Contacts of the helix formed by residues 874 - 892 (chain B) in PDB entry 2HRC
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 874 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736B CYS* 4.2 13.3 - - - +
739B ASP* 5.3 3.6 - - - +
740B HIS* 3.1 29.8 + - + -
871B LEU* 2.9 18.6 + - + +
872B ASN 3.4 1.3 - - - +
873B GLY* 1.3 75.2 - - - +
875B PRO* 1.3 72.5 - - - +
876B LEU* 2.9 26.1 - - - +
877B PHE* 2.9 32.6 + - + +
878B SER* 3.4 6.2 + - - -
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Residues in contact with PRO 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B LEU* 5.1 1.2 - - - +
873B GLY 3.3 9.9 - - - +
874B ASN* 1.3 92.0 - - - +
876B LEU* 1.3 61.1 + - - +
878B SER* 3.2 13.2 + - - +
879B LYS* 3.1 20.6 + - - +
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Residues in contact with LEU 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B LEU* 4.0 23.5 - - + +
735B GLN* 3.7 37.7 - - + +
736B CYS* 3.7 18.6 - - - -
739B ASP* 3.7 13.9 - - - +
874B ASN* 2.9 16.0 - - - +
875B PRO* 1.3 78.5 - - - +
877B PHE* 1.3 57.8 + - - +
879B LYS* 3.2 21.7 + - + +
880B ALA* 2.9 24.8 + - - +
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Residues in contact with PHE 877 (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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639B GLN* 3.3 46.4 - - + -
690B GLN* 4.7 2.5 - - - -
727B TRP* 3.8 25.8 - + - -
733B LEU* 4.2 3.6 - - + -
736B CYS* 3.6 15.2 - - - -
838B THR* 3.4 34.3 - - + -
871B LEU* 3.8 22.9 - - + -
872B ASN 4.1 3.4 - - - -
874B ASN* 2.9 18.8 + - + +
876B LEU* 1.3 78.2 - - - +
878B SER* 1.3 64.0 + - - +
880B ALA* 3.0 12.5 + - + +
881B LEU* 3.0 43.2 + - + +
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Residues in contact with SER 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B LYS 4.6 1.0 + - - -
639B GLN* 4.1 19.3 + - - +
642B GLY* 4.1 26.5 - - - -
643B MET* 4.1 3.8 - - - -
646B LEU* 3.8 5.8 - - - +
873B GLY 5.2 2.3 + - - -
874B ASN 3.4 7.5 + - - -
875B PRO* 3.2 14.0 + - - +
877B PHE* 1.3 79.0 - - - +
879B LYS* 1.3 58.3 + - - +
881B LEU* 3.3 14.0 + - - +
882B ALA* 3.0 28.1 + - - +
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Residues in contact with LYS 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B LEU* 3.5 20.6 - - + +
732B LEU* 4.0 11.4 - - + -
875B PRO 3.1 11.5 + - - +
876B LEU* 3.4 24.1 - - + +
877B PHE 3.1 0.6 - - - -
878B SER* 1.3 75.5 - - - +
880B ALA* 1.3 59.2 + - - +
882B ALA* 3.8 0.7 - - + +
883B ASP* 2.9 49.1 + - - +
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Residues in contact with ALA 880 (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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727B TRP* 5.5 2.9 - - + -
730B HIS* 4.1 6.2 - - + +
732B LEU* 3.6 33.6 - - + +
733B LEU* 4.2 11.7 - - + +
876B LEU 2.9 10.8 + - - +
877B PHE* 3.2 23.6 - - + +
879B LYS* 1.3 77.9 - - - +
881B LEU* 1.3 61.6 + - - +
883B ASP* 3.4 1.9 + - - +
884B LEU* 3.0 30.2 + - - +
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Residues in contact with LEU 881 (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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573B MET* 4.3 13.2 - - + -
639B GLN* 3.8 39.0 - - + +
643B MET* 3.9 17.7 - - + -
688B PHE* 3.6 25.9 - - + -
690B GLN* 3.8 14.8 - - - +
727B TRP* 4.0 11.2 - - + -
877B PHE* 3.0 39.8 + - + +
878B SER* 3.6 8.1 - - - +
879B LYS 3.3 0.2 - - - -
880B ALA* 1.3 77.0 - - - +
882B ALA* 1.3 61.1 + - - +
884B LEU* 3.3 3.3 + - - +
885B VAL* 3.1 27.4 + - - +
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Residues in contact with ALA 882 (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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643B MET* 3.9 18.1 - - - +
646B LEU* 3.7 30.7 - - + -
647B LEU* 3.5 10.4 - - + +
650B LEU* 3.7 12.6 - - + -
878B SER 3.0 16.8 + - - +
879B LYS 3.9 3.1 - - - +
880B ALA 3.3 0.4 - - - -
881B LEU* 1.3 78.1 - - - +
883B ASP* 1.3 57.1 + - - +
885B VAL 3.3 0.7 + - - -
886B HIS* 2.8 30.1 + - - +
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Residues in contact with ASP 883 (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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650B LEU* 3.9 19.2 - - - +
