Contacts of the helix formed by residues 963 - 979 (chain A) in PDB entry 1Y5I
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 ASN 963 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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923A GLU* 3.7 18.6 + - - +
956A LEU 3.9 3.6 - - - +
957A THR* 2.9 33.3 + - - +
959A ALA 3.0 13.3 + - - +
960A PRO 3.7 2.4 - - - +
961A GLU 3.7 1.0 - - - -
962A THR* 1.3 80.3 - - - +
964A GLY* 1.3 59.2 + - - +
965A GLN* 3.0 19.4 + - - +
966A VAL* 2.8 29.5 + - + +
967A ALA 2.9 10.0 + - - -
992A GLU 3.6 2.5 - - - -
993A LYS* 3.7 32.1 - - + +
995A ARG* 6.0 0.2 - - - +
1007A ILE* 3.8 2.2 - - - +
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Residues in contact with GLY 964 (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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963A ASN* 1.3 71.1 - - - +
965A GLN* 1.3 61.2 + - - +
967A ALA* 3.5 6.6 - - - +
968A VAL* 3.0 29.5 + - - +
986A ALA 5.3 0.4 - - - -
989A LYS 3.3 25.1 - - - -
990A GLU* 3.5 7.6 - - - -
992A GLU 2.7 15.7 + - - -
1007A ILE* 3.3 12.3 - - - +
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Residues in contact with GLN 965 (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 SER* 3.2 32.1 + - - -
923A GLU* 3.8 8.5 + - - +
963A ASN* 3.0 14.1 + - - +
964A GLY* 1.3 77.2 - - - +
966A VAL* 1.3 63.3 + - - +
968A VAL* 3.5 3.3 + - - +
969A LYS* 3.3 30.8 + - + +
990A GLU* 3.3 24.8 + - + +
993A LYS* 3.0 24.8 + - - +
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Residues in contact with VAL 966 (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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918A TRP* 3.5 30.1 - - + +
920A THR* 4.7 1.1 - - - +
923A GLU* 3.4 41.3 - - + +
957A THR 3.8 7.0 - - - +
958A LEU 3.3 24.9 - - - +
959A ALA 4.0 0.7 - - - +
960A PRO* 3.7 16.4 - - + -
963A ASN* 2.8 12.3 + - + +
965A GLN* 1.3 74.3 - - - +
967A ALA* 1.3 60.6 + - - +
969A LYS* 3.1 8.4 + - - +
970A ALA* 2.8 28.2 + - - +
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Residues in contact with ALA 967 (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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960A PRO* 3.2 32.8 - - - +
963A ASN 2.9 8.2 + - - +
964A GLY* 3.3 8.9 + - - +
966A VAL* 1.3 77.1 - - - +
968A VAL* 1.3 56.7 + - - +
970A ALA* 3.3 1.4 + - - +
971A TRP* 3.0 36.8 + - - -
986A ALA* 3.7 18.4 - - + -
1007A ILE* 3.8 12.3 - - + -
1008A SER 4.1 6.1 - - - +
1010A PRO* 5.5 0.2 - - - -
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Residues in contact with VAL 968 (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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964A GLY 3.0 19.6 + - - +
965A GLN 3.5 3.8 + - - +
967A ALA* 1.3 75.5 - - - +
969A LYS* 1.3 58.9 + - + +
971A TRP* 3.5 3.8 + - - -
972A ALA* 3.0 27.5 + - + +
983A THR* 4.0 15.2 - - + +
986A ALA* 3.7 31.9 - - + +
987A LEU* 3.9 26.0 - - + +
990A GLU* 4.0 22.7 - - + +
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Residues in contact with LYS 969 (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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918A TRP* 4.2 18.1 - - + +
919A ASN* 2.7 37.2 + - + +
920A THR* 4.0 0.6 - - - +
922A SER* 3.6 11.1 + - - -
923A GLU* 2.7 34.5 + - - -
965A GLN* 3.3 23.9 + - + +
966A VAL* 3.1 12.4 + - - +
968A VAL* 1.3 78.4 - - + +
970A ALA* 1.3 58.0 + - - +
972A ALA* 3.5 8.1 + - - +
973A ALA* 3.0 27.4 + - - +
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Residues in contact with ALA 970 (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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916A ILE* 3.4 12.0 - - - +
918A TRP* 3.8 30.0 - - + -
960A PRO* 4.1 10.3 - - + -
966A VAL 2.8 16.3 + - - +
967A ALA 3.6 4.0 - - - +
969A LYS* 1.3 76.2 - - - +
971A TRP* 1.3 64.6 + - - +
973A ALA* 3.3 2.1 + - - +
974A LEU* 3.1 17.8 + - - +
1010A PRO* 3.5 24.9 - - + -
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Residues in contact with TRP 971 (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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967A ALA 3.0 26.1 + - - +
968A VAL 4.0 2.0 - - - +
970A ALA* 1.3 73.2 - - - +
