Contacts of the helix formed by residues 930 - 950 (chain A) in PDB entry 3AR2
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 930 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806A ALA 3.2 12.9 + - - -
809A PHE* 3.2 10.7 - - - +
810A ASN* 2.9 40.1 + - - +
811A PRO* 4.2 8.1 - - + -
916A LEU* 3.6 22.3 - - + +
927A PRO 3.8 4.5 + - - +
928A TRP 4.1 1.8 - - - -
929A VAL* 1.3 77.2 - - - +
931A ILE* 1.3 60.8 + - - +
932A TRP* 2.9 14.4 + - - +
933A LEU* 2.7 39.2 + - + +
934A LEU* 3.5 15.1 + - - +
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Residues in contact with ILE 931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928A TRP* 3.1 28.9 - - + +
929A VAL 3.3 10.3 + - - +
930A ASN* 1.3 69.7 - - - +
932A TRP* 1.3 79.8 + - + +
934A LEU* 2.9 26.8 + - + +
935A GLY* 3.0 12.8 + - - +
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Residues in contact with TRP 932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A ALA* 3.9 2.6 - - + +
809A PHE* 4.4 22.7 - + + -
930A ASN* 2.9 12.5 + - - +
931A ILE* 1.3 87.2 - - + +
933A LEU* 1.3 52.8 + - - +
935A GLY* 3.7 2.5 + - - +
936A SER* 2.6 33.1 + - - -
1011A PC1 3.7 88.6 + - - +
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Residues in contact with LEU 933 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A PRO* 3.3 30.3 - - + +
806A ALA* 3.7 8.5 - - + +
807A LEU* 3.9 12.6 - - + -
912A ALA* 3.8 26.0 - - + +
913A LEU* 4.6 10.8 - - + -
916A LEU* 3.7 26.9 - - + -
927A PRO 5.7 0.4 - - - +
930A ASN* 2.7 30.0 + - - +
931A ILE 3.1 0.2 - - - -
932A TRP* 1.3 72.0 - - - +
934A LEU* 1.3 55.7 + - + +
936A SER* 3.0 2.8 + - - -
937A ILE* 2.7 59.3 + - + +
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Residues in contact with LEU 934 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913A LEU* 4.2 21.1 - - + -
927A PRO* 3.3 22.9 - - + +
928A TRP* 3.6 28.5 - - + +
930A ASN 3.6 11.4 - - - +
931A ILE* 2.9 17.3 + - + +
933A LEU* 1.3 78.7 - - + +
935A GLY* 1.3 57.7 + - - +
937A ILE* 3.0 9.1 + - + +
938A CYS* 2.9 38.5 + - - +
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Residues in contact with GLY 935 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931A ILE* 3.0 15.1 + - - +
932A TRP* 4.1 3.4 - - - -
934A LEU* 1.3 76.4 - - - +
936A SER* 1.3 56.0 + - - +
938A CYS* 4.0 5.5 - - - +
939A LEU* 3.1 26.0 + - - +
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Residues in contact with SER 936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A LEU* 3.7 42.3 + - - +
803A PRO* 3.8 7.1 - - - +
806A ALA* 3.8 3.8 - - - +
932A TRP 2.6 21.1 + - - -
933A LEU* 3.0 9.5 + - - -
935A GLY* 1.3 76.9 - - - +
937A ILE* 1.3 65.9 + - - +
939A LEU* 3.1 7.9 + - - +
940A SER* 3.0 26.9 + - - -
1011A PC1 4.3 6.1 + - - -
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Residues in contact with ILE 937 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A PRO* 4.7 1.8 - - + -
909A MET* 3.5 60.9 - - + +
912A ALA* 4.1 6.5 - - + -
913A LEU* 4.6 12.1 - - + -
933A LEU* 2.7 47.3 + - + +
934A LEU* 3.4 12.6 - - + +
936A SER* 1.3 73.0 - - - +
938A CYS* 1.3 57.7 + - - +
940A SER* 3.2 2.6 + - - -
941A MET* 2.8 43.0 + - + +
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Residues in contact with CYS 938 (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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934A LEU* 2.9 22.4 + - - +
935A GLY* 4.2 5.2 - - - +
937A ILE* 1.3 80.5 - - - +
939A LEU* 1.3 63.1 + - - +
940A SER 3.1 0.4 - - - -
941A MET* 4.1 7.6 - - - -
942A SER* 2.7 35.2 + - - +
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Residues in contact with LEU 939 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A LEU* 3.5 32.3 - - + -
935A GLY 3.1 21.0 + - - +
936A SER* 3.1 6.9 + - - +
938A CYS* 1.3 76.5 - - - +
940A SER* 1.3 59.2 + - - +
942A SER* 4.1 3.3 - - - -
943A LEU* 2.9 50.5 + - + +
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Residues in contact with SER 940 (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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797A LEU 5.0 0.7 + - - -
798A VAL* 3.1 45.4 + - - +
802A LEU* 5.7 0.2 - - - +
803A PRO* 3.3 19.6 - - - +
909A MET* 4.1 5.2 - - - -
936A SER 3.0 12.9 + - - -
937A ILE 3.6 3.6 - - - -
939A LEU* 1.3 76.9 - - - +
941A MET* 1.3 58.3 + - - +
942A SER 3.1 1.6 - - - -
943A LEU* 3.1 8.4 + - - +
944A HIS* 2.9 32.4 + - - +
