Contacts of the helix formed by residues 765 - 780 (chain B) in PDB entry 2IVS
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 765 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911A GLY 3.6 3.0 + - - -
912A ARG* 3.6 24.5 - - - +
913A ILE 3.3 18.8 - - - -
914A PRO* 4.0 1.1 - - - -
915A VAL* 3.9 3.0 - - - +
763B ASN 3.6 0.8 + - - -
764B ALA* 1.3 76.5 - - - +
766B PRO* 1.3 70.1 - - - +
767B SER* 3.5 6.2 + - - -
768B GLU* 3.0 31.5 + - - +
769B LEU* 3.1 21.8 + - - +
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Residues in contact with PRO 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A GLN* 3.5 22.7 - - - +
911A GLY 3.4 16.6 - - - +
913A ILE 3.1 16.8 - - - +
915A VAL* 3.7 13.9 - - + -
918A MET* 3.5 30.1 - - + -
923A LEU* 4.1 7.6 - - + +
702B LEU* 3.3 21.0 - - + +
765B SER* 1.3 86.0 - - - +
767B SER* 1.3 57.2 + - - +
769B LEU* 3.4 1.1 + - + -
770B ARG* 2.8 27.9 + - - +
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Residues in contact with SER 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A GLN* 3.7 25.8 - - - +
911A GLY 3.0 19.3 + - - -
912A ARG* 3.9 14.9 - - - +
765B SER* 3.2 3.7 + - - -
766B PRO* 1.3 76.7 - - - +
768B GLU* 1.3 59.4 + - - +
770B ARG* 3.6 2.4 - - - +
771B ASP* 2.9 36.1 + - - +
912B ARG* 3.7 26.0 + - - -
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Residues in contact with GLU 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B GLU 4.7 6.7 - - - +
735B PHE* 3.5 41.0 - - + +
760B LEU* 4.0 8.9 - - + +
761B LYS* 6.1 0.2 - - - +
763B ASN 4.1 3.1 - - - +
764B ALA* 3.3 9.9 - - - -
765B SER* 3.0 37.9 + - - +
767B SER* 1.3 74.9 + - - +
769B LEU* 1.3 61.2 + - - +
771B ASP* 3.3 6.9 + - - +
772B LEU* 3.0 25.3 + - - +
912B ARG* 5.6 2.7 - - - +
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Residues in contact with LEU 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A VAL* 5.3 7.6 - - + -
957A PRO* 6.0 0.4 - - + -
958A GLU* 3.8 24.5 - - + +
961A PHE* 3.9 15.7 - - + -
702B LEU* 4.0 14.4 - - + -
706B VAL* 3.8 14.8 - - + -
760B LEU* 3.8 28.8 - - + +
764B ALA* 5.5 0.2 - - + -
765B SER 3.1 12.9 + - - +
766B PRO 3.8 6.3 - - - +
768B GLU* 1.3 74.0 - - - +
770B ARG* 1.3 65.4 + - - +
772B LEU* 3.2 6.2 + - + +
773B LEU* 3.1 31.4 + - + +
800B LEU* 3.9 27.6 - - + -
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Residues in contact with ARG 770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A GLN* 3.9 24.7 - - + +
702B LEU* 3.8 16.7 - - + +
766B PRO 2.8 21.4 + - - +
767B SER* 3.6 5.4 - - - +
769B LEU* 1.3 72.9 - - - +
771B ASP* 1.3 62.7 + - - +
773B LEU* 3.3 3.4 + - - +
774B SER* 2.8 35.9 + - - -
897B ARG* 5.7 5.2 - - - +
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Residues in contact with ASP 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B GLU* 2.8 19.5 - - - +
735B PHE* 3.7 13.1 - - + +
767B SER 2.9 17.6 + - - +
768B GLU* 3.3 9.0 + - - +
770B ARG* 1.3 79.6 - - - +
772B LEU* 1.3 57.0 + - - +
774B SER* 3.4 1.4 + - - -
775B GLU* 2.9 25.3 + - - +
894B GLY* 3.2 32.4 - - - +
895B LEU* 4.0 0.4 - - - -
897B ARG* 3.9 7.6 + - - -
912B ARG* 2.5 45.7 + - - -
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Residues in contact with LEU 772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B PHE* 5.2 0.9 - - + -
735B PHE* 3.6 35.5 - - + -
758B LYS 4.5 5.2 - - - +
759B MET* 4.3 8.3 - - - -
760B LEU* 4.0 33.7 - - + +
768B GLU 3.0 10.9 + - - +
769B LEU* 3.2 9.6 + - + +
771B ASP* 1.3 74.8 - - - +
773B LEU* 1.3 77.4 + - + +
775B GLU* 3.2 1.9 + - - +
776B PHE* 3.0 22.5 + - - +
800B LEU* 4.5 23.1 - - + +
802B LEU* 3.4 37.9 - - + +
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Residues in contact with LEU 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B LEU* 3.9 21.5 - - + -
705B SER* 3.8 30.3 - - - +
