Contacts of the helix formed by residues 945 - 966 (chain A) in PDB entry 7CN9
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 LEU 945 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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724A THR* 4.6 1.3 - - - +
726A ILE* 3.6 30.1 - - + -
822A LEU* 4.3 19.3 - - + +
825A LYS* 3.7 35.2 - - + -
826A VAL* 5.3 8.3 - - + -
938A LEU* 3.7 27.6 - - + +
943A SER* 4.5 0.2 - - - +
944A ALA* 1.3 89.6 - - + +
946A GLY* 1.3 63.7 + - - +
947A LYS 3.1 3.3 + - - -
948A LEU* 3.7 9.5 + - + -
949A GLN* 3.3 30.3 + - + +
1061A VAL* 5.7 1.8 - - + -
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Residues in contact with GLY 946 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943A SER* 4.5 10.0 + - - +
944A ALA 3.5 6.7 + - - +
945A LEU* 1.3 77.7 - - - +
947A LYS* 1.3 58.2 + - - +
949A GLN* 3.7 5.4 - - - +
950A ASP* 2.8 30.4 + - - +
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Residues in contact with LYS 947 (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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725A GLU* 4.5 8.1 - - - +
726A ILE* 3.6 41.1 - - + +
727A LEU* 5.4 2.2 - - - -
728A PRO* 5.4 7.4 - - + -
944A ALA 5.8 0.2 - - - +
945A LEU 3.1 0.8 - - - -
946A GLY* 1.3 77.9 - - - +
948A LEU* 1.3 64.6 + - + +
950A ASP* 2.9 10.3 + - - +
951A VAL* 2.8 30.5 + - + +
776B LYS* 5.2 11.7 - - - +
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Residues in contact with LEU 948 (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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726A ILE* 3.5 46.9 - - + -
727A LEU 3.9 3.8 - - - +
728A PRO* 3.9 31.6 - - + -
826A VAL* 5.8 3.4 - - + -
945A LEU* 3.7 11.8 + - + +
947A LYS* 1.3 74.2 - - + +
949A GLN* 1.3 70.3 + - + +
950A ASP 2.9 1.3 - - - -
951A VAL* 2.9 14.7 + - + +
952A VAL* 2.9 28.3 + - + +
1056A ALA* 4.2 23.6 - - + -
1057A PRO* 5.0 9.6 - - + -
1058A HIS* 6.1 2.2 - - + +
1059A GLY* 5.1 5.2 - - - +
1060A VAL 4.8 2.2 - - - +
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Residues in contact with GLN 949 (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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825A LYS* 4.5 3.9 + - + +
826A VAL* 3.0 37.4 - - + +
827A THR* 3.0 44.1 + - - +
828A LEU 5.3 0.2 + - - -
945A LEU* 3.3 23.7 + - + +
946A GLY* 3.8 5.6 - - - +
947A LYS 3.4 0.2 - - - -
948A LEU* 1.3 77.7 - - - +
950A ASP* 1.3 54.6 + - - +
952A VAL* 3.1 13.0 - - - +
953A ASN* 2.4 48.9 + - - +
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Residues in contact with ASP 950 (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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946A GLY 2.8 17.6 + - - +
947A LYS* 2.9 15.7 + - - +
949A GLN* 1.3 75.2 - - - +
951A VAL* 1.3 60.3 + - - +
953A ASN* 3.7 5.8 - - - +
954A GLN* 2.8 49.2 + - - +
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Residues in contact with VAL 951 (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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728A PRO* 3.6 37.9 - - + -
730A SER 5.0 5.8 - - - +
731A MET* 5.5 4.6 - - + +
947A LYS* 2.8 16.1 + - + +
948A LEU* 2.9 25.3 + - + +
950A ASP* 1.3 79.9 - - + +
952A VAL* 1.3 69.0 + - + +
954A GLN* 3.1 13.5 - - - +
955A ASN* 3.0 25.3 + - - +
1018A ILE* 5.8 3.4 - - + -
1058A HIS* 4.9 9.0 - - + -
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Residues in contact with VAL 952 (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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826A VAL* 6.0 0.2 - - + -