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Residues in contact with MET 941 (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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905A VAL* 3.6 21.1 - - + -
906A THR* 3.4 30.5 - - - +
909A MET* 3.9 26.7 - - - -
937A ILE* 2.8 24.8 + - + +
938A CYS* 4.0 9.4 - - - +
940A SER* 1.3 73.8 - - - +
942A SER* 1.3 60.0 + - - +
944A HIS* 3.6 12.8 - - + +
945A PHE* 3.0 43.5 + - + -
967A TRP* 5.0 2.0 - - + -
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Residues in contact with SER 942 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938A CYS* 2.7 24.8 + - - +
939A LEU* 4.1 4.3 - - - -
941A MET* 1.3 74.5 - - - +
943A LEU* 1.3 57.0 + - - +
944A HIS 2.9 4.7 - - - -
945A PHE* 2.8 26.1 + - - +
946A LEU* 3.2 23.3 + - - +
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Residues in contact with LEU 943 (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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96A LEU* 5.6 7.6 - - + -
794A TRP* 3.1 34.4 - - + -
797A LEU* 5.0 13.2 - - + -
798A VAL* 5.0 3.1 - - + -
939A LEU* 2.9 42.5 + - + +
940A SER* 3.5 9.2 - - - +
942A SER* 1.3 75.9 - - - +
944A HIS* 1.3 60.2 + - - +
946A LEU* 3.7 32.6 - - + +
947A ILE* 3.8 1.2 - - - +
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Residues in contact with HIS 944 (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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794A TRP* 2.8 39.6 + + + +
798A VAL* 5.0 0.7 - - + -
901A LEU* 4.2 24.7 - - + -
902A SER* 3.0 33.6 + - - -
905A VAL* 4.3 20.5 - - + +
940A SER 2.9 15.6 + - - +
941A MET* 3.6 11.7 - - + +
943A LEU* 1.3 74.5 - - - +
945A PHE* 1.3 62.2 + + - +
946A LEU 3.2 1.8 - - - -
947A ILE* 3.0 25.6 + - + +
948A LEU* 3.4 25.0 + - + +
959A LEU* 4.9 2.7 - - + -
967A TRP* 4.3 10.5 - + - -
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Residues in contact with PHE 945 (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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941A MET* 3.0 35.2 - - + +
942A SER* 2.8 15.9 + - - +
944A HIS* 1.3 76.9 - + + +
946A LEU* 1.3 64.4 + - + +
948A LEU* 3.0 15.3 + - - +
949A TYR* 3.1 38.5 + + + +
967A TRP* 3.5 52.9 - + - -
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Residues in contact with LEU 946 (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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942A SER* 3.2 32.2 + - - +
943A LEU* 3.7 26.2 - - + +
944A HIS 3.2 0.8 - - - -
945A PHE* 1.3 78.2 - - + +
947A ILE* 1.3 60.4 + - + +
948A LEU 3.3 0.2 - - - -
949A TYR 4.2 0.2 - - - -
950A VAL* 3.3 34.0 + - + +
953A LEU* 3.0 28.3 - - + +
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Residues in contact with ILE 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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794A TRP* 3.2 45.3 - - + +
943A LEU 3.8 1.8 - - - +
944A HIS* 3.0 11.1 + - - +
946A LEU* 1.3 80.2 - - - +
948A LEU* 1.3 56.9 + - + +
949A TYR 3.5 0.2 - - - -
953A LEU* 3.5 24.2 - - + -
954A PRO* 3.1 28.3 - - - +
957A PHE* 3.5 49.8 - - + -
959A LEU* 3.6 27.6 - - + -
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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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898A THR* 3.6 28.0 - - + -
902A SER* 3.7 12.1 - - - +
944A HIS* 3.9 21.3 - - + +
945A PHE* 3.0 6.3 + - - +
947A ILE* 1.3 79.1 - - - +
949A TYR* 1.3 74.7 + - + +
950A VAL 3.9 0.4 - - - -
954A PRO* 4.6 8.7 - - - +
959A LEU* 3.9 24.0 - - + -
960A LYS 4.6 3.8 - - - +
961A ALA* 3.1 28.4 + - - +
962A LEU* 3.8 10.5 - - + -
967A TRP* 3.4 34.1 - - + -
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Residues in contact with TYR 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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945A PHE* 3.1 36.5 + + + +
948A LEU* 1.3 120.1 - - + +
950A VAL* 1.3 65.1 + - + +
951A ASP 3.7 4.4 + - - -
954A PRO* 5.0 1.8 - - - -
961A ALA* 4.0 16.6 - - + -
962A LEU 3.2 22.2 + - - -
964A LEU* 5.8 4.8 - - + +
967A TRP* 3.2 16.5 + - - -
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Residues in contact with VAL 950 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945A PHE 5.1 0.2 - - - +
946A LEU* 3.3 38.9 + - + +
948A LEU 3.9 0.6 - - - -
949A TYR* 1.3 80.4 - - + +
951A ASP* 1.3 53.2 + - - +
952A PRO* 2.7 30.0 - - + +
953A LEU* 2.8 23.2 + - + +
954A PRO* 3.2 5.8 - - - +
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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