Contacts of the helix formed by residues 973 - 985 (chain A) in PDB entry 5C51
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 973 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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967A MET* 4.9 0.9 - - - -
972A ARG* 1.3 94.4 - - + +
974A THR* 1.3 63.7 + - - +
975A GLN* 3.3 27.5 + - + +
976A GLN* 3.3 65.3 - - + +
977A GLU* 2.8 26.3 + - - +
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Residues in contact with THR 974 (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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963A GLU* 3.6 19.8 + - - -
967A MET* 4.0 20.1 - - - -
972A ARG 4.3 0.2 + - - -
973A LEU* 1.3 71.8 - - - +
975A GLN* 1.3 79.9 + - + +
977A GLU* 3.6 7.0 - - - +
978A ALA* 2.9 29.5 + - - +
981A LYS* 4.3 1.2 + - - -
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Residues in contact with GLN 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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973A LEU* 3.3 20.1 - - + +
974A THR* 1.3 88.7 + - + +
976A GLN* 1.3 62.2 + - + +
978A ALA* 3.1 7.9 + - - +
979A ALA* 2.9 26.2 + - - +
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Residues in contact with GLN 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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972A ARG* 4.8 4.7 - - - +
973A LEU* 3.3 34.9 - - + +
975A GLN* 1.3 78.2 - - + +
977A GLU* 1.3 61.3 + - - +
979A ALA* 3.1 10.6 + - - +
980A GLU* 2.9 36.8 + - + +
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Residues in contact with GLU 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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966A LEU* 4.6 9.4 - - + +
967A MET* 3.9 26.7 - - + +
970A ASN* 3.9 14.6 - - - +
972A ARG* 3.2 37.4 + - - +
973A LEU 2.8 28.7 + - - +
974A THR* 3.6 5.4 - - - +
976A GLN* 1.3 80.9 - - - +
978A ALA* 1.3 58.2 + - - +
980A GLU* 3.0 11.5 + - + +
981A LYS* 2.9 55.6 + - - +
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Residues in contact with ALA 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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963A GLU* 5.6 4.9 - - - +
974A THR* 2.9 20.7 + - - +
975A GLN* 3.1 7.8 + - - +
977A GLU* 1.3 75.0 - - - +
979A ALA* 1.3 58.0 + - - +
981A LYS* 3.6 16.3 - - + +
982A ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 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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975A GLN 2.9 12.7 + - - +
976A GLN* 3.2 14.1 - - - +
977A GLU 3.1 0.2 - - - -
978A ALA* 1.3 74.9 - - - +
980A GLU* 1.3 61.5 + - - +
982A ALA* 3.3 6.9 + - - +
983A GLN* 2.9 44.4 + - - +
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Residues in contact with GLU 980 (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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938A THR* 5.8 3.8 - - - -
939A VAL 6.0 2.2 - - - +
966A LEU* 4.5 12.8 - - + -
976A GLN* 2.9 26.0 + - + +
977A GLU* 3.0 11.2 + - + +
979A ALA* 1.3 77.3 - - - +
981A LYS* 1.3 57.0 + - - +
983A GLN* 3.2 27.0 + - - +
984A GLN* 2.9 34.6 + - + +
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Residues in contact with LYS 981 (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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949A PHE* 5.3 4.3 - - + -
959A GLN* 5.0 6.7 - - + +
962A ALA* 4.1 12.6 - - + +
963A GLU* 3.2 57.5 + - + +
966A LEU* 3.9 17.5 - - + -
967A MET* 4.5 2.6 - - - +
974A THR* 4.3 4.0 + - - -
977A GLU* 2.9 51.3 + - - +
978A ALA* 3.6 14.1 - - - +
980A GLU* 1.3 75.5 - - - +
982A ALA* 1.3 52.1 + - - +
984A GLN* 2.9 8.3 + - - +
985A MET* 2.7 51.6 + - + +
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Residues in contact with ALA 982 (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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978A ALA 2.9 18.9 + - - +
979A ALA* 3.6 7.4 - - - +
981A LYS* 1.3 76.0 - - - +
983A GLN* 1.3 61.9 + - + +
984A GLN 3.6 0.2 + - - -
985A MET* 3.6 15.9 + - - +
986A TYR* 4.1 5.7 + - - +
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Residues in contact with GLN 983 (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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979A ALA* 2.9 29.0 + - - +
980A GLU* 3.4 32.1 + - - +
982A ALA* 1.3 77.9 - - + +
984A GLN* 1.3 60.4 + - + +
985A MET 3.7 0.2 + - - -
986A TYR* 3.4 24.9 - - - +
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Residues in contact with GLN 984 (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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935A THR* 5.7 8.7 - - - +
938A THR* 4.8 16.2 - - - +
949A PHE* 4.9 21.8 - - + -
953A ARG* 4.6 15.8 + - - -
966A LEU* 6.3 1.3 - - + -
980A GLU* 2.9 19.6 + - + +
981A LYS* 2.9 8.3 + - - +
983A GLN* 1.3 78.3 - - + +
985A MET* 1.3 59.6 + - + +
986A TYR* 3.0 19.3 + - - -
987A ALA* 3.7 15.9 + - - +
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Residues in contact with MET 985 (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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949A PHE* 6.1 2.0 - - + -
953A ARG* 5.9 2.5 - - - -
957A ALA* 3.3 39.0 - - + +
959A GLN* 4.1 19.1 - - + -
962A ALA* 4.0 24.5 - - + -
981A LYS* 2.7 35.5 + - + +
982A ALA* 4.0 11.4 - - - +
983A GLN 3.4 1.0 - - - -
984A GLN* 1.3 72.8 - - - +
986A TYR* 1.3 62.6 + - - +
987A ALA 3.1 3.0 + - - -
988A ALA* 3.7 12.6 + - - +
989A THR* 3.2 26.2 + - + +
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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