Contacts of the helix formed by residues 856 - 873 (chain A) in PDB entry 6S1M
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 ASP 856 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850A ARG* 3.3 19.7 + - + +
851A LEU* 4.8 1.5 - - - +
854A ASP* 3.2 13.6 - - + +
855A ARG* 1.3 78.0 - - - +
857A PRO* 1.3 61.0 - - - +
858A GLU* 2.7 45.3 + - - +
859A GLY* 3.1 14.7 + - - -
860A ALA* 3.5 14.6 + - - +
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Residues in contact with PRO 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851A LEU* 4.4 18.4 - - + -
855A ARG 3.4 11.2 - - - +
856A ASP* 1.3 84.8 - - - +
858A GLU* 1.3 75.8 + - - +
860A ALA* 3.3 9.4 + - + +
861A VAL* 2.9 32.9 + - + +
973A ILE* 5.9 7.0 - - + -
974A LEU* 5.8 6.1 - - + -
978A ARG* 4.3 12.2 + - - +
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Residues in contact with GLU 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A ASP* 2.7 27.4 + - - +
857A PRO* 1.3 86.3 - - - +
859A GLY* 1.3 59.0 + - - +
861A VAL* 3.4 7.3 + - - +
862A ALA* 3.0 28.6 + - - +
985A ARG* 5.3 9.8 + - - +
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Residues in contact with GLY 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850A ARG* 5.0 12.7 - - - -
856A ASP* 3.1 18.9 + - - -
858A GLU* 1.3 75.4 - - - +
860A ALA* 1.3 56.8 + - - +
862A ALA* 3.8 6.5 - - - +
863A HIS* 2.9 29.8 + - - +
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Residues in contact with ALA 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A SER* 4.9 10.2 + - - +
850A ARG* 4.4 15.1 - - + +
851A LEU* 4.6 6.7 - - + -
856A ASP 3.5 12.9 + - - +
857A PRO* 3.3 13.6 + - + +
858A GLU 3.2 0.6 - - - -
859A GLY* 1.3 74.7 - - - +
861A VAL* 1.3 59.3 + - - +
863A HIS* 3.3 6.5 + - - +
864A ALA* 3.0 29.6 + - - +
970A PHE* 4.1 26.5 - - + -
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Residues in contact with VAL 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A PRO* 2.9 21.8 + - + +
858A GLU* 3.8 4.5 - - - +
860A ALA* 1.3 74.4 - - - +
862A ALA* 1.3 58.1 + - - +
864A ALA* 3.4 5.9 + - - +
865A GLN* 2.9 28.9 + - - +
970A PHE* 5.4 1.8 - - + -
978A ARG* 3.3 31.2 - - - +
982A VAL* 5.5 1.6 - - + -
985A ARG* 1.9 83.4 - - - +
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Residues in contact with ALA 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A GLU 3.0 17.6 + - - +
859A GLY* 3.8 7.4 - - - +
861A VAL* 1.3 77.1 - - - +
863A HIS* 1.3 57.3 + - - +
865A GLN* 3.5 11.5 + - - +
866A ASP* 3.0 28.4 + - - +
985A ARG* 5.5 0.7 - - - +
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Residues in contact with HIS 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A LEU* 3.8 16.8 - - + +
846A ALA* 3.7 30.4 - - + +
847A SER* 5.2 3.4 + - - +
850A ARG* 5.2 17.0 - - + -
859A GLY 2.9 19.4 + - - +
860A ALA* 3.5 7.9 - - - +
861A VAL 3.2 0.2 - - - -
862A ALA* 1.3 73.9 - - - +
864A ALA* 1.3 60.2 + - - +
866A ASP* 3.1 7.5 + - + +
867A VAL* 3.0 47.3 + - + +
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Residues in contact with ALA 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A LEU* 4.4 21.1 - - + +
847A SER* 5.2 0.9 - - - +
860A ALA 3.0 16.1 + - - +
861A VAL* 4.0 5.4 - - - +
863A HIS* 1.3 75.5 - - - +
865A GLN* 1.3 57.2 + - - +
867A VAL* 3.3 2.9 + - - +
868A ILE* 3.0 40.0 + - + +
966A LEU* 5.0 15.7 - - + -
970A PHE* 5.1 11.9 - - + -
982A VAL* 5.3 9.4 - - + -
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Residues in contact with GLN 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861A VAL* 2.9 19.0 + - - +
862A ALA* 3.5 9.0 - - - +
864A ALA* 1.3 77.2 - - - +
866A ASP* 1.3 54.2 + - - +
