Contacts of the helix formed by residues 784 - 802 (chain B) in PDB entry 5QSY
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 ASN 784 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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729B MET 5.2 4.2 + - - -
731B GLU* 3.7 47.8 - - + +
782B ASN* 3.1 22.0 + - - +
783B VAL* 1.3 87.8 - - - +
785B THR* 1.3 63.8 + - - +
786B PRO* 4.2 1.3 - - + -
787B VAL* 3.3 8.5 + - + +
788B LYS* 3.2 20.1 + - - +
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Residues in contact with THR 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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783B VAL 3.6 3.8 + - - -
784B ASN* 1.3 68.1 - - - +
786B PRO* 1.4 77.2 - - + +
788B LYS* 2.8 16.1 + - - +
789B GLU* 2.7 51.3 + - + +
836B HIS* 3.9 22.2 + - + +
864B LYS* 4.9 4.0 - - - +
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Residues in contact with PRO 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B GLU* 3.5 36.3 - - - +
732B GLN* 5.0 2.7 - - - +
735B VAL* 4.0 12.3 - - + -
784B ASN* 3.7 3.6 - - + -
785B THR* 1.4 95.0 - - + +
787B VAL* 1.3 57.0 + - - +
789B GLU* 3.0 13.8 + - - +
790B GLN* 2.8 30.1 + - - +
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Residues in contact with VAL 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B GLU* 3.7 44.0 - - + +
734B VAL* 3.5 27.1 - - + -
735B VAL* 3.8 11.7 - - + -
738B LEU* 4.3 3.0 - - + +
779B CYS* 3.9 11.1 - - - +
782B ASN* 3.4 33.4 - - + +
784B ASN* 3.3 9.1 + - + +
785B THR 3.1 1.0 - - - -
786B PRO* 1.3 75.8 - - - +
788B LYS* 1.3 62.4 + - - +
790B GLN* 4.3 1.0 - - - +
791B ALA* 3.2 22.7 + - - +
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Residues in contact with LYS 788 (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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779B CYS 4.1 6.5 - - - +
780B LEU* 3.0 32.5 - - - +
781B SER* 4.8 1.1 - - - -
782B ASN 3.2 27.4 - - - +
783B VAL 4.5 5.8 + - - -
784B ASN 3.2 3.9 + - - +
785B THR* 2.8 21.8 + - - +
787B VAL* 1.3 78.5 - - - +
789B GLU* 1.3 61.5 + - - +
791B ALA* 3.6 2.5 - - - +
792B PHE* 3.0 23.9 + - - +
832B PHE* 3.9 16.4 - - + -
836B HIS* 3.4 33.6 + - + +
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Residues in contact with GLU 789 (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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785B THR* 2.7 37.9 + - + +
786B PRO* 3.6 13.8 - - - +
788B LYS* 1.3 69.5 - - - +
790B GLN* 1.3 65.1 + - - +
792B PHE* 3.2 2.6 + - - +
793B MET* 2.9 30.1 + - + +
832B PHE* 4.1 21.1 - - + -
836B HIS* 4.8 6.1 - - + -
864B LYS* 3.0 43.5 + - + +
868B LEU* 4.4 18.9 - - + +
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Residues in contact with GLN 790 (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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735B VAL* 3.9 30.7 - - + +
738B LEU* 4.0 16.2 - - + -
739B GLN* 3.1 37.2 + - - +
786B PRO 2.8 19.1 + - - +
787B VAL 4.3 1.8 - - - +
789B GLU* 1.3 72.3 - - - +
791B ALA* 1.3 65.6 - - - +
793B MET* 3.3 10.0 + - - +
794B LEU* 2.9 53.1 + - + +
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Residues in contact with ALA 791 (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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738B LEU* 4.2 8.4 - - + +
776B CYS* 3.5 32.7 - - - +
779B CYS* 3.7 15.5 - - + -
780B LEU* 4.1 7.2 - - + -
787B VAL 3.2 19.0 + - - +
788B LYS 3.6 3.6 - - - +
790B GLN* 1.3 78.2 - - - +
792B PHE* 1.3 57.5 + - - +
794B LEU* 3.3 2.1 + - - +
795B LEU* 2.9 36.0 + - - +
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Residues in contact with PHE 792 (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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780B LEU* 3.9 10.0 - - + +
788B LYS 3.0 16.7 + - - +
789B GLU 3.5 3.1 - - - +
791B ALA* 1.3 73.3 - - - +
793B MET* 1.3 68.8 + - - +
795B LEU* 3.2 6.6 + - - +
796B CYS* 3.0 49.7 + - - -
829B LEU* 3.8 35.0 - - + -
832B PHE* 3.4 39.3 - + + -
833B VAL* 3.8 21.5 - - + -
868B LEU* 3.5 48.9 - - + -
872B PHE* 4.1 4.9 - + + -
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Residues in contact with MET 793 (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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789B GLU* 2.9 24.8 + - + +
790B GLN* 3.7 13.7 - - - +
792B PHE* 1.3 75.1 - - - +
794B LEU* 1.3 57.3 + - + +
796B CYS* 3.3 3.5 + - - +
797B ASP* 2.9 31.1 + - + +
867B ASN* 3.9 27.4 - - + +
868B LEU* 3.6 28.5 - - + -
871B ALA* 3.7 22.0 - - + -
