Contacts of the helix formed by residues 926 - 937 (chain A) in PDB entry 4YZ9
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 PRO 926 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836A GLU* 3.8 40.4 - - + +
839A LEU* 3.4 21.3 - - + +
908A LYS* 5.6 1.3 - - - -
925A LEU* 1.3 95.1 - - + +
927A ASP* 1.3 82.1 + - - +
928A ASP 3.5 1.3 - - - -
929A PHE* 3.2 1.2 + - - +
930A VAL* 2.9 27.5 + - - +
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Residues in contact with ASP 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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835A LEU* 3.8 33.5 - - + +
836A GLU* 4.6 3.3 + - - +
924A SER* 3.1 7.8 + - - +
926A PRO* 1.3 92.3 - - - +
928A ASP* 1.3 65.7 + - - +
930A VAL* 3.3 4.3 - - - +
931A CYS* 3.0 32.1 + - - -
955B ARG* 4.6 13.7 + - - -
879C THR* 5.8 0.7 - - - +
880C VAL* 6.1 0.5 - - - +
881C PRO* 6.1 5.2 - - + +
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Residues in contact with ASP 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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922A LEU 3.5 11.4 - - - +
923A GLY 3.4 14.1 - - - +
924A SER* 2.7 28.1 + - - -
927A ASP* 1.3 79.4 - - - +
929A PHE* 1.3 65.5 + - - +
931A CYS* 4.0 4.7 - - - +
932A TYR* 3.0 24.3 + - - +
879C THR* 3.0 24.6 + - - -
881C PRO* 4.6 4.8 - - - +
921C THR* 3.0 41.4 - - - +
936C ARG* 5.7 0.3 + - - -
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Residues in contact with PHE 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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839A LEU* 3.7 29.6 - - + -
904A MET* 3.6 28.7 - - + -
907A LYS* 4.0 19.7 - - + -
908A LYS* 3.8 10.8 - - + -
911A TYR* 4.6 6.7 - + - -
922A LEU* 3.6 40.8 - - + -
923A GLY 3.4 11.6 + - - +
925A LEU* 3.3 27.6 - - + -
926A PRO 3.2 4.0 + - - +
928A ASP* 1.3 78.8 - - - +
930A VAL* 1.3 62.8 + - - +
932A TYR* 3.2 10.5 - - - +
933A PHE* 3.2 46.1 - + - -
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Residues in contact with VAL 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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835A LEU* 3.7 35.7 - - + +
838A GLN* 4.3 6.5 - - + +
839A LEU* 3.8 39.3 - - + +
842A PHE* 4.2 11.9 - - + -
904A MET* 5.3 1.6 - - + -
926A PRO 2.9 17.5 + - - +
927A ASP 3.3 11.4 - - - +
929A PHE* 1.3 75.7 - - - +
931A CYS* 1.3 64.4 + - - +
933A PHE* 3.4 5.0 + - - +
934A THR* 2.9 46.1 + - + +
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Residues in contact with CYS 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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801A GLU* 5.6 5.6 - - - -
835A LEU* 3.8 32.5 - - - -
927A ASP 3.0 22.0 + - - +
928A ASP* 4.0 6.5 - - - +
930A VAL* 1.3 75.6 - - - +
932A TYR* 1.3 56.5 + - - +
934A THR* 3.3 9.6 - - - -
935A SER* 2.5 40.1 + - - -
879C THR* 4.4 16.6 - - - +
936C ARG* 4.1 19.0 + - - +
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Residues in contact with TYR 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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878A ILE* 3.3 10.5 - - + +
879A THR* 3.2 40.3 + - + +
882A LEU* 3.1 23.2 - - + +
