Contacts of the helix formed by residues 772 - 789 (chain B) in PDB entry 5PWM
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 LEU 772 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A PHE* 4.0 9.8 - - + +
800A TYR* 5.3 10.1 - - + +
848A TYR* 4.7 6.3 - - - +
853A PHE* 3.7 26.9 - - + -
904A MES 5.1 4.7 - - - +
770B GLN* 2.8 26.1 + - + +
771B MET* 1.3 74.6 - - - +
773B PRO* 1.3 76.3 - - + +
774B GLU* 3.2 4.5 - - + +
775B GLU* 3.0 10.7 + - + +
776B GLN* 2.9 19.4 + - - +
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Residues in contact with PRO 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A ARG* 4.1 8.5 - - - +
848A TYR* 4.3 3.1 - - + -
851A ASP* 4.0 10.8 - - - +
853A PHE* 3.9 42.8 - - + -
904A MES 3.6 31.2 - - - +
772B LEU* 1.3 87.3 - - + +
774B GLU* 1.3 57.2 + - - +
776B GLN* 3.5 8.0 + - + +
777B LEU* 3.0 27.9 + - - +
903B EDO 3.8 14.9 - - - -
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Residues in contact with GLU 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A MES 3.5 31.2 + - - +
750B ILE* 3.8 26.2 - - + +
753B ARG* 2.8 44.8 + - - -
772B LEU* 3.1 3.2 + - + +
773B PRO* 1.3 77.2 - - - +
775B GLU* 1.3 66.2 + - - +
777B LEU* 3.3 6.8 + - - +
778B LYS* 2.9 36.7 + - - +
903B EDO 3.8 20.2 + - - +
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Residues in contact with GLU 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B ARG* 3.5 36.3 + - + -
770B GLN 3.4 26.5 - - - +
771B MET* 4.2 6.5 - - - -
772B LEU* 3.0 11.5 + - + +
774B GLU* 1.3 80.2 - - - +
776B GLN* 1.3 65.6 + - - +
778B LYS* 3.2 18.3 + - - +
779B CYS* 3.0 28.8 + - - -
830B VAL* 4.3 9.9 - - + -
872B PHE* 3.4 24.7 - - - -
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Residues in contact with GLN 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A LYS* 4.0 17.2 - - - +
771B MET* 3.6 33.7 - - + +
772B LEU 2.9 12.4 + - - +
773B PRO* 3.5 13.2 - - + +
775B GLU* 1.3 75.8 - - - +
777B LEU* 1.3 57.6 + - - +
779B CYS* 3.3 4.3 + - - +
780B GLU* 3.0 58.1 + - - +
822B LEU* 3.1 42.3 + - - +
825B GLN* 4.9 14.0 - - - +
827B TYR 5.0 1.4 - - - +
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Residues in contact with LEU 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B PRO* 4.4 2.7 - - + -
743B ILE* 3.6 21.0 - - + +
746B ARG* 3.7 55.4 - - + +
747B ILE* 4.2 10.5 - - + -
750B ILE* 4.0 22.4 - - + -
773B PRO 3.0 17.6 + - - +
774B GLU* 3.7 5.8 - - - +
776B GLN* 1.3 78.7 - - - +
778B LYS* 1.3 57.1 + - - +
780B GLU* 3.2 21.6 + - - +
781B PHE* 2.9 30.0 + - - +
903B EDO 4.0 11.2 - - - +
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Residues in contact with LYS 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B ILE* 3.8 22.9 - - + -
750B ILE* 4.4 24.9 - - + +
751B GLN* 6.0 5.4 - - - +
769B ARG* 4.7 8.9 - - - +
774B GLU* 2.9 26.0 + - - +
775B GLU* 3.2 27.5 + - - +
777B LEU* 1.3 75.9 - - - +
779B CYS* 1.4 55.8 + - - +
781B PHE* 3.3 3.1 + - - +
782B LEU* 2.9 28.2 + - - +
871B ILE* 3.8 29.4 + - + +
872B PHE* 3.6 26.8 - - + +
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Residues in contact with CYS 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B MET* 3.8 27.8 - - + -
775B GLU 3.0 20.9 + - - +
776B GLN 3.7 4.0 - - - +
778B LYS* 1.4 71.8 - - - +
780B GLU* 1.3 60.8 + - - +
782B LEU* 3.3 2.4 + - - -
783B LEU* 2.9 26.7 + - - +
822B LEU* 4.1 5.6 - - + -
830B VAL* 4.2 8.5 - - - -
833B PHE* 3.4 46.5 - - + -
872B PHE* 4.1 16.2 - - - -
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Residues in contact with GLU 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A LYS* 2.7 30.7 + - - -
730B ILE* 3.8 25.0 - - + +
731B PRO* 3.5 17.0 - - - +
743B ILE* 3.9 9.6 - - + -
776B GLN* 3.0 33.8 + - - +
777B LEU* 3.2 32.1 + - - +
779B CYS* 1.3 74.6 - - - +
781B PHE* 1.3 57.7 + - - +
783B LEU* 3.3 3.2 + - - +
784B LEU* 2.9 28.9 + - - +
822B LEU* 4.0 21.8 - - + +
823B ASN* 5.7 0.5 - - - -
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Residues in contact with PHE 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743B ILE* 3.6 29.2 - - + -
744B PHE* 3.6 57.0 - + - -
