Contacts of the helix formed by residues 932 - 944 (chain A) in PDB entry 3N56
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 THR 932 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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882A PHE* 3.4 10.5 - - - -
930A THR 3.9 9.2 - - - +
931A LEU* 1.3 77.3 - - - +
933A LYS* 1.3 62.4 + - - +
934A GLU* 3.2 14.8 + - + +
935A ASP* 2.9 50.1 + - - +
936A ILE* 3.6 5.0 + - - +
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Residues in contact with LYS 933 (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 ILE* 2.6 31.4 + - + -
875A GLU* 2.9 25.1 + - - +
877A MET* 3.1 26.6 + - - +
879A GLU* 4.1 21.9 + - - +
882A PHE* 3.4 41.0 - - + -
932A THR* 1.3 74.4 - - - +
934A GLU* 1.3 57.8 + - + +
935A ASP 3.4 0.2 - - - -
936A ILE* 3.7 5.9 + - - +
937A ILE* 3.3 28.7 + - + +
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Residues in contact with GLU 934 (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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932A THR* 3.4 13.5 - - - +
933A LYS* 1.3 76.6 - - + +
935A ASP* 1.3 60.9 + - - +
936A ILE 3.3 0.4 - - - -
937A ILE* 3.6 12.3 - - + +
938A LYS* 2.7 44.6 + - + +
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Residues in contact with ASP 935 (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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807A PHE* 3.9 24.4 - - + -
930A THR 4.5 0.9 - - - +
931A LEU* 3.7 10.0 - - + +
932A THR* 2.9 44.8 + - - +
934A GLU* 1.3 80.0 - - - +
936A ILE* 1.3 60.3 + - + +
938A LYS* 3.2 7.2 + - - +
939A PHE* 2.9 31.7 + - - +
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Residues in contact with ILE 936 (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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807A PHE* 4.3 15.0 - - + +
810A LEU* 3.6 41.3 - - + -
811A PHE* 4.5 15.7 - - + +
814A ILE* 4.5 9.4 - - + -
874A ILE* 4.4 28.3 - - + -
882A PHE* 4.5 7.9 - - + -
931A LEU* 3.8 17.5 - - + -
932A THR 3.6 11.1 + - - +
933A LYS 3.8 9.9 - - - +
934A GLU 3.3 0.2 - - - -
935A ASP* 1.3 81.6 - - - +
937A ILE* 1.3 59.8 + - + +
939A PHE* 3.7 7.7 - - + +
940A TYR* 2.9 28.2 + - + +
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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
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871A GLU* 5.4 2.7 - - + +
874A ILE* 3.8 29.2 - - + +
875A GLU* 3.4 42.2 - - - +
933A LYS* 3.3 22.1 + - + +
934A GLU* 3.4 11.9 + - + +
935A ASP 3.2 0.6 - - - -
936A ILE* 1.3 75.4 - - + +
938A LYS* 1.3 66.0 + - - +
940A TYR* 3.3 9.1 + - + +
941A LYS* 2.9 43.9 + - + +
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Residues in contact with LYS 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 GLU* 2.7 30.0 + - + +
935A ASP* 3.5 7.9 - - - +
937A ILE* 1.3 71.5 - - - +
939A PHE* 1.3 56.3 + - - +
941A LYS* 3.2 8.1 + - - +
942A GLU* 2.9 34.3 + - + +
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Residues in contact with PHE 939 (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 THR* 4.2 18.8 - - + -
804A GLU* 4.2 20.4 - - - -
807A PHE* 3.7 51.6 - + + -
808A LEU* 3.9 21.3 - - + -
811A PHE* 4.4 9.4 - + + -
935A ASP 2.9 16.6 + - - +
936A ILE* 3.7 9.0 - - + +
938A LYS* 1.3 73.8 - - - +
940A TYR* 1.3 67.0 + - + +
942A GLU* 4.8 4.0 - - - -
943A MET* 3.0 47.7 + - + +
944A LEU* 3.7 22.9 - - + -
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Residues in contact with TYR 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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811A PHE* 3.7 37.9 - + + -
867A LEU* 3.5 35.3 + - + +
868A ILE* 4.2 5.2 + - - +
870A MET* 6.2 0.2 - - + -
871A GLU* 3.7 47.4 + - + -
874A ILE* 6.1 1.8 - - + -
936A ILE* 2.9 18.9 + - + +
937A ILE* 3.7 9.9 - - + +
939A PHE* 1.3 80.7 - - - +
941A LYS* 1.3 65.0 + - + +
944A LEU* 2.9 38.8 + - + -
945A ALA* 2.9 47.7 + - + +
946A VAL* 4.8 2.3 + - - +
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Residues in contact with LYS 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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871A GLU* 4.1 20.6 - - - +
875A GLU* 5.1 3.4 - - - -
937A ILE* 2.9 35.8 + - + +
938A LYS* 3.4 7.2 - - - +
940A TYR* 1.3 83.9 - - + +
942A GLU* 1.3 57.4 + - - +
945A ALA* 4.0 9.9 - - + +
947A ASP* 5.0 0.9 - - - +
948A ALA* 3.4 22.9 - - - +
949A PRO* 3.9 2.8 - - - +
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Residues in contact with GLU 942 (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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938A LYS* 2.9 18.5 + - + +
939A PHE* 4.2 3.4 - - - +
941A LYS* 1.3 78.6 - - - +
943A MET* 1.3 75.3 + - + +
948A ALA* 3.2 13.3 - - - +
949A PRO* 3.4 16.2 - - + +
950A ARG* 3.3 51.9 + - - +
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Residues in contact with MET 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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795A TYR* 5.4 1.7 - - - +
796A GLN 5.4 2.0 - - - +
797A THR* 4.4 24.7 - - + +
804A GLU* 4.3 22.9 - - - +
939A PHE* 3.0 35.3 + - + +
942A GLU* 1.3 96.2 - - + +
944A LEU* 1.3 70.8 + - + +
948A ALA* 3.7 3.8 - - - -
950A ARG* 3.3 55.8 - - - +
951A ARG* 3.3 27.7 - - - +
952A HIS 4.5 1.2 + - - -
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Residues in contact with LEU 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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795A TYR* 3.8 33.0 - - + -
796A GLN 6.0 0.2 - - - +
797A THR* 4.3 17.7 - - + -
808A LEU* 5.5 1.6 - - + -
811A PHE* 3.7 36.6 - - + -
846A LEU* 4.3 14.1 - - + -
867A LEU* 4.7 9.1 - - + +
939A PHE* 3.7 26.7 - - + -
940A TYR* 2.9 27.8 + - + +
943A MET* 1.3 82.7 - - + +
945A ALA* 1.3 58.2 + - - +
951A ARG* 2.4 32.7 + - - +
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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
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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