706B VAL* 3.9 18.6 - - + +
709B PHE* 3.6 45.5 - - + -
769B LEU* 3.1 19.5 + - + +
770B ARG* 3.9 3.1 - - - +
772B LEU* 1.3 84.3 - - + +
774B SER* 1.3 57.9 + - - +
776B PHE* 3.4 4.4 + - - +
777B ASN* 2.7 45.7 + - - +
800B LEU* 4.5 5.4 - - + -
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Residues in contact with SER 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770B ARG* 2.8 22.6 + - - -
771B ASP* 3.6 5.2 - - - -
773B LEU* 1.3 73.4 - - - +
775B GLU* 1.3 59.4 + - - +
777B ASN* 3.2 4.6 + - - +
778B VAL* 2.9 36.8 + - - +
893B PHE 4.6 1.6 + - - -
894B GLY 4.1 6.0 + - - -
896B SER 4.0 5.4 + - - -
897B ARG* 3.2 27.3 + - - -
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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
----------------------------------------------------------
735B PHE* 3.1 19.0 - - + -
758B LYS* 2.9 29.6 + - - -
771B ASP 2.9 13.3 + - - +
772B LEU 3.2 7.6 + - - +
774B SER* 1.3 74.7 - - - +
776B PHE* 1.3 58.2 + - - +
778B VAL* 4.0 0.2 - - - +
779B LEU* 3.0 52.4 + - + +
788B ILE* 5.3 1.4 - - - +
802B LEU* 4.3 11.1 - - + +
804B VAL* 5.7 1.6 - - - -
892B ASP* 3.5 10.9 + - - -
893B PHE* 2.7 41.4 + - + +
894B GLY* 4.0 7.4 - - - +
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Residues in contact with PHE 776 (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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709B PHE* 3.4 33.7 - + + -
717B TRP* 4.0 21.1 - + + -
772B LEU 3.0 8.5 + - - +
773B LEU* 3.5 8.7 - - - +
774B SER 3.3 0.2 - - - -
775B GLU* 1.3 77.1 - - - +
777B ASN* 1.3 72.0 + - - +
779B LEU* 5.0 0.4 - - - -
780B LYS* 3.2 59.6 + - + +
790B LEU* 3.8 31.1 - - + +
792B GLY 4.6 0.7 - - - -
793B ALA* 3.8 16.8 - - + -
802B LEU* 3.7 32.5 - - + +
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Residues in contact with ASN 777 (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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705B SER* 5.9 3.8 - - - -
709B PHE* 5.7 1.2 - - - -
773B LEU* 2.7 38.4 + - - +
774B SER* 3.2 5.6 + - - +
776B PHE* 1.3 83.3 - - - +
778B VAL* 1.3 61.2 + - + +
780B LYS* 2.9 38.4 + - - +
781B GLN* 3.2 24.8 + - - +
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Residues in contact with VAL 778 (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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774B SER* 2.9 24.1 + - - +
775B GLU 4.0 2.5 - - - +
777B ASN* 1.3 74.2 - - + +
779B LEU* 1.3 62.0 + - - +
780B LYS 3.1 2.0 - - - -
781B GLN* 2.9 34.9 + - - +
782B VAL* 3.6 7.8 - - + +
870B LEU* 4.0 35.9 - - + -
893B PHE* 3.7 29.8 - - + -
896B SER* 3.5 25.6 - - - +
898B ASP* 5.4 4.5 - - + +
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Residues in contact with LEU 779 (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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717B TRP* 5.0 2.1 - - - -
775B GLU* 3.0 45.0 + - + +
776B PHE 4.3 1.3 - - - +
778B VAL* 1.3 77.9 - - - +
780B LYS* 1.3 60.4 + - - +
781B GLN 3.1 0.7 + - - -
782B VAL* 3.4 24.2 + - + +
787B VAL* 4.1 7.4 - - + -
788B ILE* 3.7 34.5 - - + +
790B LEU* 3.7 34.5 + - + +
804B VAL* 4.4 12.6 - - + -
893B PHE* 3.6 34.8 - - + -
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Residues in contact with LYS 780 (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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717B TRP* 3.4 60.8 - - + +
776B PHE* 3.2 42.5 + - + +
777B ASN* 2.9 38.3 + - - +
778B VAL 3.1 1.0 + - - -
779B LEU* 1.3 77.5 - - - +
781B GLN* 1.3 60.4 + - + +
782B VAL 3.3 1.8 + - - +
790B LEU* 3.6 10.3 - - + +
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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
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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