Contacts of the helix formed by residues 927 - 940 (chain A) in PDB entry 5Y36
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 ILE 927 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727A LEU* 3.8 33.2 - - + +
728A ALA* 4.2 6.5 - - + -
733A ILE* 4.0 21.1 - - + -
763A MET* 3.6 54.1 - - + +
764A ALA* 4.8 1.3 - - - +
765A ARG* 3.9 37.7 - - + +
925A ARG* 4.1 4.5 - - - +
926A GLN* 1.3 81.8 - - - +
928A THR* 1.4 64.2 + - + +
929A LYS 3.3 1.2 + - - -
930A HIS* 3.6 6.9 + - - -
931A VAL* 3.4 11.5 + - + +
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Residues in contact with THR 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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761A ILE 5.5 0.2 - - - +
762A GLU* 5.0 0.4 - - - -
763A MET* 3.1 42.8 - - + +
925A ARG* 2.6 26.7 + - + +
926A GLN* 4.7 0.2 - - - -
927A ILE* 1.4 75.7 - - + +
929A LYS* 1.3 63.1 + - - +
930A HIS 3.3 1.5 + - - -
931A VAL* 3.4 17.0 + - + -
932A ALA* 4.1 1.0 + - - +
957A THR* 3.5 38.4 + - + +
958A LEU 5.1 5.4 - - - +
959A LYS* 2.7 19.7 + - - +
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Residues in contact with LYS 929 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A GLN* 3.4 14.3 + - - +
927A ILE 3.3 0.2 - - - -
928A THR* 1.3 81.2 + - - +
930A HIS* 1.4 78.3 + - + +
932A ALA* 5.0 2.9 + - - +
933A GLN* 3.7 22.2 + - - +
957A THR* 5.7 0.2 - - - -
1008A PHE* 4.1 35.1 - - + -
1009A VAL* 5.2 7.6 - - + -
30C T 5.1 1.4 + - - -
31C G 3.7 33.3 + - - +
32C G 5.1 10.3 + - - +
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Residues in contact with HIS 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A LEU* 3.7 35.4 - - + -
926A GLN 5.3 1.1 - - - -
927A ILE* 3.6 2.9 + - - -
929A LYS* 1.4 96.1 + - + +
931A VAL* 1.4 63.9 + - - +
932A ALA 3.4 2.2 - - - -
933A GLN* 2.7 38.8 + - - +
934A ILE* 3.2 27.1 + - + +
30C T 4.7 1.8 + - - -
31C G 3.4 30.5 + - - -
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Residues in contact with VAL 931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 4.8 1.8 - - + -
727A LEU* 4.3 11.2 - - + -
737A ILE* 4.8 8.4 - - + +
740A THR* 5.8 2.2 - - + -
761A ILE* 4.1 30.1 - - + -
763A MET* 3.5 42.0 - - + -
927A ILE 3.4 18.6 + - - +
928A THR* 3.4 15.0 + - - +
930A HIS* 1.4 77.2 - - - +
932A ALA* 1.4 63.9 + - - +
934A ILE* 3.5 5.8 + - - +
935A LEU* 3.3 20.8 + - + +
957A THR* 4.6 3.4 - - + -
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Residues in contact with ALA 932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928A THR 4.1 2.9 + - - +
929A LYS 5.3 3.1 - - - +
930A HIS 3.4 0.2 - - - -
931A VAL* 1.4 79.9 - - - +
933A GLN* 1.4 53.9 + - + +
935A LEU* 3.5 1.7 + - - +
936A ASP* 2.8 38.8 + - - +
955A VAL* 3.7 39.1 - - + +
957A THR* 3.8 19.3 - - + +
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Residues in contact with GLN 933 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929A LYS* 3.7 20.9 + - - +
930A HIS* 2.7 41.5 + - + +
931A VAL 3.3 0.4 - - - -
932A ALA* 1.4 75.2 - - + +
934A ILE* 1.3 59.1 + - + +
936A ASP* 3.7 6.5 - - - +
937A SER* 3.0 30.1 + - - -
