Contacts of the helix formed by residues 924 - 936 (chain A) in PDB entry 4RIB
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 SER 924 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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906A TRP* 3.8 11.0 - - - -
922A PHE* 3.0 13.2 + - - +
923A THR* 1.3 81.9 + - - +
925A LEU* 1.3 64.6 + - - +
926A GLN* 3.0 13.5 + - - +
927A GLN* 3.0 21.9 + - - +
928A ALA 3.4 13.2 + - - -
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Residues in contact with LEU 925 (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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902A VAL* 3.8 22.2 - - + -
903A ALA* 4.0 12.3 - - + -
906A TRP* 3.6 57.3 - - + +
907A HIS* 3.6 35.7 - - + +
924A SER* 1.3 72.1 - - - +
926A GLN* 1.3 67.1 + - - +
928A ALA* 3.1 12.6 + - - +
929A GLN* 3.1 24.8 + - - +
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Residues in contact with GLN 926 (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 ARG* 3.4 27.9 - - - +
924A SER* 3.0 11.6 + - - +
925A LEU* 1.3 79.7 - - - +
927A GLN* 1.3 57.7 + - - +
929A GLN* 2.9 33.1 + - - +
930A ASP* 3.2 26.0 + - - +
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Residues in contact with GLN 927 (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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829A GLN* 4.3 12.2 + - - +
830A GLY 4.7 3.0 + - - -
831A ILE* 3.3 31.0 - - + +
921A ARG 4.8 0.2 - - - +
922A PHE* 3.3 8.6 - - + -
923A THR* 2.7 51.2 + - - +
924A SER* 3.0 14.8 + - - +
925A LEU 3.3 0.2 - - - -
926A GLN* 1.3 75.9 - - - +
928A ALA* 1.3 62.3 + - - +
930A ASP* 3.4 13.9 + - - +
931A LEU* 3.4 21.7 + - - +
964A TRP* 3.9 21.4 - - + -
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Residues in contact with ALA 928 (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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841A LEU* 4.9 4.7 - - + +
844A LEU* 5.3 3.4 - - + -
902A VAL* 4.4 15.5 - - + +
906A TRP* 4.3 8.1 - - + -
922A PHE* 4.1 31.8 - - + -
924A SER 3.4 8.7 + - - +
925A LEU* 3.1 15.2 + - - +
927A GLN* 1.3 79.7 - - - +
929A GLN* 1.3 59.9 + - - +
931A LEU* 3.6 3.5 + - - +
932A VAL* 3.2 25.2 + - - +
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Residues in contact with GLN 929 (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 ARG* 3.0 57.5 + - + +
902A VAL* 4.5 7.6 - - + -
903A ALA* 3.4 22.0 - - - +
925A LEU* 3.1 25.0 + - - +
926A GLN* 2.9 27.3 + - - +
928A ALA* 1.3 74.8 - - - +
930A ASP* 1.3 65.7 + - - +
932A VAL* 3.0 20.3 - - - +
933A SER* 3.1 15.4 + - - -
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Residues in contact with ASP 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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829A GLN* 6.0 0.9 - - - +
899A ARG* 3.7 10.0 + - - +
926A GLN* 3.3 30.7 + - - +
927A GLN* 3.4 21.4 + - - +
929A GLN* 1.3 75.0 - - - +
931A LEU* 1.3 64.1 + - - +
933A SER* 3.1 13.2 + - - -
934A CYS* 3.1 19.8 + - - -
964A TRP* 4.1 20.0 + - + +
969A ARG* 4.3 20.5 + - - +
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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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831A ILE* 4.7 1.6 - - + -
837A THR* 4.0 17.0 - - + -
841A LEU* 4.7 4.5 - - + -
922A PHE* 3.6 29.4 - - + -
927A GLN 3.4 12.8 + - - +
928A ALA 3.8 5.6 - - - +
929A GLN 3.2 0.6 - - - -
930A ASP* 1.3 80.0 - - - +
932A VAL* 1.3 58.0 + - + +
934A CYS* 3.3 7.9 + - + +
935A LEU* 3.0 51.4 + - + +
962A VAL* 3.6 28.7 - - + -
964A TRP* 3.7 34.5 - - + -
971A PHE* 5.4 1.6 - - + -
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Residues in contact with VAL 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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841A LEU* 4.0 25.4 - - + -
845A LEU* 5.2 4.9 - - + -
898A LEU* 3.7 15.3 - - + +
899A ARG* 4.7 13.0 - - - +
902A VAL* 4.2 25.8 - - + -
928A ALA 3.2 14.8 - - - +
929A GLN* 3.0 24.2 - - - +
931A LEU* 1.3 73.1 - - - +
933A SER* 1.3 59.6 + - - +
935A LEU* 4.2 4.3 - - - -
936A GLY* 2.9 27.9 + - - -
940A LEU* 3.7 21.9 - - + +
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Residues in contact with SER 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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895A GLU* 3.3 36.8 + - - +
898A LEU* 5.4 0.2 - - - -
899A ARG* 2.8 37.5 + - - +
929A GLN 3.1 8.0 + - - -
930A ASP 3.1 11.1 + - - -
932A VAL* 1.3 79.4 - - - +
934A CYS* 1.3 62.0 + - - +
936A GLY* 3.8 7.8 + - - -
969A ARG* 3.4 17.5 - - - -
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Residues in contact with CYS 934 (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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930A ASP 3.1 16.3 + - - -
931A LEU* 3.3 6.0 + - + +
933A SER* 1.3 75.1 - - - +
935A LEU* 1.3 65.6 - - + +
936A GLY* 4.6 0.3 - - - -
964A TRP* 4.0 26.0 - - + -
969A ARG* 3.4 51.1 - - - +
971A PHE* 3.0 33.5 - - + -
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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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838A PHE* 5.0 17.3 - - + -
841A LEU* 3.8 23.6 - - + -
931A LEU* 3.0 49.6 + - + +
932A VAL* 4.0 3.4 - - - +
934A CYS* 1.3 79.9 - - - +
936A GLY* 1.3 67.5 + - - +
939A VAL* 3.4 35.1 - - + +
940A LEU* 4.0 17.7 - - + -
962A VAL* 5.2 2.0 - - + -
971A PHE* 3.5 29.0 - - + -
973A LEU* 5.1 8.5 - - + -
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Residues in contact with GLY 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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895A GLU* 5.6 2.5 - - - -
898A LEU* 3.9 5.6 - - - -
932A VAL 2.9 18.1 + - - -
933A SER 4.1 7.0 - - - -
934A CYS 3.5 0.6 - - - -
935A LEU* 1.3 84.2 - - - +
937A GLY* 1.3 68.5 + - - +
938A PRO* 3.0 7.2 - - - +
939A VAL 2.9 12.8 + - - -
940A LEU* 3.5 7.2 + - - +
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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