Contacts of the helix formed by residues 903 - 919 (chain A) in PDB entry 1OY6
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 LEU 903 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545A TYR* 3.4 33.2 + - + +
899A PHE 4.0 9.0 - - - +
900A SER 3.4 6.3 + - - +
901A VAL 3.0 1.0 + - - -
902A MET* 1.3 87.7 - - + +
904A VAL* 1.3 60.5 + - - +
905A VAL 3.0 2.5 - - - -
906A PRO* 2.8 20.5 - - - +
907A LEU* 2.9 16.1 - - - +
1023A PRO* 3.8 25.6 - - + -
1024A VAL 5.5 0.9 - - - +
1027A VAL* 3.4 30.7 - - + -
1030A ARG* 4.3 10.3 - - - +
1031A ARG* 4.5 16.2 - - - +
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Residues in contact with VAL 904 (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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900A SER 4.5 0.8 + - - +
901A VAL* 3.0 26.0 - - + +
903A LEU* 1.3 74.0 - - - +
905A VAL* 1.3 64.4 + - - +
907A LEU* 3.1 21.9 + - + +
908A GLY 3.3 3.1 + - - -
938A SER* 2.9 58.8 + - - +
939A ALA* 4.3 1.1 - - - +
941A ASN* 5.5 0.7 - - + -
942A ALA* 3.4 21.8 - - + +
1014A ALA 5.2 0.4 - - - +
1018A ALA* 4.0 9.0 - - + -
1024A VAL* 3.5 30.3 - - + +
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Residues in contact with VAL 905 (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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901A VAL* 3.8 6.7 - - + +
902A MET* 3.3 35.9 - - + +
903A LEU 3.0 1.2 - - - -
904A VAL* 1.3 80.0 - - - +
906A PRO* 1.3 66.5 - - + +
908A GLY* 3.7 0.3 + - - -
909A VAL* 3.1 28.9 + - + +
934A THR* 5.3 0.3 - - - +
935A ILE* 3.8 37.5 - - + +
938A SER* 4.7 2.5 + - - -
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Residues in contact with PRO 906 (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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545A TYR* 3.9 15.9 - - + +
548A ILE* 4.4 5.2 - - + +
549A VAL* 3.9 25.1 - - + -
552A MET* 3.9 19.9 - - + +
902A MET 4.3 2.0 - - - +
903A LEU* 2.8 28.7 - - - +
905A VAL* 1.3 86.4 - - + +
907A LEU* 1.3 61.5 + - - -
908A GLY 3.4 0.4 - - - -
909A VAL* 3.9 9.4 - - + -
910A ILE* 3.1 26.2 + - - +
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Residues in contact with LEU 907 (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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545A TYR* 3.5 18.4 - - + -
548A ILE* 5.5 2.5 - - + -
903A LEU* 2.9 29.6 - - + +
904A VAL* 3.1 13.6 + - + +
906A PRO* 1.3 76.9 - - - +
908A GLY* 1.3 57.2 + - - +
910A ILE* 3.0 18.8 - - - +
1013A THR* 2.8 20.6 - - - +
1014A ALA* 4.5 3.4 - - - +
1017A LEU* 3.5 11.9 - - + -
1018A ALA* 3.4 21.1 - - + +
1022A VAL* 3.3 36.6 - - + -
1023A PRO* 4.8 1.6 - - + -
1024A VAL* 3.3 28.7 - - + -
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Residues in contact with GLY 908 (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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904A VAL 3.3 6.4 + - - -
905A VAL 4.3 0.2 - - - -
907A LEU* 1.3 79.4 - - - +
909A VAL* 1.3 64.0 + - - +
910A ILE 3.3 0.4 - - - -
911A GLY 3.1 6.2 + - - -
934A THR* 3.5 13.2 - - - -
938A SER* 4.2 2.5 - - - -
1010A GLY* 3.0 40.6 - - - +
1014A ALA* 3.6 14.5 - - - +
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Residues in contact with VAL 909 (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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552A MET* 4.0 12.8 - - + -
556A PHE* 5.5 4.5 - - + -
905A VAL* 3.1 22.3 + - + +
906A PRO* 3.8 6.0 + - + -
907A LEU 3.5 0.2 - - - -
908A GLY* 1.3 74.1 - - - +
910A ILE* 1.3 65.6 + - - +
912A ALA* 3.6 3.1 - - - +
913A LEU* 3.0 39.9 + - + +
931A LEU* 3.7 22.2 - - + -
934A THR* 4.1 7.4 - - + -
935A ILE* 3.7 30.1 - - + -
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Residues in contact with ILE 910 (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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548A ILE* 4.0 24.2 - - + +
551A GLY* 4.2 1.6 - - - -
552A MET* 3.4 44.5 - - + +
555A LEU* 3.6 17.7 - - + -
906A PRO 3.1 16.7 + - - +
907A LEU* 3.0 24.9 - - - +
909A VAL* 1.3 75.6 - - - +
911A GLY* 1.3 58.3 + - - +
913A LEU* 3.6 2.8 - - - +
914A LEU* 3.1 32.7 + - + +
1013A THR* 3.5 14.6 - - + -
