Contacts of the helix formed by residues 928 - 943 (chain A) in PDB entry 3H0G
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 GLN 928 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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925A SER* 5.8 1.2 + - - -
926A SER* 3.4 19.6 + - - +
927A VAL* 1.3 84.1 - - + +
929A ASP* 1.3 63.9 + - - +
930A LEU 3.4 0.4 - - - -
931A LEU* 2.8 20.9 + - + +
932A ASP* 2.8 39.1 + - - +
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Residues in contact with ASP 929 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922A GLU* 4.3 10.0 - - - +
924A ASP* 3.8 20.0 - - - +
925A SER* 4.1 12.3 - - - -
927A VAL 2.4 22.1 + - - +
928A GLN* 1.3 73.7 - - - +
930A LEU* 1.3 66.9 + - + +
931A LEU 2.7 5.9 + - - -
932A ASP* 2.9 20.1 + - - +
933A GLU* 3.2 19.8 + - + +
985A LEU* 5.6 5.3 - - - +
986A PRO* 6.0 7.0 - - + -
987A SER* 4.9 13.0 - - - -
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Residues in contact with LEU 930 (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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906A ASP 6.2 0.7 - - - -
907A LEU* 4.6 33.0 - - + +
924A ASP* 5.0 24.2 - - + +
927A VAL* 4.6 23.3 - - + +
929A ASP* 1.3 80.9 - - + +
931A LEU* 1.3 64.2 + - + +
933A GLU* 3.9 15.2 - - - +
934A GLU* 3.9 20.4 - - - +
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Residues in contact with LEU 931 (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 VAL* 4.2 15.9 - - + -
928A GLN* 2.8 30.5 + - + +
929A ASP 2.7 0.8 + - - -
930A LEU* 1.3 81.4 - - + +
932A ASP* 1.3 63.6 + - - +
933A GLU 3.1 2.5 + - - -
934A GLU* 3.4 10.0 + - - +
935A TYR* 3.3 20.4 + - - +
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Residues in contact with ASP 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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928A GLN 2.8 18.4 + - - +
929A ASP* 2.9 12.0 + - - +
931A LEU* 1.3 73.7 - - - +
933A GLU* 1.3 65.9 + - - +
935A TYR* 3.3 10.4 + - - +
936A THR* 3.0 31.4 + - - +
986A PRO* 5.5 1.8 - - + +
987A SER* 4.0 15.6 + - - -
990A ILE* 2.8 36.9 - - + +
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Residues in contact with GLU 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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905A ILE* 3.2 53.3 - - + +
929A ASP* 3.4 18.6 - - + +
930A LEU* 3.9 9.9 - - + +
931A LEU 3.1 0.2 - - - -
932A ASP* 1.3 86.2 - - - +
934A GLU* 1.3 59.4 + - + +
935A TYR 3.4 0.2 - - - -
936A THR* 3.1 17.7 - - - +
937A GLN* 4.0 5.7 + - - +
986A PRO* 3.7 25.2 - - - +
990A ILE* 5.6 0.3 - - - +
1031A VAL* 3.8 28.3 - - - +
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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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905A ILE 4.6 10.7 - - - +
906A ASP* 3.6 19.6 - - - +
907A LEU* 5.7 0.3 - - - +
930A LEU* 3.9 16.8 - - - +
931A LEU* 3.4 11.2 + - - +
932A ASP 3.3 0.2 - - - -
933A GLU* 1.3 79.4 - - + +
935A TYR* 1.3 61.1 + - - +
936A THR 3.5 0.4 - - - -
937A GLN* 3.8 10.5 + - - +
938A LEU* 3.1 33.5 + - + +
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Residues in contact with TYR 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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931A LEU 3.3 16.0 + - - +
932A ASP* 3.3 10.9 + - - +
934A GLU* 1.3 78.1 - - - +
936A THR* 1.3 68.8 + - - +
938A LEU* 3.2 30.6 + - + +
939A VAL* 3.6 15.0 + - + +