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Residues in contact with LEU 794 (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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738B LEU* 3.7 46.4 - - + +
739B GLN* 3.9 11.2 - - - +
742B HIS* 3.4 38.3 - - + +
772B PHE* 4.2 8.7 - - + -
776B CYS* 4.2 8.7 - - - -
790B GLN* 2.9 37.8 + - + +
791B ALA 3.7 3.8 - - - +
793B MET* 1.3 75.9 - - + +
795B LEU* 1.3 52.2 + - - +
797B ASP* 3.4 4.3 + - + +
798B LEU* 2.7 46.7 + - + +
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Residues in contact with LEU 795 (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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773B LEU* 3.6 33.9 - - + +
776B CYS* 3.6 27.6 - - + +
777B GLN* 4.1 2.2 - - - +
780B LEU* 3.6 32.5 - - + -
791B ALA 2.9 20.5 + - - +
792B PHE* 3.2 6.0 + - - +
794B LEU* 1.3 76.6 - - - +
796B CYS* 1.3 55.5 + - - +
798B LEU* 3.1 5.2 + - - +
799B LEU* 2.8 43.0 + - + +
825B LEU* 4.4 19.5 - - + -
829B LEU* 4.1 18.2 - - + -
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Residues in contact with CYS 796 (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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792B PHE* 3.0 56.3 + - - +
793B MET 3.8 2.2 - - - +
795B LEU* 1.3 77.5 - - - +
797B ASP* 1.3 61.6 + - - +
800B MET* 3.4 22.9 + - - +
829B LEU* 4.6 4.7 - - - -
871B ALA* 3.8 27.8 - - + +
872B PHE* 4.1 6.7 - - - -
875B LEU* 3.7 32.2 - - + +
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Residues in contact with ASP 797 (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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742B HIS* 3.1 30.1 + - + +
746B LEU* 4.8 2.9 - - - +
793B MET* 2.9 17.8 + - + +
794B LEU* 3.9 5.4 - - + +
796B CYS* 1.3 77.5 - - - +
798B LEU* 1.3 56.0 + - - +
800B MET* 3.5 8.2 - - - +
801B ILE* 3.0 49.6 + - - +
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Residues in contact with LEU 798 (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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742B HIS* 3.7 24.2 - - + +
745B ILE* 4.3 14.8 - - + -
746B LEU* 5.3 0.4 - - + -
769B VAL* 5.2 2.9 - - + +
772B PHE* 3.5 34.8 - - + -
773B LEU* 4.2 28.4 - - + +
776B CYS* 4.8 3.6 - - - -
794B LEU* 2.7 30.9 + - + +
795B LEU 3.1 3.8 + - - +
797B ASP* 1.3 69.7 - - - +
799B LEU* 1.3 59.6 + - - +
801B ILE* 3.3 5.8 + - + -
802B PHE* 3.0 60.5 + - + +
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Residues in contact with LEU 799 (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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773B LEU* 4.5 18.8 - - + -
795B LEU* 2.8 27.8 + - + +
798B LEU* 1.3 68.7 - - - +
800B MET* 1.3 66.5 + - - +
802B PHE* 3.1 22.1 - - - +
803B SER* 3.4 9.4 - - - -
819B PHE* 4.6 14.5 - - + +
821B PRO* 4.0 37.0 - - + -
825B LEU* 4.5 9.4 - - + -
829B LEU* 3.7 29.4 - - + -
875B LEU* 3.6 24.2 - - + -
880B ILE* 4.1 8.3 - - + +
881B VAL* 5.4 0.4 - - + -
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Residues in contact with MET 800 (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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796B CYS 3.4 17.9 + - - +
797B ASP* 3.5 11.0 + - - +
799B LEU* 1.3 77.8 - - - +
801B ILE* 1.3 63.0 + - + +
803B SER* 3.4 13.5 + - - -
805B GLN* 4.3 10.2 - - - +
874B LYS* 3.3 67.1 - - + +
875B LEU* 3.9 12.6 - - + +
878B TYR* 4.0 31.6 - - + -
880B ILE* 4.3 7.6 - - + -
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Residues in contact with ILE 801 (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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742B HIS* 4.5 2.9 - - + -
746B LEU* 3.6 24.5 - - + -
749B LEU* 3.4 31.2 - - + -
797B ASP* 3.0 50.7 + - - +
798B LEU* 3.7 6.5 - - + +
799B LEU 3.2 0.4 - - - -
800B MET* 1.3 79.9 - - + +
802B PHE* 1.3 73.9 + - + +
803B SER 3.6 3.1 + - - -
805B GLN* 5.5 0.3 - - - +
806B LEU* 3.7 21.5 + - - +
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Residues in contact with PHE 802 (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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745B ILE* 3.8 25.4 - - + -
746B LEU* 5.7 1.1 - - + -
749B LEU* 3.9 37.2 - - + -
765B LEU* 4.6 2.9 - - + -
769B VAL* 3.9 31.6 - - + -
773B LEU* 6.0 0.9 - - + -
798B LEU* 3.0 35.2 + - + +
799B LEU 3.1 10.6 - - - +
801B ILE* 1.3 85.8 - - + +
803B SER* 1.3 57.0 + - - +
806B LEU* 3.7 14.1 - - + -
817B LEU* 3.3 39.0 - - + +
818B VAL* 4.3 1.3 - - - -
819B PHE* 3.1 35.2 + - + +
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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