921A THR* 3.3 28.0 - - - +
922A LEU* 3.7 13.0 - - + -
928A ASP 3.0 14.5 + - - +
929A PHE* 3.2 13.0 - - - +
930A VAL 3.2 0.2 - - - -
931A CYS* 1.3 76.7 - - - +
933A PHE* 1.3 98.8 + + - +
935A SER* 3.0 15.1 + - - -
936A ARG* 3.3 45.8 + - - +
936C ARG* 4.7 5.3 - - - +
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Residues in contact with PHE 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 TRP* 6.4 0.7 - + - -
878A ILE* 4.5 4.0 - - + -
882A LEU* 4.1 15.7 - - + -
900A LEU* 4.4 7.9 - - + -
903A ALA* 5.8 2.2 - - + -
904A MET* 3.7 52.5 - - + -
907A LYS* 5.7 2.7 - - + -
922A LEU* 3.9 11.9 - - + -
929A PHE* 3.2 50.9 - + - -
930A VAL* 3.4 3.9 + - - +
932A TYR* 1.3 103.5 - + - +
934A THR* 1.3 60.4 + - + +
935A SER 3.2 1.6 - - - -
936A ARG 3.2 0.5 + - - -
937A PHE* 2.8 55.8 + + + +
940A LEU* 4.8 4.3 - - + -
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Residues in contact with THR 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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800A HIS* 3.4 46.6 + - + +
801A GLU* 5.6 0.5 + - - -
835A LEU* 5.9 1.2 - - - +
838A GLN* 4.4 3.8 + - - +
842A PHE* 4.2 18.8 - - + -
930A VAL* 2.9 37.4 + - + +
931A CYS* 3.3 13.2 - - - +
933A PHE* 1.3 76.3 - - + +
935A SER* 1.3 63.8 + - - +
937A PHE 4.0 7.4 - - - +
938A PRO* 3.4 23.6 - - - +
940A LEU* 5.8 1.3 - - + -
941A LEU* 5.2 0.7 - - + +
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Residues in contact with SER 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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798A GLU 5.0 2.6 - - - +
800A HIS* 5.2 2.9 - - - +
871A LYS* 5.8 0.3 + - - -
931A CYS* 2.5 25.1 + - - -
932A TYR* 3.0 11.8 + - - -
934A THR* 1.3 81.0 + - - +
936A ARG* 1.3 64.3 + - - +
937A PHE 3.7 0.2 + - - -
938A PRO* 4.2 8.1 - - - +
935C SER* 4.7 11.2 + - - +
936C ARG* 3.4 42.0 + - - +
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Residues in contact with ARG 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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871A LYS* 3.7 21.4 + - - +
877A ASN* 3.3 30.9 + - + +
878A ILE* 4.5 1.7 - - - +
879A THR* 4.6 13.7 - - - +
932A TYR* 3.3 59.2 + - - +
933A PHE 3.2 1.8 + - - -
935A SER* 1.3 81.8 + - - +
937A PHE* 1.3 80.7 + - + +
938A PRO* 3.7 2.5 - - - -
928C ASP 5.8 0.2 + - - -
931C CYS* 4.2 22.6 + - - +
932C TYR* 4.8 3.8 - - - +
935C SER* 3.5 38.8 + - - -
936C ARG* 5.7 4.0 - - - +
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Residues in contact with PHE 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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800A HIS* 4.9 0.7 - - - -
869A VAL 3.7 23.3 - - - +
870A VAL* 3.8 19.5 - - - -
871A LYS* 4.7 2.5 - - + +
874A TRP* 3.8 26.0 - - + -
877A ASN* 3.6 32.8 - - + -
878A ILE* 4.2 15.5 - - + -
900A LEU* 4.2 21.8 - - + -
933A PHE* 2.8 34.7 + + + +
934A THR* 3.4 8.9 - - - +
936A ARG* 1.3 93.7 - - + +
938A PRO* 1.3 67.6 - - - +
939A HIS 3.2 3.1 - - - -
940A LEU* 3.1 30.1 + - + +
941A LEU 4.8 0.5 + - - -
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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