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Residues in contact with THR 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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903A TYR 5.7 1.3 - - - +
905A ILE* 4.8 3.1 - - + -
932A ASP 3.0 15.8 + - - +
933A GLU* 3.1 32.3 - - - +
935A TYR* 1.3 78.2 - - - +
937A GLN* 1.3 69.0 + - + +
939A VAL* 3.1 7.9 + - - +
940A ALA* 2.9 26.6 + - - +
990A ILE* 4.6 11.0 - - - +
1030A ALA* 4.7 10.2 - - + +
1031A VAL* 4.2 23.9 + - + +
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Residues in contact with GLN 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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899A PHE* 4.6 17.7 - - + -
900A GLU* 4.9 3.5 - - - +
903A TYR* 4.7 6.0 - - + +
904A ARG* 3.0 59.8 + - - +
905A ILE* 4.3 2.2 + - + +
933A GLU 4.1 13.1 + - - +
934A GLU* 3.8 9.6 + - - +
935A TYR 3.2 0.6 - - - -
936A THR* 1.3 80.6 - - + +
938A LEU* 1.3 61.9 + - + +
939A VAL 3.1 0.2 - - - -
940A ALA* 3.7 11.7 - - + +
941A ASP* 2.7 43.3 + - + +
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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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934A GLU* 3.1 26.3 + - + +
935A TYR* 3.5 26.9 - - + +
936A THR 3.2 0.8 - - - -
937A GLN* 1.3 77.2 - - + +
939A VAL* 1.3 62.3 + - + +
941A ASP* 3.8 10.0 - - + +
942A ARG* 3.1 41.2 + - - +
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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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935A TYR* 3.6 14.1 + - + +
936A THR 3.1 7.3 + - - +
938A LEU* 1.3 81.7 - - + +
940A ALA* 1.3 59.1 + - - +
941A ASP 2.9 6.0 + - - -
942A ARG* 3.2 24.8 + - + +
943A GLU* 2.8 44.7 - - + +
1026A ARG* 3.9 21.1 - - - +
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Residues in contact with ALA 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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891A SER* 6.2 0.3 - - - -
899A PHE* 3.8 17.6 - - + -
903A TYR* 5.2 14.1 - - + -
936A THR* 2.9 17.6 + - - +
937A GLN* 3.5 11.9 + - + -
939A VAL* 1.3 76.2 - - - +
941A ASP* 1.3 57.5 + - - +
943A GLU* 3.8 14.0 - - - +
944A LEU* 3.7 12.6 + - - +
1026A ARG* 4.2 23.3 - - + +
1030A ALA* 5.2 4.3 - - + -
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Residues in contact with ASP 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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899A PHE* 4.9 7.6 - - + -
937A GLN* 2.7 26.9 + - + +
938A LEU* 3.8 10.9 - - - +
940A ALA* 1.3 78.3 - - - +
942A ARG* 1.3 61.3 + - - +
943A GLU 2.9 8.2 + - - -
944A LEU* 3.2 19.4 + - - +
945A LEU* 3.6 12.6 + - - +
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Residues in contact with ARG 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 LEU* 3.1 33.0 + - - +
939A VAL* 3.2 20.9 + - + +
941A ASP* 1.3 77.7 - - - +
943A GLU* 1.3 59.7 + - + +
945A LEU* 4.4 6.3 - - - +
946A CYS* 3.7 21.3 + - - +
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Residues in contact with GLU 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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939A VAL* 2.8 29.4 - - + +
940A ALA* 3.8 9.0 - - - +
941A ASP 2.9 0.6 - - - -
942A ARG* 1.3 82.2 - - + +
944A LEU* 1.3 58.3 + - - +
945A LEU 3.3 2.0 - - - -
946A CYS 3.3 13.3 - - - +
947A LYS* 2.8 27.8 + - - +
1023A ILE* 3.2 45.4 - - + +
1026A ARG* 2.8 48.3 + - - +
1027A SER* 5.5 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
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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