 1.3 85.5 - - + +
761A PHE* 1.3 50.1 + - - +
763A ARG* 3.3 24.4 + - - +
764A PHE* 2.7 35.2 + - - +
767A ARG* 5.9 2.8 - - - +
399B ARG* 5.1 11.7 - - - +
401B GLU* 4.0 31.3 + - + +
405B ARG* 4.3 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 761 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A LEU* 4.8 0.9 - - + -
630A LEU* 4.1 17.9 - - + -
710A VAL* 3.7 20.9 - - + -
714A ILE* 4.5 1.3 - - + -
743A LEU* 4.2 8.3 - - + -
746A ARG* 4.1 3.1 - - + -
747A ALA* 3.4 37.7 - - + -
750A TYR* 2.9 45.9 + + + -
757A GLY 3.4 14.8 + - - +
758A LEU* 3.4 14.8 + - + +
759A PHE 3.2 0.4 - - - -
760A ARG* 1.3 76.6 - - - +
762A LEU* 1.3 62.5 + - + +
764A PHE* 3.1 6.9 - + - +
765A ILE* 2.9 60.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 762 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A LEU* 4.8 12.6 - - + +
630A LEU* 4.3 22.2 - - + -
631A LYS* 4.2 29.8 - - + -
634A ASP* 3.7 35.4 - - + +
638A GLN* 5.9 1.1 - - - +
758A LEU* 3.0 27.1 + - + +
759A PHE* 3.1 8.2 + - + +
761A PHE* 1.3 83.8 - - + +
763A ARG* 1.3 51.8 + - + +
765A ILE* 3.1 6.8 + - - +
766A GLU* 2.7 48.4 + - + +
816B ARG* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 763 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A PHE* 3.1 44.7 + - + +
760A ARG* 3.7 29.1 - - - +
762A LEU* 1.3 75.5 - - + +
764A PHE* 1.3 57.4 + - - +
766A GLU* 2.9 23.4 + - - +
767A ARG* 2.7 55.8 + - - +
399B ARG* 5.8 0.6 - - - +
400B TYR* 2.5 30.1 + - - -
401B GLU* 2.7 30.3 + - - +
434B ILE* 4.8 4.0 - - - +
818B PHE* 5.8 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 764 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASP* 5.0 4.9 - - - -
136A THR* 3.6 31.4 - - + +
137A GLU* 4.5 18.6 - - + -
140A LEU* 4.1 19.0 - - + +
746A ARG* 5.0 10.3 - - + -
749A GLN* 6.3 0.9 - - + -
750A TYR* 4.0 31.9 - + + -
753A THR* 5.1 5.2 - - - -
755A PHE* 4.6 10.1 - + + -
760A ARG 2.7 18.5 + - - +
761A PHE* 3.1 18.2 - + - +
763A ARG* 1.3 74.7 - - - +
765A ILE* 1.3 69.2 + - + +
767A ARG* 3.2 21.4 + - - +
768A MET* 3.3 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 765 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A TYR* 6.5 0.2 - - + -
618A PHE* 3.4 26.2 - - + -
627A LEU* 3.6 18.6 - - + -
743A LEU* 3.5 23.3 - - + -
746A ARG* 5.7 7.6 - - + -
761A PHE* 2.9 51.5 + - + +
762A LEU* 3.6 8.3 - - - +
764A PHE* 1.3 81.2 - - + +
766A GLU* 1.3 66.5 + - + +
768A MET* 3.2 11.8 + - - +
769A GLN* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 766 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A LYS* 5.2 12.8 - - - +
762A LEU* 2.7 36.5 + - + +
763A ARG* 2.9 29.8 + - - +
765A ILE* 1.3 71.1 - - - +
767A ARG* 1.3 65.7 + - - +
769A GLN* 3.2 17.8 - - - +
770A GLU* 3.0 25.2 + - - +
818B PHE* 5.5 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 767 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A THR* 6.4 0.7 - - + -
140A LEU* 3.7 34.3 - - + +
143A ASP* 4.3 11.3 + - - +
760A ARG* 5.9 2.4 - - - +
763A ARG* 2.7 41.8 + - + +
764A PHE 3.2 7.4 - - - +
765A ILE 3.1 0.2 - - - -
766A GLU* 1.3 73.8 - - - +
768A MET* 1.3 69.0 + - + +
769A GLN 2.9 0.5 + - - -
770A GLU* 2.9 48.8 + - - +
771A ARG* 3.1 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 768 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A THR* 3.9 30.5 - - + +
618A PHE* 3.8 10.8 - - + -
746A ARG* 3.8 36.8 - - - +
764A PHE* 3.5 39.3 - - + +
765A ILE* 3.2 12.0 + - - +
767A ARG* 1.3 76.4 - - + +
769A GLN* 1.3 63.0 + - - +
771A ARG* 4.6 3.8 - - - -
772A GLY 3.5 2.5 + - - +
773A ASP* 2.6 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 769 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A PHE* 3.4 46.8 - - + +
627A LEU* 4.1 11.5 - - - +
631A LYS* 5.3 8.7 - - - +
765A ILE* 3.0 31.7 + - - +
766A GLU* 3.2 20.2 - - - +
767A ARG 2.9 0.4 + - - -
768A MET* 1.3 79.5 - - - +
770A GLU* 1.3 65.5 + - - +
771A ARG* 3.0 5.7 + - - +
773A ASP* 4.7 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 770 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A GLU* 3.0 6.9 + - - +
767A ARG* 2.9 43.7 + - - +
769A GLN* 1.3 76.3 - - - +
771A ARG* 1.3 99.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 771 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 4.7 17.3 - - - -
140A LEU* 5.5 2.4 - - - +
143A ASP* 3.0 37.1 + - - +
182A LYS* 5.6 1.5 - - - +
767A ARG* 3.1 48.8 + - - +
768A MET* 3.9 2.9 - - - +
769A GLN 3.0 3.7 + - - +
770A GLU* 1.3 112.1 + - + +
772A GLY* 1.3 70.0 - - - +
773A ASP* 3.7 1.8 - - - +
----------------------------------------------------------
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