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Residues in contact with ILE 934 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A LEU* 5.9 0.2 - - + -
723A HIS* 3.5 29.9 + - + +
724A ILE* 4.1 18.8 - - + -
726A ASN* 3.8 12.6 - - + +
727A LEU* 3.5 41.7 - - + -
737A ILE* 4.4 20.2 - - + -
741A VAL* 4.6 6.1 - - + -
930A HIS* 3.2 9.0 + - + +
931A VAL* 3.8 7.0 - - - +
932A ALA 3.5 0.2 - - - -
933A GLN* 1.3 75.9 - - + +
935A LEU* 1.4 63.2 + - - +
937A SER* 3.3 18.8 - - - -
938A ARG* 3.7 10.5 + - - +
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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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740A THR* 5.4 1.8 - - + -
741A VAL* 4.1 31.8 - - + +
744A VAL* 3.9 23.3 - - + -
745A ASP* 4.6 0.7 - - - +
759A ILE* 4.0 11.2 - - + -
761A ILE* 3.6 29.8 - - + -
931A VAL* 3.3 10.8 + - + +
932A ALA* 3.8 6.7 - - - +
934A ILE* 1.4 78.2 - - - +
936A ASP* 1.4 63.3 + - - +
938A ARG* 3.0 6.2 + - + -
939A MET* 3.0 45.3 + - + +
955A VAL* 3.6 20.0 - - + -
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Residues in contact with ASP 936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932A ALA 2.8 23.5 + - - +
933A GLN* 3.7 8.2 - - - +
935A LEU* 1.4 71.0 - - - +
937A SER* 1.3 61.7 + - - +
939A MET* 4.4 5.6 - - - -
940A ASN* 2.7 56.7 + - - +
951A ARG* 2.8 28.7 + - - -
953A VAL 4.1 3.5 - - - +
955A VAL* 4.5 10.6 + - + +
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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
----------------------------------------------------------
715A GLY* 5.9 1.2 - - - -
716A GLN* 5.2 5.2 + - - +
723A HIS* 3.0 25.8 + - - -
933A GLN 3.0 14.5 + - - -
934A ILE* 3.3 15.7 - - - -
936A ASP* 1.3 77.1 + - - +
938A ARG* 1.4 56.3 + - - +
940A ASN 5.0 0.7 - - - -
941A THR* 3.1 21.5 + - - +
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Residues in contact with ARG 938 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A ASP* 2.9 28.9 + - - +
720A LEU* 3.6 41.5 - - - +
723A HIS* 3.5 35.1 + - + +
741A VAL* 3.6 13.2 - - + +
745A ASP* 3.1 33.7 + - - +
934A ILE* 3.7 4.9 + - - +
935A LEU 3.0 8.3 + - - +
937A SER* 1.4 75.8 - - - +
939A MET* 1.3 62.1 + - + +
940A ASN 3.5 0.2 - - - -
941A THR* 3.0 28.5 + - - +
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Residues in contact with MET 939 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A VAL* 4.0 13.5 - - + -
745A ASP* 3.2 27.8 - - - +
748A VAL* 3.8 33.9 - - + -
755A LYS* 5.2 7.8 + - - +
759A ILE* 4.3 0.7 - - + -
935A LEU* 3.0 37.0 + - + +
936A ASP* 4.1 5.2 - - - +
938A ARG* 1.3 79.3 - - + +
940A ASN* 1.3 57.4 + - - +
941A THR* 3.4 3.2 + - - -
952A GLU* 6.1 0.2 - - - +
953A VAL* 3.9 51.1 - - + +
955A VAL* 4.9 0.9 - - + -
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Residues in contact with ASN 940 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936A ASP* 2.7 41.7 + - - +
937A SER 5.0 0.7 - - - -
939A MET* 1.3 76.3 - - - +
941A THR* 1.3 59.3 + - - +
942A LYS* 2.9 18.1 + - - +
943A TYR* 5.1 5.9 + - - -
951A ARG* 4.1 15.1 - - + +
952A GLU* 3.3 15.6 + - - +
953A VAL* 2.8 45.0 + - - +
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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