868A ILE* 3.4 6.4 + - - +
869A SER* 2.7 38.0 + - - -
985A ARG* 2.9 74.9 - - + +
988A HIS* 5.5 5.1 - - - +
989A THR* 3.5 18.7 - - + +
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Residues in contact with ASP 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862A ALA 3.0 17.9 + - - +
863A HIS* 3.7 7.2 - - + +
865A GLN* 1.3 75.3 - - - +
867A VAL* 1.3 60.6 + - + +
869A SER* 3.8 6.1 - - - -
870A ASP* 2.9 35.2 + - - +
875A ARG* 5.7 2.6 + - - -
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Residues in contact with VAL 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A LEU* 3.9 24.5 - - + +
843A LEU* 3.8 40.6 - - + -
863A HIS* 3.0 27.4 + - + +
864A ALA 3.7 5.8 - - - +
865A GLN 3.3 0.2 - - - -
866A ASP* 1.3 81.0 - - + +
868A ILE* 1.3 57.2 + - + +
870A ASP* 3.8 3.3 - - - +
871A LEU* 3.0 27.5 + - - +
876A ILE* 4.8 6.3 - - + +
962A LEU* 5.1 3.1 - - + -
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Residues in contact with ILE 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A LEU* 5.7 1.1 - - + -
864A ALA* 3.0 23.4 + - + +
865A GLN* 3.9 5.6 - - + +
867A VAL* 1.3 77.0 - - + +
869A SER* 1.3 58.0 + - - +
871A LEU* 3.2 9.9 + - + +
872A LEU* 3.0 40.7 + - + +
958A LEU* 4.0 26.5 - - + -
962A LEU* 4.3 18.2 - - + -
966A LEU* 4.9 16.4 - - + -
982A VAL* 5.3 10.1 - - + +
985A ARG 6.1 0.2 - - - -
986A GLY* 5.1 15.3 - - - +
989A THR* 4.6 11.4 - - - +
990A ARG* 5.4 4.7 - - + +
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Residues in contact with SER 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A GLN 2.7 22.3 + - - -
866A ASP* 3.8 7.4 - - - -
868A ILE* 1.3 77.2 - - - +
870A ASP* 1.3 57.2 + - - +
872A LEU* 3.3 3.2 + - - +
873A CYS* 3.0 40.6 + - - -
875A ARG* 6.0 0.2 - - - -
989A THR* 3.3 35.4 - - - +
992A LYS* 5.3 8.9 + - - -
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Residues in contact with ASP 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866A ASP* 2.9 26.6 + - - +
867A VAL* 4.1 1.6 - - - +
869A SER* 1.3 73.8 - - - +
871A LEU* 1.3 63.6 + - - +
873A CYS* 4.0 2.9 - - - +
874A ASN 3.5 1.4 + - - -
875A ARG* 2.6 89.8 + - - +
876A ILE* 3.3 21.6 - - + +
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Residues in contact with LEU 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839A LEU* 4.5 21.1 - - + -
867A VAL 3.0 13.7 + - - +
868A ILE* 3.3 10.1 - - - +
870A ASP* 1.3 78.8 - - - +
872A LEU* 1.3 74.6 + - + +
874A ASN* 3.3 17.8 + - - +
876A ILE* 3.8 14.5 - - + +
881A LEU* 6.0 3.6 - - + -
954A THR* 3.7 40.4 - - + +
957A TYR* 4.7 14.6 - - + +
958A LEU* 4.7 7.4 - - + -
962A LEU* 3.6 31.0 - - + -
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Residues in contact with LEU 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868A ILE* 3.0 24.9 + - + +
869A SER* 3.3 2.9 + - - +
871A LEU* 1.3 93.4 - - + +
873A CYS* 1.3 57.6 + - - +
874A ASN* 3.2 11.5 - - - +
954A THR* 4.2 17.1 + - - +
955A GLN* 5.1 4.5 - - - +
958A LEU* 4.0 20.0 - - + -
989A THR 3.8 7.4 - - - +
990A ARG* 3.8 42.0 - - + +
992A LYS 3.7 13.7 - - - +
993A THR* 3.8 10.8 - - + -
994A VAL 3.3 18.6 + - - +
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Residues in contact with CYS 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869A SER* 3.0 28.4 + - - +
870A ASP* 4.5 5.2 - - - +
871A LEU 3.3 0.4 - - - -
872A LEU* 1.3 74.3 - - - +
874A ASN* 1.3 69.2 + - - +
875A ARG* 3.5 27.1 + - - +
992A LYS* 3.8 28.9 - - - -
994A VAL* 3.4 32.2 - - + +
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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
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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