730B HIS* 4.1 15.0 - - + +
731B HIS* 5.1 3.9 + - + -
732B LEU* 3.1 25.6 - - - +
879B LYS* 2.9 31.6 + - - +
880B ALA 3.8 3.6 - - - +
882B ALA* 1.3 74.5 - - - +
884B LEU* 1.3 60.2 + - - +
886B HIS* 3.7 7.1 + - - +
887B SER* 2.9 38.3 + - - +
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Residues in contact with LEU 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B PHE* 3.7 20.6 - - + -
724B ILE* 3.8 13.4 - - + +
726B ARG 5.4 0.2 - - - +
727B TRP* 3.3 59.2 - - + -
730B HIS* 3.4 31.2 + - + -
880B ALA 3.0 18.6 + - - +
881B LEU* 3.5 5.2 - - - +
882B ALA 3.3 0.2 - - - -
883B ASP* 1.3 76.0 - - - +
885B VAL* 1.3 57.1 + - - +
887B SER* 3.9 4.1 - - - -
888B HIS* 3.0 29.6 + - - +
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Residues in contact with VAL 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B ILE* 3.5 29.8 - - + -
643B MET* 4.1 11.4 - - - -
647B LEU* 3.8 16.2 - - + -
686B ILE* 4.0 5.4 - - + -
688B PHE* 3.6 27.6 - - + -
724B ILE* 3.8 11.7 - - + -
881B LEU 3.1 16.1 + - - +
882B ALA 3.8 3.6 - - - +
884B LEU* 1.3 76.5 - - - +
886B HIS* 1.3 57.3 + - - +
888B HIS* 3.2 2.1 + - - +
889B ILE* 2.9 44.9 + - + +
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Residues in contact with HIS 886 (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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647B LEU* 4.1 9.1 - - + +
650B LEU* 3.5 42.2 + - + +
651B SER* 4.0 21.8 + - - -
882B ALA 2.8 18.5 + - - +
883B ASP* 3.7 10.6 + - - +
885B VAL* 1.3 78.0 - - - +
887B SER* 1.3 62.4 + - - +
889B ILE* 3.3 6.5 + - + +
890B GLN* 3.0 55.9 + - + +
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Residues in contact with SER 887 (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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730B HIS* 5.7 1.2 + - - -
883B ASP* 2.9 24.7 + - - +
884B LEU* 4.0 5.2 - - - -
886B HIS* 1.3 74.0 + - - +
888B HIS* 1.3 63.9 + - - +
890B GLN* 3.3 8.8 + - - +
891B SER* 2.9 27.4 + - - -
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Residues in contact with HIS 888 (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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684B ARG* 3.9 7.3 + - - -
686B ILE* 3.9 26.2 - - + +
722B SER* 2.8 32.1 + - - -
723B THR 3.4 19.8 + - - -
724B ILE* 3.5 24.5 - - + +
884B LEU 3.0 19.6 + - - +
885B VAL 3.2 4.0 + - - +
887B SER* 1.3 76.7 - - - +
889B ILE* 1.3 63.1 + - - +
891B SER* 2.9 20.2 + - - -
892B ASN* 3.3 6.6 + - - -
893B GLU* 3.2 34.0 + - + +
895B CYS* 5.6 0.7 - - - -
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Residues in contact with ILE 889 (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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569B THR* 4.6 5.6 - - + -
647B LEU* 5.3 0.7 - - + -
651B SER* 4.5 9.6 - - - +
654B THR* 3.8 39.5 - - + +
657B HIS* 4.5 7.4 - - - +
684B ARG* 3.8 24.9 + - - +
686B ILE* 3.9 21.3 - - + -
885B VAL* 2.9 37.2 + - + +
886B HIS* 3.6 7.0 - - - +
888B HIS* 1.3 77.5 - - - +
890B GLN* 1.3 65.6 + - + +
892B ASN* 3.3 21.1 + - - +
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Residues in contact with GLN 890 (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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651B SER* 6.0 0.2 - - - +
886B HIS* 3.0 54.4 + - + +
887B SER* 3.3 7.0 + - - +
889B ILE* 1.3 79.3 - - + +
891B SER* 1.3 60.6 + - - +
892B ASN* 3.3 10.0 + - - -
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Residues in contact with SER 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B SER 2.9 15.4 + - - -
888B HIS* 2.9 19.1 + - - -
890B GLN* 1.3 76.3 - - - +
892B ASN* 1.3 69.4 + - - +
893B GLU* 3.0 41.3 + - - +
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Residues in contact with ASN 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B ARG* 5.1 8.7 + - - +
888B HIS 3.3 2.6 + - - -
889B ILE* 3.3 16.8 + - - +
890B GLN 3.9 10.9 + - - -
891B SER* 1.3 78.2 + - - +
893B GLU* 1.3 65.4 + - - +
894B LEU* 3.7 9.2 + - - +
923B LEU* 5.0 13.4 - - + +
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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
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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