827A THR* 5.8 2.5 - - - +
828A LEU* 5.8 7.9 - - + +
948A LEU* 2.9 21.2 + - + +
949A GLN* 3.1 30.5 - - - +
951A VAL* 1.3 84.9 - - + +
953A ASN* 1.3 62.1 + - - +
955A ASN* 3.2 11.8 + - - +
956A ALA* 2.9 27.3 + - - +
1057A PRO* 6.3 1.3 - - + -
1058A HIS* 3.9 34.8 - - + +
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Residues in contact with ASN 953 (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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827A THR* 4.5 11.0 + - - -
949A GLN* 2.4 48.2 + - - +
950A ASP* 3.8 6.7 - - - +
952A VAL* 1.3 78.5 - - - +
954A GLN* 1.3 53.7 + - - +
956A ALA* 3.5 8.7 - - - +
957A GLN* 2.6 46.1 + - - +
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Residues in contact with GLN 954 (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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950A ASP* 2.8 35.3 + - - +
951A VAL* 3.1 15.9 - - - +
952A VAL 3.1 0.2 - - - -
953A ASN* 1.3 73.0 - - - +
955A ASN* 1.3 68.0 + - - +
957A GLN* 3.0 23.9 + - - +
958A ALA* 3.0 24.8 + - - +
1014A ARG* 3.5 39.5 + - - +
1017A GLU* 4.5 5.1 + - - +
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Residues in contact with ASN 955 (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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731A MET* 3.5 29.1 - - + +
732A THR* 3.5 20.6 - - + +
734A THR* 3.4 26.9 - - - +
951A VAL 3.0 8.3 + - - +
952A VAL* 3.2 12.7 + - - +
954A GLN* 1.3 79.3 - - - +
956A ALA* 1.3 63.9 + - - +
958A ALA* 3.4 6.6 + - - +
959A LEU* 2.8 37.0 + - - +
1007A TYR* 5.5 0.3 + - - -
1011A GLN* 4.7 0.5 - - - +
1014A ARG* 5.7 1.1 - - - +
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Residues in contact with ALA 956 (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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952A VAL 2.9 16.8 + - - +
953A ASN* 3.0 13.0 + - - +
955A ASN* 1.3 82.8 - - - +
957A GLN* 1.3 61.3 + - - +
959A LEU* 3.0 11.7 + - + +
960A ASN* 2.9 29.3 + - - +
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Residues in contact with GLN 957 (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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950A ASP 4.9 0.2 - - - +
953A ASN* 2.6 38.4 + - - +
954A GLN* 3.0 37.6 + - - +
956A ALA* 1.3 69.3 - - - +
958A ALA* 1.3 71.4 + - + +
960A ASN* 3.2 4.8 + - - +
961A THR* 2.8 33.3 + - + +
765B ARG* 6.1 3.8 - - - +
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Residues in contact with ALA 958 (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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731A MET* 6.3 0.4 - - + -
954A GLN 3.0 18.0 + - - +
955A ASN* 3.5 7.0 - - - +
957A GLN* 1.3 76.6 - - + +
959A LEU* 1.3 63.5 + - - +
961A THR* 2.2 25.5 + - - -
962A LEU* 2.9 10.3 + - - +
1007A TYR* 4.4 21.2 - - + -
1011A GLN* 5.9 2.0 - - - +
1014A ARG* 4.5 22.4 - - - +
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Residues in contact with LEU 959 (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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734A THR* 5.9 5.4 - - + -
853A GLN 4.6 15.0 - - - +
858A LEU* 3.7 34.3 - - + -
955A ASN* 2.8 26.1 + - - +
956A ALA* 3.1 14.8 - - + +
958A ALA* 1.3 74.7 - - - +
960A ASN* 1.3 61.2 + - + +
962A LEU* 2.8 34.7 + - + +
963A VAL* 2.8 20.9 + - + +
1007A TYR* 5.0 5.8 - - - +
