Contacts of the helix formed by residues 931 - 942 (chain A) in PDB entry 3E0D
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 931 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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896A ASN 5.7 1.8 + - - -
927A GLU* 3.5 24.5 + - - +
928A GLN 5.8 0.4 - - - +
929A VAL 3.7 5.6 + - - +
930A VAL* 1.3 75.3 - - - +
932A LYS* 1.3 57.8 + - - +
933A ARG* 3.1 15.2 + - - +
934A ALA* 2.8 38.4 + - - +
935A LEU* 2.9 26.4 + - - +
18C C 6.5 1.3 - - - -
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Residues in contact with LYS 932 (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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927A GLU* 3.6 17.0 + - - +
931A ASN* 1.3 74.0 - - - +
933A ARG* 1.3 62.0 + - - +
935A LEU* 3.4 10.7 + - - +
936A GLU* 3.0 47.2 + - + +
957A LEU* 5.1 8.1 - - + -
958A GLU* 3.9 37.5 + - + +
961A LEU* 4.0 21.3 - - + -
18C C 5.9 2.9 - - - +
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Residues in contact with ARG 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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896A ASN* 3.0 43.2 + - + +
931A ASN* 3.1 10.0 + - - +
932A LYS* 1.3 76.3 - - - +
934A ALA* 1.3 64.0 + - - +
936A GLU* 3.2 25.1 + - - +
937A SER* 3.3 13.9 + - - -
16C G 5.0 3.6 + - - -
17C C 3.7 47.4 + - - +
18C C 5.6 3.2 + - - +
15D G 6.4 0.2 - - - -
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Residues in contact with ALA 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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896A ASN* 4.5 5.6 - - - +
897A VAL* 3.8 33.2 - - + +
898A GLY 5.3 1.1 - - - +
901A ALA* 5.6 2.7 - - + -
929A VAL 5.7 0.4 - - - +
930A VAL* 3.9 17.3 - - + -
931A ASN* 2.8 32.4 + - - +
933A ARG* 1.3 69.6 - - - +
935A LEU* 1.3 66.8 + - - +
936A GLU 3.2 0.3 + - - -
937A SER* 3.2 5.7 + - - -
938A LEU* 3.1 21.1 + - - +
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Residues in contact with LEU 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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918A LEU* 5.8 0.9 - - + -
921A PHE* 3.7 27.4 - - + -
922A LEU* 3.6 34.3 - - + -
925A LEU 6.0 0.7 - - - +
930A VAL* 3.5 28.7 - - + +
931A ASN 2.9 16.8 + - - +
932A LYS* 3.6 13.0 - - - +
934A ALA* 1.3 71.9 - - - +
936A GLU* 1.3 62.4 + - - +
938A LEU* 3.3 9.1 + - + +
939A VAL* 3.1 26.0 + - - +
944A LEU* 4.2 4.7 - - + +
957A LEU* 4.1 17.9 - - + -
961A LEU* 3.8 23.8 - - + -
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Residues in contact with GLU 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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932A LYS* 3.0 46.5 + - - +
933A ARG* 3.4 17.7 - - - +
934A ALA 3.1 0.4 - - - -
935A LEU* 1.3 73.4 - - - +
937A SER* 1.3 67.2 + - - +
939A VAL* 3.3 5.6 + - - +
940A LYS* 3.0 37.1 + - - +
954A LEU* 4.0 15.3 - - + +
957A LEU* 3.9 18.8 - - + -
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Residues in contact with SER 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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894A VAL* 3.8 17.5 - - - -
895A LYS* 4.7 0.6 - - - +
896A ASN* 2.8 46.3 + - - +
897A VAL 4.9 0.4 - - - -
933A ARG 3.3 1.0 + - - -
934A ALA 3.2 8.5 + - - -
936A GLU* 1.3 76.6 - - - +
938A LEU* 1.3 53.7 + - - +
940A LYS* 2.9 13.5 + - - +
941A ALA* 2.7 35.0 + - - +
1004A GLU* 5.2 4.0 + - - -
1005A ALA* 3.6 12.4 - - - +
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Residues in contact with LEU 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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873A VAL* 4.5 4.7 - - + -
891A LEU* 4.5 12.3 - - + +
894A VAL* 3.8 16.7 - - + +
897A VAL* 3.7 22.7 - - + -
905A ILE* 4.0 25.4 - - + -
921A PHE* 4.0 23.6 - - + -
930A VAL* 4.4 11.9 - - + -
934A ALA 3.1 6.7 + - - +
935A LEU* 3.3 11.0 - - - +
937A SER* 1.3 79.7 - - - +
939A VAL* 1.3 57.7 + - - +
941A ALA* 3.6 0.9 + - - +
942A GLY 3.5 1.7 + - - -
943A ALA* 3.1 51.3 + - + +
944A LEU* 3.8 11.6 + - + -
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Residues in contact with VAL 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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918A LEU* 5.5 0.7 - - + -
935A LEU 3.1 15.8 + - - +
936A GLU 3.5 6.7 - - - +
937A SER 3.2 0.2 - - - -
938A LEU* 1.3 73.5 - - - +
940A LYS* 1.3 60.0 + - - +
942A GLY* 3.0 21.1 + - - -
944A LEU* 3.5 23.8 - - + -
945A ASP* 4.0 2.1 - - - +
950A ARG* 3.8 40.7 - - + +
953A LEU* 3.9 23.1 - - + -
954A LEU* 3.9 15.5 - - + -
957A LEU* 4.5 20.4 - - + -
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Residues in contact with LYS 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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936A GLU* 3.0 30.9 + - - +
937A SER* 2.9 11.3 + - - +
939A VAL* 1.3 76.9 - - - +
941A ALA* 1.3 61.2 + - - +
950A ARG* 3.4 20.5 + - - +
954A LEU* 4.3 22.0 - - + -
1001A TYR* 3.7 56.0 - - + +
1002A GLU* 3.7 14.4 + - - -
1004A GLU* 2.9 33.6 + - - +
1005A ALA* 3.8 12.1 - - + -
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Residues in contact with ALA 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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870A PRO* 3.5 20.1 - - - +
871A PRO* 3.8 23.9 - - + +
894A VAL* 3.8 19.7 - - + -
937A SER 2.7 17.8 + - - +
938A LEU 3.8 6.7 - - - +
939A VAL 3.2 0.2 - - - -
940A LYS* 1.3 74.1 - - - +
942A GLY* 1.3 58.7 + - - +
950A ARG* 3.9 4.7 + - - -
1002A GLU* 4.0 5.4 - - - +
1005A ALA* 3.7 7.1 - - + +
1006A LEU* 3.9 19.6 - - + +
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Residues in contact with GLY 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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870A PRO* 4.5 4.8 - - - +
871A PRO 3.1 12.9 - - - +
872A ASP* 4.7 2.4 - - - +
939A VAL 3.0 8.3 + - - -
940A LYS 3.2 0.4 - - - -
941A ALA* 1.3 78.9 - - - +
943A ALA* 1.3 60.7 + - - +
944A LEU 3.1 6.7 + - - -
945A ASP* 3.3 36.1 + - - +
950A ARG* 3.4 13.5 - - - -
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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