Contacts of the helix formed by residues 848 - 863 (chain D) in PDB entry 1SO2
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 848 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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830D ASN* 4.3 2.6 - - - +
846D ASP 3.9 2.6 + - - -
847D ARG* 1.3 71.0 - - - +
849D VAL* 1.3 65.1 + - - +
850D LEU 3.4 2.5 - - - -
851D GLU* 3.4 7.2 + - - -
852D ASN* 2.9 29.2 + - - -
891D LEU* 3.8 18.7 + - - +
894D ASP* 2.9 30.7 + - - +
896D LYS* 5.9 4.0 - - - +
897D LYS* 3.6 24.6 - - - -
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Residues in contact with VAL 849 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830D ASN* 3.3 16.3 + - + +
833D LEU* 4.1 16.6 - - + -
834D VAL* 4.3 11.0 - - + -
840D GLN* 3.3 41.3 - - + +
841D ALA* 3.8 11.4 - - + +
844D TYR* 4.0 8.8 - - + -
846D ASP* 3.7 34.8 - - - +
847D ARG 2.6 9.3 + - - +
848D SER* 1.3 72.6 - - - +
850D LEU* 1.3 64.0 + - - +
852D ASN* 3.5 2.9 + - - +
853D HIS* 3.1 20.1 + - - +
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Residues in contact with LEU 850 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D 666 6.1 4.0 - - + -
825D HIS* 3.6 16.2 - - + +
826D PRO* 3.4 34.1 - - + -
828D ARG 3.3 20.6 - - - +
829D THR* 4.3 1.3 - - - -
830D ASN* 3.0 29.3 + - - +
833D LEU* 3.6 19.7 - - + -
840D GLN* 5.3 4.9 - - - +
849D VAL* 1.3 73.6 - - - +
851D GLU* 1.3 72.3 + - - +
853D HIS* 3.2 8.6 + - + +
854D HIS* 2.8 48.6 + - + +
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Residues in contact with GLU 851 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D MG 4.1 11.6 - - - -
830D ASN* 3.2 16.9 + - - -
848D SER* 3.4 7.2 + - - +
850D LEU* 1.3 86.9 - - - +
852D ASN* 1.3 67.7 + - - +
854D HIS* 3.0 13.7 + - + +
855D ALA* 3.0 25.1 + - - +
890D ILE* 3.7 7.5 - - + +
891D LEU* 3.9 22.9 - - + -
893D THR* 3.7 24.6 - - - +
894D ASP* 3.0 46.0 - - + +
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Residues in contact with ASN 852 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844C TYR* 5.1 1.7 - - - +
845C ASN* 3.2 21.6 + - - +
847C ARG* 4.9 6.5 + - - +
844D TYR* 3.3 34.8 + - + +
847D ARG* 3.0 29.3 + - - +
848D SER* 2.9 22.2 + - - +
849D VAL 3.7 1.3 - - - +
851D GLU* 1.3 71.7 - - - +
853D HIS* 1.3 56.4 + - - +
856D ALA* 2.8 34.7 + - - +
891D LEU* 3.1 23.2 - - - +
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Residues in contact with HIS 853 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843C LEU* 6.3 0.2 - - - +
823D TYR 4.4 6.5 - - - -
824D ASP* 3.0 38.3 + - + -
826D PRO* 5.9 0.9 - - + -
840D GLN* 3.3 36.8 + - + +
843D LEU* 6.3 0.2 - - - +
844D TYR* 4.0 18.2 + - + -
849D VAL 3.1 13.8 + - - +
850D LEU* 3.2 11.7 - - + +
851D GLU 3.1 0.2 - - - -
852D ASN* 1.3 75.5 - - - +
854D HIS* 1.3 64.8 + + - +
856D ALA* 4.7 0.4 - - - -
857D SER* 2.8 55.6 + - - -
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Residues in contact with HIS 854 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D MG 4.0 3.7 - - - -
820D MET 3.9 7.2 - - - +
821D HIS 3.0 33.9 - - - +
822D ASP* 3.4 24.3 + - - -
823D TYR* 2.6 35.4 + - - +
824D ASP 4.4 1.1 - - - -
825D HIS* 3.7 24.1 - + + -
826D PRO* 4.9 0.2 - - + -
850D LEU* 2.8 49.7 + - + +
851D GLU* 3.0 11.9 + - + +
853D HIS* 1.3 79.6 - + - +
855D ALA* 1.3 61.8 + - - +
857D SER* 3.8 1.4 - - - -
858D ALA* 3.1 22.7 + - - +
890D ILE* 4.3 2.7 - - + -
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Residues in contact with ALA 855 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845C ASN* 3.6 17.9 - - - +
851D GLU 3.0 10.0 + - - +
852D ASN 4.0 1.1 - - - +
854D HIS* 1.3 78.3 - - - +
856D ALA* 1.3 60.8 + - - +