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Residues in contact with ASN 960 (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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956A ALA 2.9 16.7 + - - +
957A GLN* 4.2 3.6 - - - +
959A LEU* 1.3 77.3 - - + +
961A THR* 1.3 58.1 + - + +
963A VAL* 3.1 21.6 + - - +
964A LYS* 2.8 35.5 + - - +
569C ILE* 5.8 3.8 - - - +
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Residues in contact with THR 961 (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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957A GLN* 2.8 21.5 + - + +
958A ALA* 2.2 35.2 + - - -
960A ASN* 1.3 71.4 - - + +
962A LEU* 1.3 63.0 + - - -
963A VAL 3.0 0.7 + - - -
964A LYS* 3.1 4.7 + - - +
965A GLN* 2.3 41.8 + - - +
1007A TYR* 5.7 0.2 - - - -
758B SER* 5.1 7.0 - - - +
762B GLN* 4.9 9.7 - - + +
765B ARG* 3.6 32.8 - - - +
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Residues in contact with LEU 962 (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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736A VAL* 4.7 9.2 - - + -
741A TYR* 3.1 49.0 + - + +
858A LEU* 5.4 9.6 - - + -
958A ALA 3.4 6.3 - - - +
959A LEU* 2.8 23.1 + - + +
961A THR* 1.3 78.2 + - - +
963A VAL* 1.3 66.1 + - + +
965A GLN* 3.2 22.9 - - + +
966A LEU* 3.6 0.3 - - - +
1004A LEU* 4.8 5.2 - - + -
1007A TYR* 3.3 58.3 - - + +
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Residues in contact with VAL 963 (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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853A GLN 5.8 2.2 - - - +
856A ASN* 5.5 8.7 - - - +
858A LEU* 5.0 9.2 - - + -
959A LEU* 2.8 30.9 + - + +
960A ASN* 3.2 27.4 - - - +
961A THR 3.0 0.2 - - - -
962A LEU* 1.3 78.1 - - + +
964A LYS* 1.3 61.7 + - - +
966A LEU* 2.7 36.6 - - + +
569C ILE* 4.7 24.2 - - + -
570C ALA* 4.9 9.9 - - + +
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Residues in contact with LYS 964 (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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49A HIS* 5.0 17.7 - - + -
960A ASN* 2.8 25.8 + - - +
961A THR* 3.1 4.2 + - - +
963A VAL* 1.3 74.8 - - - +
965A GLN* 1.3 59.7 + - - +
966A LEU* 3.0 0.7 - - - -
967A SER* 2.1 58.3 + - - +
758B SER* 5.6 4.0 - - - +
569C ILE* 4.6 2.0 - - - +
570C ALA* 2.9 41.1 - - - +
571C ASP 4.2 1.6 - - - +
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Residues in contact with GLN 965 (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 TYR* 4.3 6.3 - - - +
961A THR* 2.3 43.2 + - - +
962A LEU* 3.2 21.5 - - - +
963A VAL 2.8 1.2 + - - -
964A LYS* 1.3 76.4 - - - +
966A LEU* 1.3 54.6 + - + +
967A SER* 3.4 1.8 + - - -
968A SER* 2.7 39.2 + - - -
970A PHE* 5.0 5.9 - - + -
1000A ARG* 6.1 1.3 - - - +
1003A SER* 4.4 27.3 - - - +
1004A LEU* 6.2 0.2 - - + -
756B TYR 5.3 2.1 - - - +
757B GLY* 5.5 1.6 - - - -
758B SER* 3.7 23.2 + - - -
759B PHE* 4.9 14.6 + - - +
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Residues in contact with LEU 966 (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 TYR* 3.7 19.5 - - + +
856A ASN* 4.0 24.9 - - + +
962A LEU 3.6 11.0 - - - +
963A VAL* 2.7 30.1 - - + +
964A LYS 2.9 1.2 + - - -
965A GLN* 1.3 70.5 - - + +
967A SER* 1.3 53.9 - - - +
968A SER* 2.9 5.2 + - - +
975A SER* 2.2 31.2 + - - +
1000A ARG* 2.8 45.3 + - - +
570C ALA* 4.1 20.6 - - + -
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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