747B ILE* 3.8 30.5 - - + -
751B GLN* 5.9 0.7 - - - -
777B LEU 2.9 16.6 + - - +
778B LYS 3.6 3.8 - - - +
780B GLU* 1.3 76.4 - - - +
782B LEU* 1.3 58.1 + - - +
784B LEU* 3.1 7.8 + - + +
785B LYS* 2.9 43.0 + - + +
870B ASN* 6.1 0.4 - - - -
871B ILE* 3.5 34.1 - - + -
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Residues in contact with LEU 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B LYS 2.9 16.4 + - - +
779B CYS 3.6 4.7 - - - +
781B PHE* 1.3 77.8 - - - +
783B LEU* 1.3 62.7 + - - +
785B LYS* 3.2 3.5 + - - +
786B VAL* 3.2 19.6 + - + +
833B PHE* 3.7 14.4 - - + -
864B PHE* 3.5 41.1 - - + +
867B ASN* 3.6 29.4 - - + -
868B PHE* 3.6 39.7 - - + +
871B ILE* 3.8 10.6 - - + +
872B PHE* 4.2 9.6 - - + -
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Residues in contact with LEU 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B ILE* 3.8 11.9 - - + -
779B CYS 2.9 16.9 + - - +
780B GLU 3.6 4.5 - - - +
782B LEU* 1.3 77.0 - - - +
784B LEU* 1.3 64.0 + - - +
786B VAL* 3.1 5.9 + - - +
787B TYR* 3.1 43.8 + - + -
815B LEU* 3.9 11.4 - - + +
818B VAL* 4.2 5.6 - - + -
819B LYS* 3.7 40.6 - - + +
822B LEU* 3.9 15.5 - - + -
833B PHE* 4.1 8.9 - - + -
837B MET* 3.8 34.3 - - + -
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Residues in contact with LEU 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B VAL* 3.9 16.6 - - + -
724B PHE* 4.4 5.2 - - + -
728B CYS 3.7 12.3 - - - +
729B HIS* 3.9 4.3 - - - -
730B ILE* 3.6 38.0 - - + +
743B ILE* 4.1 14.4 - - + -
744B PHE* 3.7 29.2 - - + -
780B GLU 2.9 14.8 + - - +
781B PHE* 3.1 17.0 + - + +
783B LEU* 1.3 76.5 - - - +
785B LYS* 1.3 65.0 + - + +
787B TYR* 3.1 7.0 + - - +
788B CYS* 2.9 34.8 + - - -
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Residues in contact with LYS 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744B PHE* 4.3 17.1 - - + -
781B PHE* 2.9 51.3 + - + +
782B LEU 3.2 6.9 + - - +
784B LEU* 1.3 73.3 - - + +
786B VAL* 1.3 62.5 + - - +
788B CYS* 3.3 24.8 + - - +
789B ASP* 3.8 2.6 + - - +
863B ILE* 4.1 9.7 - - - +
867B ASN* 2.9 47.7 + - + +
871B ILE* 4.6 5.6 - - + -
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Residues in contact with VAL 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B LEU* 3.2 13.8 + - + +
783B LEU 3.1 8.7 + - - +
785B LYS* 1.3 76.9 - - + +
787B TYR* 1.3 62.8 + - - +
789B ASP* 3.1 16.5 + - - +
792B SER* 3.3 13.2 - - - -
815B LEU* 4.1 28.9 - - + -
837B MET* 3.8 20.6 - - + -
841B PHE* 4.8 1.6 - - + -
860B VAL* 3.8 27.4 - - + -
863B ILE* 4.4 6.5 - - + -
864B PHE* 3.9 31.4 - - + +
867B ASN* 5.9 0.2 - - - +
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Residues in contact with TYR 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B VAL* 3.7 25.0 - - + +
708B CYS* 5.5 0.7 - - - -
728B CYS 5.7 1.6 - - - +
730B ILE* 3.9 11.2 - - + -
783B LEU* 3.1 48.8 + - + -
784B LEU* 3.1 8.0 + - - +
786B VAL* 1.3 76.7 - - - +
788B CYS* 1.3 61.1 + - - +
789B ASP 3.2 2.1 + - - +
792B SER* 3.1 22.9 + - - -
796B ALA* 4.4 9.6 - - + -
815B LEU* 3.1 36.9 + - + -
816B ASN* 2.6 30.4 + - - -
819B LYS* 3.9 26.6 - - - -
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Residues in contact with CYS 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B GLU* 4.2 8.7 - - - +
707B VAL* 3.6 34.8 - - - +
709B ASN* 4.7 5.4 - - - +
744B PHE* 4.8 7.0 - - - -
784B LEU* 2.9 38.3 + - - -
785B LYS* 3.4 23.6 - - - +
786B VAL 3.2 0.6 - - - -
787B TYR* 1.3 77.2 - - - +
789B ASP* 1.3 60.7 + - - +
790B SER* 3.6 1.9 + - - -
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Residues in contact with ASP 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785B LYS 3.8 1.8 + - - +
786B VAL 3.1 11.5 + - - +
787B TYR 3.1 3.6 - - - +
788B CYS* 1.3 78.6 - - - +
790B SER* 1.4 65.4 + - - +
791B LYS* 2.9 44.4 + - - +
792B SER* 2.7 32.5 + - - +
860B VAL* 5.2 5.4 - - + -
863B ILE* 3.9 36.4 - - + +
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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) + - + + + + + -
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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