1017A LEU* 4.7 1.3 - - + -
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Residues in contact with GLY 911 (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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908A GLY 3.1 5.5 + - - -
910A ILE* 1.3 82.2 - - - +
912A ALA* 1.3 63.6 + - - +
914A LEU* 3.5 8.7 - - - +
915A ALA 3.1 19.6 + - - -
1009A GLY* 3.2 20.9 - - - -
1013A THR* 3.2 26.9 - - - -
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Residues in contact with ALA 912 (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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908A GLY 3.2 4.5 + - - +
909A VAL* 3.2 8.6 + - - +
911A GLY* 1.3 74.1 - - - +
913A LEU* 1.3 65.4 + - - +
915A ALA* 3.6 2.1 + - - +
916A ALA* 3.4 14.6 + - - +
927A PHE* 3.3 17.7 - - + -
930A GLY 5.2 0.4 - - - +
931A LEU* 3.8 22.7 - - + -
934A THR* 4.1 7.0 - - - +
1006A GLY* 3.1 20.3 - - - +
1009A GLY 3.9 0.2 - - - -
1010A GLY* 3.2 20.8 - - - +
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Residues in contact with LEU 913 (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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552A MET* 3.4 41.5 - - + +
555A LEU* 3.4 31.0 - - + +
556A PHE* 3.5 28.9 - - + -
559A LEU* 3.9 11.6 - - + +
909A VAL* 3.0 32.8 + - + +
910A ILE* 3.6 4.7 - - - +
912A ALA* 1.3 76.5 - - - +
914A LEU* 1.3 54.9 + - - +
916A ALA* 3.2 3.6 + - - +
917A THR* 2.6 37.3 + - - -
927A PHE* 3.6 15.6 - - + -
931A LEU* 5.2 0.9 - - + -
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Residues in contact with LEU 914 (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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555A LEU* 4.0 19.3 - - + -
910A ILE* 3.1 24.2 + - + +
911A GLY* 3.2 10.5 + - - +
913A LEU* 1.3 78.5 - - - +
915A ALA* 1.3 60.7 + - + +
917A THR* 4.0 3.9 - - - -
918A PHE* 3.1 36.8 + - + +
1013A THR* 5.5 3.6 - - + +
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Residues in contact with ALA 915 (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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911A GLY 3.1 6.2 + - - +
912A ALA 4.0 0.9 - - - +
914A LEU* 1.3 80.3 - - + +
916A ALA* 1.3 62.6 + - - +
918A PHE* 3.5 6.8 + - - +
919A ARG* 3.4 19.2 + - - +
1005A THR* 3.2 39.8 - - + +
1008A MET* 6.0 0.2 - - + -
1009A GLY* 3.5 22.4 - - - -
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Residues in contact with ALA 916 (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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559A LEU* 4.3 9.2 - - + -
912A ALA 3.4 13.3 + - - +
913A LEU 3.2 4.3 + - - +
915A ALA* 1.3 79.7 - - - +
917A THR* 1.3 58.8 + - - +
919A ARG 2.9 16.3 - - - +
921A LEU* 3.0 45.1 + - + +
922A THR 4.9 0.9 - - - +
927A PHE* 4.1 25.1 - - + -
1005A THR* 4.3 1.1 - - - +
1006A GLY* 5.1 3.6 - - - -
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Residues in contact with THR 917 (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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555A LEU* 3.6 25.1 + - + +
558A ARG 6.3 0.4 - - - -
559A LEU* 3.3 25.1 - - + +
913A LEU 2.6 23.1 + - - -
914A LEU* 4.1 5.6 - - - -
915A ALA 3.3 0.2 - - - -
916A ALA* 1.3 76.6 - - - +
918A PHE* 1.3 64.4 + - - +
919A ARG 3.6 3.1 - - - +
921A LEU 5.2 0.2 - - - -
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Residues in contact with PHE 918 (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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914A LEU* 3.1 24.5 + - + +
915A ALA* 3.7 8.3 - - - +
917A THR* 1.3 77.4 - - - +
919A ARG* 1.3 69.5 + - + +
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Residues in contact with ARG 919 (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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915A ALA 3.4 8.1 + - - +
916A ALA 2.9 17.8 - - - +
917A THR 3.6 4.0 - - - +
918A PHE* 1.3 89.2 - - + +
920A GLY* 1.3 61.6 + - - +
921A LEU* 3.1 29.6 + - + +
990A VAL* 3.2 41.5 + - - +
991A ILE* 4.3 18.5 - - - +
1001A ASN* 3.6 14.3 - - - +
1005A THR* 3.4 19.1 + - + +
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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