Contacts of the helix formed by residues 902 - 923 (chain A) in PDB entry 6CIM
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 CYS 902 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891A PRO* 3.9 33.7 - - + -
892A VAL* 4.2 1.8 - - - -
895A SER* 4.5 5.4 - - - -
898A PRO* 3.4 25.5 + - - +
901A GLU* 1.3 79.6 - - + +
903A PRO* 1.3 67.0 - - - +
904A GLU 3.2 2.9 - - - -
905A SER* 3.1 26.8 + - - +
906A LEU 3.1 13.5 + - - -
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Residues in contact with PRO 903 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A PRO 3.7 7.2 - - - +
899A ALA* 3.7 15.3 - - - +
900A LYS 3.8 10.1 - - - +
901A GLU 3.6 7.2 - - - +
902A CYS* 1.3 88.2 - - - +
904A GLU* 1.3 58.2 + - + +
906A LEU* 3.4 5.0 + - + +
907A CYS* 2.9 36.8 + - - +
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Residues in contact with GLU 904 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902A CYS 3.2 0.8 - - - -
903A PRO* 1.3 78.2 - - + +
905A SER* 1.3 61.0 + - - +
907A CYS* 3.2 6.0 + - + +
908A GLN* 2.9 52.3 + - + +
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Residues in contact with SER 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A LYS* 4.0 19.3 + - - +
891A PRO* 4.0 12.7 - - - +
892A VAL* 3.4 22.0 - - - +
902A CYS* 3.1 25.8 + - - +
904A GLU* 1.3 79.3 - - - +
906A LEU* 1.3 56.5 + - - +
908A GLN* 3.4 2.4 + - - -
909A TYR* 2.9 26.3 + - - +
912A ASN* 4.9 1.5 + - - +
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Residues in contact with LEU 906 (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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892A VAL* 3.5 30.2 - - + +
898A PRO* 4.2 6.5 - - + +
899A ALA* 4.0 30.1 - - + +
902A CYS 3.1 12.9 + - - +
903A PRO* 3.8 7.4 - - + +
905A SER* 1.3 77.1 - - - +
907A CYS* 1.3 64.7 + - - +
908A GLN 3.4 0.3 + - - -
909A TYR* 3.4 13.2 + - + +
910A SER 4.9 0.7 + - - -
944A PRO* 5.1 12.3 - - + +
947A ILE* 3.7 31.6 - - + -
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Residues in contact with CYS 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903A PRO* 2.9 23.0 + - - +
904A GLU* 3.2 7.4 + - + +
906A LEU* 1.3 82.2 - - - +
908A GLN* 1.3 75.2 + - - +
909A TYR 3.7 0.3 + - - -
910A SER* 4.6 5.0 + - - -
911A PHE* 5.3 1.4 + - - +
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Residues in contact with GLN 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A GLU* 2.9 39.0 + - + +
905A SER* 3.7 0.9 - - - +
907A CYS* 1.3 90.4 + - - +
909A TYR* 1.3 62.5 + - - +
910A SER 3.3 2.7 - - - -
911A PHE* 3.3 23.5 + - + +
912A ASN* 2.6 49.2 + - - +
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Residues in contact with TYR 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A LYS 5.8 0.2 - - - -
889A MET* 3.6 30.9 - - + +
892A VAL* 3.8 24.5 - - + -
893A TRP* 3.4 32.1 - + - -
905A SER 2.9 15.1 + - - +
906A LEU* 3.7 10.3 - - + +
907A CYS 3.4 2.2 - - - -
908A GLN* 1.3 77.4 - - - +
910A SER* 1.3 58.5 + - - +
912A ASN* 3.2 6.4 + - - +
913A SER* 2.9 36.4 + - - -
939A THR* 2.4 28.0 + - - +
940A LEU 4.9 2.2 - - - -
943A VAL* 3.2 33.8 - - + +
944A PRO* 3.3 26.5 - - + -
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Residues in contact with SER 910 (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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742A VAL* 5.3 3.3 - - - +
743A PHE* 5.7 0.7 - - - -
906A LEU 4.9 0.8 + - - -
907A CYS 4.6 4.5 + - - -
908A GLN 3.3 0.8 - - - -
909A TYR* 1.3 82.2 - - - +
911A PHE* 1.3 64.4 + - - +
913A SER* 3.0 9.0 + - - -
914A GLN* 3.0 44.4 + - - +
944A PRO* 4.5 15.4 - - - +
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Residues in contact with PHE 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A LEU* 6.4 0.2 - - + -
907A CYS 5.3 1.0 + - - +
908A GLN* 3.3 27.1 + - + +
910A SER* 1.3 77.1 - - - +
912A ASN* 1.3 73.9 + - - +
914A GLN* 3.4 16.2 + - + +
915A ARG* 3.0 37.1 + - + +
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Residues in contact with ASN 912 (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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885A LEU* 4.2 15.5 - - + +
888A LYS* 4.1 38.1 + - + +
889A MET* 4.0 17.3 - - + +
905A SER* 4.9 1.6 + - - +
908A GLN* 2.6 45.5 + - - +
909A TYR* 3.7 5.4 - - - +
911A PHE* 1.3 91.5 - - - +
913A SER* 1.3 60.4 + - - +
915A ARG* 3.4 5.2 + - - +
916A PHE* 2.8 28.9 + - - +
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Residues in contact with SER 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A VAL* 3.4 26.0 - - - +
889A MET* 3.8 20.9 - - - -
909A TYR* 2.9 22.9 + - - -
910A SER* 3.0 17.0 + - - -
912A ASN* 1.3 72.9 - - - +
914A GLN* 1.3 64.7 + - - +
916A PHE* 3.4 4.5 - - - +
917A ALA* 2.9 19.6 + - - +
940A LEU* 3.8 23.1 + - - +
