Contacts of the helix formed by residues 756 - 768 (chain B) in PDB entry 4HPF
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 SER 756 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B VAL* 4.8 3.2 + - - +
722B GLY 3.6 25.8 + - - +
723B ASP* 4.1 4.7 - - - +
755B GLY* 1.3 69.3 - - - -
757B LEU* 1.3 59.0 + - - +
758B ASP* 3.5 11.1 + - - +
759B TYR* 3.1 21.6 + - - +
760B LEU* 2.8 31.2 + - - +
778B GLY 3.7 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 757 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B LEU* 4.2 15.0 - - + -
701B THR* 3.9 27.8 - - + +
755B GLY 3.2 6.8 + - - -
756B SER* 1.3 70.6 + - - +
758B ASP* 1.3 63.7 + - - +
760B LEU* 4.3 6.3 - - + +
761B GLN* 2.6 50.8 + - + +
775B ILE* 5.3 6.7 - - + -
777B PRO* 4.2 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 758 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B ASP* 5.3 0.2 - - - -
724B ALA* 4.6 18.9 - - + +
756B SER* 3.2 10.0 + - - +
757B LEU* 1.3 86.1 + - - +
759B TYR* 1.3 60.3 + - - +
761B GLN* 3.5 13.5 + - - +
762B ARG* 3.4 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 759 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B VAL* 4.1 22.7 - - + -
721B PHE 3.7 16.4 - - - -
722B GLY* 3.8 14.8 - - - -
723B ASP 3.6 35.3 - - - +
726B SER* 4.0 9.9 - - - -
727B ALA 2.8 23.2 + - - -
728B PRO* 4.0 4.7 - - + -
729B MET* 2.8 49.6 + - + +
756B SER* 3.1 13.4 + - - +
758B ASP* 1.3 78.7 - - - +
760B LEU* 1.3 67.9 + - + +
762B ARG* 3.3 25.2 + - - +
763B GLU* 3.8 12.8 + - + +
803B PRO* 4.1 3.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 760 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B LEU* 6.0 0.2 - - + -
720B VAL* 3.5 27.8 - - + -
731B LEU* 3.7 25.6 - - + -
753B PHE* 4.0 20.4 - - + -
755B GLY* 4.0 22.2 - - - +
756B SER 2.8 18.9 + - - +
757B LEU* 3.0 4.9 + - + +
759B TYR* 1.3 77.5 - - + +
761B GLN* 1.3 64.8 + - - +
762B ARG 3.1 2.0 - - - -
763B GLU* 3.2 15.4 + - + +
764B TRP* 3.2 12.8 + - - +
767B LEU* 5.9 1.6 - - + +
775B ILE* 3.7 40.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 761 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B LEU* 3.5 29.3 - - + +
757B LEU* 2.6 30.9 + - + +
758B ASP* 3.5 13.4 + - - +
760B LEU* 1.3 72.1 - - - +
762B ARG* 1.3 79.5 + - - +
763B GLU 3.3 0.2 - - - -
764B TRP* 3.4 15.6 + - - +
765B ARG 4.5 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 762 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B ASP 2.6 30.1 + - - -
724B ALA* 2.8 22.5 + - - +
726B SER 2.8 24.5 + - - -
728B PRO* 4.8 14.9 - - + +
758B ASP 3.4 16.4 + - - +
759B TYR* 3.3 21.2 + - - +
760B LEU 3.1 1.0 - - - -
761B GLN* 1.3 94.6 - - - +
763B GLU* 1.3 60.2 + - + +
765B ARG* 4.7 5.2 + - - +
766B PHE* 4.5 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 763 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B PRO* 3.4 18.0 - - - +
729B MET 2.7 45.0 + - - +
730B GLY* 4.0 3.1 - - - -
731B LEU* 3.3 36.1 + - + -
732B ARG 4.9 0.9 + - - -
759B TYR* 3.9 18.3 + - + +
760B LEU* 3.2 11.2 + - + +
762B ARG* 1.3 76.6 - - + +
764B TRP* 1.3 58.9 + - - +
765B ARG 3.2 3.1 - - - -
766B PHE* 2.9 38.3 + - - +
767B LEU* 3.5 13.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 764 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B THR* 3.2 23.8 + - - -
696B SER* 4.3 0.7 - - - -
697B LEU* 3.4 37.0 - - + +
700B VAL* 3.4 42.6 - - + -
760B LEU 3.2 10.5 + - - +
761B GLN* 3.5 17.7 - - - +
762B ARG 3.4 1.6 - - - -
763B GLU* 1.3 76.5 - - - +
765B ARG* 1.3 64.5 + - - +
767B LEU* 3.0 35.8 + - + +
768B TRP* 3.1 42.5 + + - +
770B PHE 5.7 1.3 - - - -
773B ILE* 3.8 27.8 - - + -
775B ILE* 3.7 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 765 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A ARG* 4.7 0.8 - - - +
782A TYR* 3.6 40.3 - - + +
784A GLY* 4.5 6.9 - - - -
785A ASP* 2.7 30.7 + - - +
732B ARG* 5.6 2.8 - - - +
761B GLN 4.5 2.8 + - - +
762B ARG 4.9 3.8 - - - +
763B GLU 3.2 0.6 - - - -
764B TRP* 1.3 79.2 - - - +
766B PHE* 1.3 89.4 + - + +
767B LEU 3.6 0.2 + - - -
768B TRP* 3.2 60.1 - - + +
769B ASN* 5.4 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 766 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A TYR* 3.4 31.2 - + - -
451B GLN* 5.6 2.7 - - - -
453B HIS* 3.1 50.0 - + + -
732B ARG* 3.9 47.4 + - + +
762B ARG 4.5 10.3 - - - -
763B GLU* 2.9 26.9 + - - +
765B ARG* 1.3 93.9 - - + +
767B LEU* 1.3 63.8 + - + +
768B TRP 3.5 0.7 - - - -
770B PHE* 3.8 15.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 767 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B LEU* 3.6 24.2 - - + +
732B ARG* 3.4 39.3 - - - +
735B VAL* 3.9 14.1 - - + -
753B PHE* 3.9 28.0 - - + -
760B LEU* 5.9 1.6 - - + +
763B GLU* 4.0 14.4 - - + +
764B TRP* 3.0 34.6 + - + +
766B PHE* 1.3 79.6 - - + +
768B TRP* 1.3 66.6 + - - +
769B ASN 3.2 3.3 + - - -
770B PHE* 3.4 23.3 + - + +
773B ILE* 4.2 7.4 - - + +
775B ILE* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 768 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A ARG* 3.2 50.0 - - + -
705A THR* 5.2 6.7 - - + +
692B CYS* 4.5 3.1 - - - -
694B PRO* 3.7 38.0 + - + +
695B THR* 3.6 24.7 + - - +
696B SER* 4.9 3.0 - - - +
764B TRP* 3.1 46.4 + + - +
765B ARG* 3.2 64.8 - - - +
766B PHE 3.5 1.6 - - - -
767B LEU* 1.3 78.8 - - - +
769B ASN* 1.3 67.9 + - - +
770B PHE 3.3 9.1 + - - +
----------------------------------------------------------
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