972A ALA* 1.3 60.1 + - - +
974A LEU* 3.4 26.0 + - + +
975A SER* 3.0 31.5 + - - -
982A HIS* 3.5 39.2 - - + +
983A THR* 3.9 7.9 - - - -
985A LEU* 3.5 34.0 - - + +
986A ALA* 3.6 18.7 - - + +
1008A SER* 3.1 23.4 + - - -
1009A SER* 3.3 23.7 - - - +
1010A PRO* 3.6 28.3 - - + -
1012A TRP 4.7 2.0 - - - -
1014A GLY 5.8 0.7 - - - -
1015A LEU* 4.9 2.7 - - + -
1027A THR* 4.2 15.5 - - + -
1033A ILE* 4.1 9.6 - - + -
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Residues in contact with ALA 972 (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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968A VAL* 3.0 19.3 + - + +
969A LYS* 3.6 9.6 - - - +
971A TRP* 1.3 75.5 - - - +
973A ALA* 1.3 65.6 + - - +
975A SER* 3.2 18.1 + - - -
976A GLU* 3.4 12.7 + - - +
983A THR* 3.8 16.8 - - + +
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Residues in contact with ALA 973 (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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916A ILE* 4.0 14.8 - - + -
917A ALA 3.3 27.8 - - - +
918A TRP* 5.0 0.7 - - + -
969A LYS 3.0 14.2 + - - +
970A ALA* 3.3 10.1 + - - +
972A ALA* 1.3 76.6 - - - +
974A LEU* 1.3 63.5 + - - +
976A GLU* 3.2 24.3 + - - +
977A PHE* 3.6 10.5 - - + -
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Residues in contact with LEU 974 (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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400A TRP* 4.1 26.5 - - + -
914A LYS 5.9 1.3 - - - +
916A ILE* 3.8 26.4 - - + +
970A ALA 3.1 13.5 + - - +
971A TRP* 3.6 37.9 - - + +
972A ALA 3.2 0.2 - - - -
973A ALA* 1.3 76.0 - - - +
975A SER* 1.3 57.9 + - - +
977A PHE* 2.9 25.5 + - + +
978A THR* 3.3 14.4 + - + +
982A HIS* 4.1 8.3 - - + -
1010A PRO* 4.0 11.7 - - + +
1033A ILE* 3.7 24.9 - - + -
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Residues in contact with SER 975 (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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971A TRP 3.0 14.3 + - - -
972A ALA* 3.2 14.5 + - - -
974A LEU* 1.3 76.3 - - - +
976A GLU* 1.3 59.6 + - - +
978A THR* 3.7 3.5 + - - -
979A GLY* 2.8 30.2 + - - -
980A ARG 2.8 15.8 + - - -
981A ASP* 3.5 5.8 + - - -
982A HIS* 2.8 32.9 + - - -
983A THR* 4.2 1.5 + - - -
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Residues in contact with GLU 976 (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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397A LYS* 3.4 24.5 - - + +
398A GLY* 3.4 15.4 + - - -
972A ALA 3.4 10.3 + - - +
973A ALA* 3.2 17.2 + - - +
974A LEU 3.0 0.4 + - - -
975A SER* 1.3 79.9 - - - +
977A PHE* 1.3 64.4 + - + +
979A GLY* 3.9 2.4 + - - -
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Residues in contact with PHE 977 (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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392A PHE 4.9 0.6 - - - +
393A ARG* 3.1 45.3 - - + -
394A TRP* 3.8 20.6 - + - -
397A LYS* 3.2 30.6 - - - +
398A GLY 3.2 17.8 + - - -
400A TRP* 3.4 36.1 + + + +
915A GLY 3.4 26.0 - - - -
916A ILE* 4.0 16.2 - - + -
973A ALA* 3.6 16.8 - - + -
974A LEU* 2.9 9.2 + - + +
976A GLU* 1.3 82.2 - - + +
978A THR* 1.3 58.7 + - - +
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Residues in contact with THR 978 (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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398A GLY 3.6 3.3 - - - +
400A TRP* 3.3 34.1 - - + +
401A ASN* 3.1 30.0 + - - -
974A LEU* 3.3 19.7 + - + +
975A SER* 3.7 2.6 + - - -
977A PHE* 1.3 76.2 - - - +
979A GLY* 1.3 61.2 + - - +
980A ARG* 3.0 19.9 + - - +
982A HIS* 2.9 32.5 + - - +
1033A ILE* 4.5 7.6 - - + -
1034A PRO* 4.4 7.2 - - + -
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Residues in contact with GLY 979 (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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398A GLY* 3.9 17.2 - - - -
403A GLU* 5.2 0.9 - - - +
975A SER 2.8 14.0 + - - -
976A GLU 3.9 2.8 + - - -
977A PHE 3.4 2.6 + - - -
978A THR* 1.3 77.4 - - - +
980A ARG* 1.3 60.1 + - - +
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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