944A PRO* 5.9 0.2 - - - +
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Residues in contact with GLN 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A VAL* 4.0 16.4 - - + -
743A PHE* 3.6 40.0 - - + -
910A SER* 3.0 37.0 + - - +
911A PHE* 3.5 15.8 - - + +
913A SER* 1.3 76.9 + - - +
915A ARG* 1.3 63.6 + - - +
917A ALA* 3.3 2.3 + - - +
918A GLU* 2.9 24.6 + - - +
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Residues in contact with ARG 915 (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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881A GLU* 3.3 35.3 + - - +
885A LEU* 3.6 23.8 - - + -
911A PHE* 3.0 29.6 + - + +
912A ASN* 3.8 4.7 - - - +
914A GLN* 1.3 75.7 - - - +
916A PHE* 1.3 57.1 + - - +
918A GLU* 3.2 29.9 + - - +
919A LEU* 2.9 65.4 + - - +
922A THR* 4.9 2.4 + - - -
923A LYS* 4.9 8.3 - - - +
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Residues in contact with PHE 916 (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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800A ASN* 4.1 11.4 - - - -
803A GLU* 6.4 0.4 - - + -
804A PHE* 4.0 20.4 - + - -
882A LEU* 3.6 39.3 - - + +
885A LEU* 3.6 26.4 - - + +
886A TYR* 4.4 2.9 - - + -
889A MET* 3.9 15.7 - - + -
912A ASN 2.8 18.6 + - - +
913A SER* 3.4 8.7 - - - +
914A GLN 3.2 0.2 - - - -
915A ARG* 1.3 77.4 - - - +
917A ALA* 1.3 59.7 + - - +
919A LEU* 3.2 4.3 + - - +
920A LEU* 3.0 50.4 + - + +
936A PHE* 4.1 19.3 - + - -
940A LEU* 4.0 22.9 - - + -
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Residues in contact with ALA 917 (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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741A LEU* 3.7 31.5 - - + +
742A VAL* 3.5 30.5 - - + -
913A SER 2.9 7.3 + - - +
914A GLN* 3.9 2.7 - - - +
916A PHE* 1.3 79.3 - - + +
918A GLU* 1.3 57.0 + - - +
920A LEU* 3.3 4.5 + - - +
921A SER* 2.9 35.1 + - - +
940A LEU* 5.5 0.7 - - + -
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Residues in contact with GLU 918 (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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914A GLN 2.9 16.4 + - - +
915A ARG* 3.6 33.3 + - - +
917A ALA* 1.3 72.8 - - - +
919A LEU* 1.3 60.8 + - - +
921A SER* 3.2 6.0 + - - +
922A THR* 2.9 48.6 + - + +
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Residues in contact with LEU 919 (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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878A ALA* 3.8 9.9 - - + +
881A GLU* 3.5 31.4 - - - +
882A LEU* 3.6 41.7 - - + +
885A LEU* 4.3 4.3 - - + -
915A ARG* 2.9 32.0 + - - +
916A PHE* 3.5 5.2 - - - +
918A GLU* 1.3 76.5 - - - +
920A LEU* 1.3 61.8 + - - +
922A THR* 3.8 3.4 - - - +
923A LYS* 3.1 50.3 + - + -
924A PHE* 3.5 14.4 - - + -
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Residues in contact with LEU 920 (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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741A LEU* 4.2 21.3 - - + -
803A GLU* 5.7 5.6 - - + +
807A ILE* 4.0 16.4 - - + -
882A LEU* 3.8 30.7 - - + -
916A PHE* 3.0 37.8 + - + +
917A ALA* 3.6 8.5 - - - +
918A GLU 3.3 0.2 - - - -
919A LEU* 1.3 76.8 - - - +
921A SER* 1.3 58.6 + - - +
924A PHE* 3.1 43.9 - - + +
925A LYS* 3.7 1.2 + - - -
927A ARG* 6.2 2.0 - - + -
936A PHE* 4.8 11.0 - - + -
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Residues in contact with SER 921 (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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739A GLN 5.6 1.6 + - - -
741A LEU* 5.4 4.9 - - - +
917A ALA* 2.9 23.3 + - - +
918A GLU* 3.2 8.0 + - - -
920A LEU* 1.3 78.2 - - - +
922A THR* 1.3 62.0 + - - +
925A LYS* 3.2 24.0 - - - +
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Residues in contact with THR 922 (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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915A ARG* 4.9 2.8 + - - -
918A GLU* 2.9 31.1 + - + +
919A LEU* 3.6 8.7 + - - +
921A SER* 1.3 81.9 - - - +
923A LYS* 1.3 76.7 + - - +
924A PHE 3.3 2.0 - - - -
925A LYS* 3.5 26.5 - - - +
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Residues in contact with LYS 923 (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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874A GLU 5.8 1.5 + - - +
875A ARG* 2.9 33.0 + - - +
877A GLU* 4.6 14.3 + - - +
878A ALA* 4.3 18.8 - - + +
881A GLU* 5.0 3.4 + - - -
915A ARG* 4.9 7.5 - - - +
919A LEU* 3.1 31.5 + - + +
922A THR* 1.3 88.3 + - - +
924A PHE* 1.3 67.8 + - + +
925A LYS 3.8 0.7 - - - -
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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
------------------------------------------------------------
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