Contacts of the helix formed by residues 962 - 975 (chain A) in PDB entry 3U9Y
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 ASP 962 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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958A LEU* 3.8 18.0 - - + +
959A SER* 2.8 29.5 + - - +
961A ASP* 1.3 80.2 - - - +
963A LYS* 1.3 82.1 + - - +
964A GLU* 3.0 26.4 + - - +
965A PHE* 3.1 17.7 + - + +
966A GLN* 3.2 12.9 + - - +
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Residues in contact with LYS 963 (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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961A ASP 3.5 3.2 + - - -
962A ASP* 1.3 79.7 + - - +
964A GLU* 1.3 61.8 + - + +
966A GLN* 3.1 14.2 + - - +
967A SER* 2.9 31.1 + - - -
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Residues in contact with GLU 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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958A LEU* 4.3 15.9 - - + +
962A ASP* 3.0 16.6 + - - +
963A LYS* 1.3 80.5 - - + +
965A PHE* 1.3 62.2 + - - +
967A SER* 3.7 7.0 + - - +
968A VAL* 3.3 30.8 + - + +
999A LYS* 3.2 24.6 - - - +
1151A TYR* 2.3 42.0 + - + +
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Residues in contact with PHE 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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958A LEU* 3.6 31.1 - - + +
959A SER 3.2 21.5 - - - +
960A PRO* 3.7 32.3 - - + -
962A ASP* 3.1 8.6 + - + +
964A GLU* 1.3 78.9 - - - +
966A GLN* 1.3 65.6 + - + +
969A GLU* 2.9 48.7 + - + +
994A ILE* 4.0 23.3 - - + -
995A LEU 5.5 1.3 - - - -
996A LYS* 4.5 4.9 - - - -
997A ILE* 3.5 42.2 - - + +
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Residues in contact with GLN 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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960A PRO 3.0 27.2 + - - +
961A ASP* 3.4 21.8 + - - +
962A ASP 3.2 4.0 + - - +
963A LYS* 3.1 13.6 + - - +
965A PHE* 1.3 86.7 - - + +
967A SER* 1.3 57.1 + - - +
969A GLU* 3.4 5.7 + - - +
970A GLU* 3.0 28.6 + - - +
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Residues in contact with SER 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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963A LYS 2.9 14.0 + - - -
964A GLU* 3.7 11.8 + - - +
965A PHE 3.4 0.2 - - - -
966A GLN* 1.3 73.2 - - - +
968A VAL* 1.3 70.4 + - - +
970A GLU* 3.3 7.7 + - - +
971A GLU* 3.0 23.0 + - - +
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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
----------------------------------------------------------
964A GLU* 3.3 17.8 + - + +
965A PHE 4.0 2.0 - - - +
967A SER* 1.3 79.3 + - - +
969A GLU* 1.3 63.7 + - - +
971A GLU* 3.1 9.4 + - - +
972A MET* 3.0 19.4 + - - +
997A ILE* 3.8 19.1 - - + -
1030A PHE* 5.4 0.3 - - - -
1098A PHE* 4.0 20.2 - - + -
1151A TYR* 4.0 37.2 - - + +
1153A ILE* 3.6 30.7 - - + -
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Residues in contact with GLU 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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965A PHE* 2.9 44.0 + - + +
966A GLN* 3.7 6.2 - - - +
968A VAL* 1.3 71.7 - - - +
970A GLU* 1.3 61.5 + - - +
972A MET* 3.1 9.8 + - - +
973A GLN* 2.9 56.4 + - + +
994A ILE* 3.5 21.9 + - + +
997A ILE* 3.9 10.2 - - + +
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Residues in contact with GLU 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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966A GLN 3.0 18.7 + - - +
967A SER* 3.5 8.1 - - - +
968A VAL 3.2 0.2 - - - -
969A GLU* 1.3 76.7 - - - +
971A GLU* 1.3 55.6 + - - +
973A GLN* 4.5 7.5 - - - +
974A SER* 2.6 58.4 + - - +
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Residues in contact with GLU 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 SER 3.0 12.8 + - - +
968A VAL 3.1 9.2 + - - +
970A GLU* 1.3 80.5 - - - +
972A MET* 1.3 51.1 + - - +
974A SER* 3.9 4.5 + - - -
975A THR* 2.7 52.1 + - - +
1028A MET 5.5 2.4 - - - +
1030A PHE* 3.7 7.8 - - + -
1063A GLU 5.2 0.5 - - - +
1098A PHE* 3.5 36.8 - - + -
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Residues in contact with MET 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 11.7 + - + +
969A GLU* 3.2 9.6 - - - +
971A GLU* 1.3 78.9 - - - +
973A GLN* 1.3 64.8 + - + +
975A THR* 3.5 2.8 + - - -
976A VAL* 3.8 0.7 - - - +
992A TYR* 3.3 41.6 - - + -
994A ILE* 3.8 23.1 - - + -
997A ILE* 6.2 0.2 - - + -
1030A PHE* 3.9 23.6 - - + -
1065A SER* 2.8 26.1 + - - -
1096A LEU* 3.9 15.5 - - + -
1153A ILE* 3.9 27.4 - - + -
1155A TYR* 3.9 27.1 - - + -
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Residues in contact with GLN 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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969A GLU* 2.9 49.0 + - + +
970A GLU* 4.1 9.2 - - - +
972A MET* 1.3 78.3 - - - +
974A SER* 1.3 62.6 + - - +
975A THR 3.4 0.7 + - - -
976A VAL* 3.4 19.2 + - - +
990A ASN 4.8 2.4 - - - +
991A ARG* 3.6 13.2 - - + +
992A TYR* 3.0 55.0 + - - -
994A ILE* 3.9 7.2 - - - +
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Residues in contact with SER 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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970A GLU* 2.6 45.3 + - - +
971A GLU* 3.9 9.2 + - - -
973A GLN* 1.3 77.5 - - - +
975A THR* 1.3 64.2 + - - +
976A VAL 3.4 6.3 + - - +
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Residues in contact with THR 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 GLU* 2.7 43.7 + - + +
973A GLN 3.3 0.4 - - - -
974A SER* 1.3 83.6 - - - +
976A VAL* 1.3 59.6 + - - +
1030A PHE* 3.6 1.6 - - - -
1063A GLU 3.4 21.2 + - - +
1064A ASN* 2.9 34.0 + - - +
1065A SER* 3.2 24.8 + - - -
1066A SER* 4.0 0.3 + - - -
1136A LEU* 4.6 11.7 - - + -
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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