Contacts of the helix formed by residues 962 - 975 (chain B) in PDB entry YUA9
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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958B LEU* 3.7 19.5 - - + +
959B SER* 2.8 26.8 + - - +
961B ASP* 1.3 82.6 + - - +
963B LYS* 1.3 86.2 + - - +
964B GLU* 3.1 23.8 + - - +
965B PHE* 3.0 18.6 + - + +
966B GLN* 3.2 11.7 + - - +
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Residues in contact with LYS 963 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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961B ASP 3.7 3.2 + - - -
962B ASP* 1.3 78.2 + - - +
964B GLU* 1.3 64.8 + - + +
966B GLN* 3.2 16.0 + - - +
967B SER* 3.0 31.2 + - - -
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Residues in contact with GLU 964 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958B LEU* 4.3 14.9 - - + +
962B ASP* 3.5 14.3 - - - +
963B LYS* 1.3 84.7 - - + +
965B PHE* 1.3 65.6 + - - +
967B SER* 3.2 7.5 + - - +
968B VAL* 3.2 29.0 + - + +
999B LYS* 2.6 35.7 + - - -
1151B TYR* 2.4 39.1 + - + +
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Residues in contact with PHE 965 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958B LEU* 3.7 37.2 - - + +
959B SER 3.3 11.0 - - - +
960B PRO* 3.6 39.3 - - + -
962B ASP* 3.0 12.0 + - - +
964B GLU* 1.3 79.7 - - - +
966B GLN* 1.3 61.7 + - + +
968B VAL* 3.2 2.3 + - - +
969B GLU* 2.9 47.2 + - - +
994B ILE* 4.0 24.9 - - + -
995B LEU 5.6 1.3 - - - -
996B LYS* 4.6 3.6 - - - -
997B ILE* 3.7 40.6 - - + +
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Residues in contact with GLN 966 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960B PRO 3.2 25.9 + - - +
961B ASP* 3.6 17.9 + - - +
962B ASP 3.2 8.5 + - - +
963B LYS* 3.6 15.4 - - - +
964B GLU 3.2 0.4 - - - -
965B PHE* 1.3 84.2 - - + +
967B SER* 1.3 56.8 + - - +
968B VAL 3.3 0.2 - - - -
969B GLU* 3.9 5.9 - - - +
970B GLU* 2.9 29.3 + - - +
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Residues in contact with SER 967 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963B LYS 3.0 12.5 + - - -
964B GLU* 3.2 14.4 + - - +
966B GLN* 1.3 74.3 - - - +
968B VAL* 1.3 68.0 + - - +
970B GLU* 3.9 5.9 - - - +
971B GLU* 3.2 22.9 + - - +
1098B PHE* 5.6 0.2 - - - -
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Residues in contact with VAL 968 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964B GLU* 3.2 18.1 + - + +
965B PHE 3.7 2.7 - - - +
967B SER* 1.3 79.0 + - - +
969B GLU* 1.3 59.2 + - - +
971B GLU* 3.1 7.0 + - - +
972B MET* 2.9 26.9 + - - +
997B ILE* 3.9 19.1 - - + -
1030B PHE* 5.1 1.0 - - - -
1098B PHE* 4.1 18.8 - - + -
1151B TYR* 3.9 39.7 - - + +
1153B ILE* 3.8 28.0 - - + +
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Residues in contact with GLU 969 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965B PHE* 2.9 36.7 + - + +
966B GLN* 3.9 6.6 - - - +
968B VAL* 1.3 73.6 - - - +
970B GLU* 1.3 69.2 + - - +
972B MET* 3.0 9.8 + - - +
973B GLN* 2.9 51.3 + - + +
994B ILE* 3.5 23.7 + - + +
997B ILE* 4.0 9.5 - - + +
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Residues in contact with GLU 970 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966B GLN 2.9 20.0 + - - +
967B SER* 3.9 7.2 - - - +
968B VAL 3.3 0.2 - - - -
969B GLU* 1.3 79.0 - - - +
971B GLU* 1.3 51.9 + - - +
973B GLN* 4.6 6.6 - - - +
974B SER* 2.7 56.2 + - - +
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Residues in contact with GLU 971 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967B SER 3.2 16.5 + - - +
968B VAL 3.1 5.2 + - - +
969B GLU 3.1 0.6 - - - -
970B GLU* 1.3 74.4 - - - +
972B MET* 1.3 65.5 + - - +
974B SER* 3.6 7.3 + - - -
975B THR* 2.9 38.8 + - - +
1028B MET 4.8 5.2 - - - +
1030B PHE* 3.7 7.5 - - + -
1063B GLU* 4.9 2.6 - - - +
1098B PHE* 3.5 37.2 - - + -
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Residues in contact with MET 972 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968B VAL 2.9 11.6 + - - +
969B GLU* 3.0 12.5 + - - +
971B GLU* 1.3 78.7 - - - +
973B GLN* 1.3 61.8 - - - +
975B THR* 3.4 2.9 + - - -
976B VAL* 3.7 0.5 - - - +
992B TYR* 3.4 34.1 - - + -
994B ILE* 3.8 15.3 - - + -
1030B PHE* 3.8 18.5 - - + -
1065B SER* 2.7 29.7 + - - -
1096B LEU* 3.8 25.4 - - + -
1153B ILE* 3.7 32.1 - - + -
1155B TYR* 3.8 34.5 - - + -
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Residues in contact with GLN 973 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969B GLU* 2.9 49.2 + - + +
970B GLU* 4.0 9.2 - - - +
972B MET* 1.3 75.0 - - + +
974B SER* 1.3 63.1 + - - +
975B THR 3.4 0.9 + - - -
976B VAL* 3.5 19.3 + - - +
990B ASN 4.9 2.8 - - - +
991B ARG* 3.5 14.5 - - + +
992B TYR* 2.8 54.8 + - - -
994B ILE* 4.0 6.4 - - - +
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Residues in contact with SER 974 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970B GLU* 2.7 42.3 + - - +
971B GLU* 3.6 12.1 + - - -
973B GLN* 1.3 78.4 - - - +
975B THR* 1.3 64.0 + - - +
976B VAL 3.4 5.7 + - - +
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Residues in contact with THR 975 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971B GLU* 2.9 37.5 + - + +
973B GLN 3.3 0.2 - - - -
974B SER* 1.3 84.1 - - - +
976B VAL* 1.3 59.9 + - - +
1030B PHE* 3.7 1.4 - - - -
1063B GLU 3.2 23.0 + - - +
1064B ASN* 2.9 34.4 + - - +
1065B SER* 2.9 25.4 + - - -
1066B SER* 3.8 0.3 + - - -
1136B LEU* 4.6 10.5 - - + -
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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