Contacts of the helix formed by residues 971 - 980 (chain B) in PDB entry 2PDA
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 TYR 971 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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971A TYR* 2.9 46.2 + + - -
972A GLY* 4.6 7.9 - - - -
975A ASP* 4.0 9.0 - - - -
1028A MET* 3.1 18.0 - - + +
965B TRP 3.2 4.2 + - - -
966B ALA 3.2 24.5 - - - +
967B TYR 3.8 6.5 - - - +
968B ASP 3.2 14.8 + - - +
970B GLY* 1.3 71.7 - - - +
972B GLY* 1.3 58.9 + - - +
974B LEU* 2.7 11.7 + - + +
975B ASP* 2.6 42.6 + - + +
1003B LYS* 5.0 1.1 - - - +
1023B LYS* 3.0 28.9 - - - -
1025B LEU* 3.2 28.7 - - + -
1028B MET* 3.2 10.4 - - - +
1029B VAL* 5.1 1.8 - - + -
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Residues in contact with GLY 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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62A GLN* 4.2 10.5 - - - +
968A ASP 5.5 2.8 - - - +
971A TYR* 4.7 4.7 - - - -
972A GLY* 4.4 23.7 - - - -
1003A LYS* 4.0 5.9 + - - -
968B ASP 4.6 1.2 + - - -
969B ILE 4.9 1.8 + - - -
970B GLY 3.5 0.8 - - - -
971B TYR* 1.3 81.2 - - - +
973B GLY* 1.3 55.5 + - - +
975B ASP* 3.6 7.6 - - - +
976B HIS* 3.2 23.9 + - - +
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Residues in contact with GLY 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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61A MET* 6.5 0.2 - - - -
62A GLN* 3.5 24.2 - - - +
873B ALA* 4.4 6.1 - - - -
874B GLU* 3.5 13.7 - - - -
969B ILE 5.6 0.2 + - - -
970B GLY 3.1 7.5 + - - -
971B TYR 3.0 0.8 - - - -
972B GLY* 1.3 71.7 - - - +
974B LEU* 1.3 68.4 + - - +
975B ASP 3.0 1.8 - - - -
976B HIS* 2.9 1.7 + - - -
977B VAL* 2.9 28.0 + - - +
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Residues in contact with LEU 974 (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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873B ALA* 3.9 12.0 - - + +
965B TRP* 3.8 15.3 - - + -
966B ALA* 3.4 37.9 - - + +
970B GLY 2.8 13.4 + - - +
971B TYR* 2.7 14.4 + - + +
973B GLY* 1.3 70.5 - - - +
975B ASP* 1.3 57.8 + - - +
977B VAL* 3.5 0.9 + - - +
978B LEU* 2.9 48.6 + - + +
986B VAL* 3.6 38.8 - - + -
1025B LEU* 3.9 22.7 - - + -
1029B VAL* 6.0 0.2 - - + -
1064B LEU* 5.1 2.2 - - + -
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Residues in contact with ASP 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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971A TYR* 4.0 5.8 - - + -
1003A LYS* 3.0 11.6 + - - -
1023A LYS* 2.6 30.6 + - - -
1028A MET* 3.3 21.3 - - - +
971B TYR* 2.6 31.3 + - + +
972B GLY* 3.6 8.1 - - - +
974B LEU* 1.3 77.0 - - - +
976B HIS* 1.3 55.9 + - - +
978B LEU* 3.3 7.0 + - - +
979B ALA* 2.8 28.4 + - - +
1029B VAL* 5.4 3.5 - - - +
1032B TYR* 2.9 27.0 + - - -
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Residues in contact with HIS 976 (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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60A GLU* 2.8 30.0 + - - +
61A MET* 3.5 23.4 + - - +
62A GLN* 3.3 37.8 + - + +
968A ASP* 4.8 5.6 + - - -
1003A LYS* 3.3 36.0 + - + +
877B PHE* 5.9 0.9 - + - -
972B GLY 3.2 11.4 + - - +
973B GLY* 2.9 8.3 + - - +
975B ASP* 1.3 76.9 - - - +
977B VAL* 1.3 63.9 + - + +
979B ALA* 3.1 3.1 + - - +
980B SER* 2.8 32.2 + - - -
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Residues in contact with VAL 977 (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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61A MET* 4.3 8.1 - - + -
873B ALA* 3.7 27.8 - - + +
874B GLU* 3.7 10.8 - - + +
877B PHE* 3.8 25.8 - - + -
959B ILE* 4.3 11.4 - - + -
973B GLY 2.9 15.0 + - - +
974B LEU 3.9 2.9 - - - +
976B HIS* 1.3 74.1 - - + +
978B LEU* 1.3 63.1 + - + +
980B SER* 2.5 34.0 + - - -
981B GLY 3.8 0.9 + - - -
984B VAL* 3.8 27.9 - - + +
986B VAL* 5.6 0.7 - - + -
1062B PRO* 4.7 2.1 - - - +
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Residues in contact with LEU 978 (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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974B LEU* 2.9 44.9 + - + +
975B ASP* 3.7 5.8 - - - +
977B VAL* 1.3 78.5 - - + +
979B ALA* 1.3 60.1 + - - +
981B GLY 3.3 0.9 + - - -
984B VAL* 5.2 3.6 - - + -
986B VAL* 3.6 25.1 - - + -
1029B VAL* 4.1 22.4 - - + -
1032B TYR* 5.1 5.4 - - + -
1034B TYR* 3.7 0.5 - - - -
1035B VAL* 3.2 31.6 - - + +
1062B PRO* 3.3 32.7 - - + +
1063B SER 4.2 8.5 - - - +
1064B LEU* 4.0 22.4 - - + -
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Residues in contact with ALA 979 (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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1003A LYS* 4.0 18.4 - - + -
1020A THR* 4.3 5.7 + - - +
975B ASP 2.8 16.8 + - - +
976B HIS 3.1 4.7 + - - +
978B LEU* 1.3 73.1 - - - +
980B SER* 1.3 62.0 + - - +
981B GLY 2.9 7.1 + - - -
1032B TYR* 3.3 32.7 - - + +
1034B TYR* 2.6 29.7 + - - +
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Residues in contact with SER 980 (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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1020A THR* 4.9 7.6 - - - +
877B PHE* 3.0 37.4 - - - -
976B HIS* 2.8 17.6 + - - -
977B VAL* 2.5 19.4 + - - +
979B ALA* 1.3 79.2 - - - +
981B GLY* 1.3 57.1 + - - +
982B GLU* 3.1 21.6 + - - +
984B VAL* 5.8 0.3 - - - +
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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