858D ALA* 4.1 1.7 - - - +
859D TRP* 3.0 32.4 + - + -
887D ILE* 4.5 14.1 - - + -
890D ILE* 3.6 39.9 - - + +
891D LEU* 5.4 2.2 - - + -
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Residues in contact with ALA 856 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842C VAL* 3.2 18.7 - - - +
843C LEU* 3.1 32.7 - - + +
845C ASN* 3.3 7.2 + - - +
844D TYR* 3.7 7.2 - - - +
852D ASN 2.8 23.5 + - - +
853D HIS* 4.3 0.7 - - - +
855D ALA* 1.3 74.4 - - - +
857D SER* 1.3 60.3 + - - +
859D TRP* 4.2 2.5 - - - -
860D ASN* 3.2 23.7 + - - +
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Residues in contact with SER 857 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823D TYR* 3.7 27.0 - - - -
824D ASP* 5.0 1.2 + - - -
853D HIS* 2.8 44.8 + - - -
855D ALA 3.3 0.2 - - - -
856D ALA* 1.3 77.4 - - - +
858D ALA* 1.3 59.2 + - - +
860D ASN* 3.6 7.9 + - - +
861D LEU* 3.2 24.4 + - - +
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Residues in contact with ALA 858 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723D TYR* 3.1 20.4 + - - +
727D LEU* 4.1 8.3 - - + -
820D MET* 3.9 30.3 - - + -
823D TYR* 3.9 9.1 - - + -
854D HIS 3.1 15.9 + - - +
855D ALA 4.1 1.6 - - - +
857D SER* 1.3 76.1 - - - +
859D TRP* 1.3 53.9 + - - +
861D LEU* 2.8 9.9 + - - +
862D TYR 2.6 32.7 + - - -
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Residues in contact with TRP 859 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842C VAL* 4.0 16.2 - - + -
845C ASN* 4.8 2.2 - - - -
816D VAL* 5.5 1.1 - - + -
820D MET* 4.6 13.7 - - + -
855D ALA* 3.0 27.8 + - - +
856D ALA 4.4 0.4 - - - +
858D ALA* 1.3 77.8 - - - +
860D ASN* 1.3 53.9 + - - +
862D TYR* 3.5 36.1 - + + +
863D LEU* 2.7 47.0 + - + +
871D LEU* 4.7 2.7 - - + -
879D PHE* 4.1 15.7 - + - -
882D PHE* 4.0 21.3 - + - -
883D ARG* 3.4 57.0 + - + +
886D VAL* 3.4 36.1 - - + +
887D ILE* 4.1 10.9 - - + +
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Residues in contact with ASN 860 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842C VAL* 3.8 13.2 - - + +
856D ALA 3.2 18.0 + - - +
857D SER* 3.6 9.3 + - - +
858D ALA 3.2 0.4 - - - -
859D TRP* 1.3 77.6 - - - +
861D LEU* 1.3 65.6 + - - +
863D LEU* 3.3 5.6 + - - +
864D SER* 3.0 30.9 + - - -
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Residues in contact with LEU 861 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723D TYR* 3.9 17.9 - - + -
726D ALA* 3.9 22.2 - - + +
727D LEU* 4.1 10.8 - - + -
823D TYR* 3.4 30.7 - - + +
857D SER 3.2 9.6 + - - +
858D ALA 2.8 9.8 + - - +
860D ASN* 1.3 82.5 - - - +
862D TYR* 1.3 58.4 + - - +
863D LEU 3.0 1.3 - - - -
864D SER* 2.6 36.9 + - - +
868D TYR* 3.3 27.9 - - + +
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Residues in contact with TYR 862 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723D TYR* 3.4 28.9 - + + +
820D MET* 5.6 0.2 - - + -
858D ALA 2.6 15.4 + - - +
859D TRP* 3.1 31.2 + + + +
861D LEU* 1.3 73.6 - - - +
863D LEU* 1.3 71.9 + - + +
864D SER 3.3 0.9 + - - -
865D ARG 3.7 13.3 - - - +
868D TYR* 3.4 17.6 - - - +
869D ASN* 3.3 23.9 + - + +
870D PHE* 3.3 34.5 + + - -
871D LEU* 3.0 46.5 + - + +
879D PHE* 3.9 20.6 - + - -
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Residues in contact with LEU 863 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837C ASN* 5.8 12.1 - - + +
842C VAL* 4.2 25.6 - - + -
859D TRP* 2.7 33.7 + - + +
860D ASN* 3.4 6.1 - - - +
862D TYR* 1.3 94.0 - - + +
864D SER* 1.3 61.5 + - - +
865D ARG 3.4 4.0 - - - -
869D ASN* 6.2 1.1 - - - +
879D PHE* 4.8 13.2 - - + -
883D ARG* 4.9 8.5 - - - +
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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