Contacts of the helix formed by residues 966 - 975 (chain M) in PDB entry 6D6Q
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 966 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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910M SER* 4.3 9.6 + - - +
914M PHE* 3.3 45.5 - - + -
963M LYS 4.7 1.0 + - - -
964M PRO 2.7 6.3 + - - -
965M HIS* 1.3 80.2 - - + +
967M MET* 1.3 62.8 + - - +
968M ASP 3.3 2.7 - - - -
969M VAL* 3.3 31.1 + - + -
970M VAL* 2.9 33.1 + - + +
986M THR* 4.4 17.5 - - + +
988M VAL* 5.4 4.0 - - + -
992M SER 5.4 0.2 - - - +
993M ILE* 4.6 18.8 - - + -
996M CYS* 3.8 23.3 - - + -
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Residues in contact with MET 967 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907M ALA* 3.8 25.5 - - + +
908M LEU* 4.3 11.7 - - + -
910M SER* 3.9 7.8 + - - +
911M CYS* 3.2 36.8 - - - -
924M LEU* 3.8 14.1 - - + -
928M LEU* 3.2 47.3 - - + +
932M LEU* 3.5 14.4 - - + -
964M PRO* 3.0 30.2 + - + +
965M HIS 3.7 0.4 - - - -
966M LEU* 1.3 77.8 - - - +
968M ASP* 1.3 59.0 + - - +
970M VAL* 3.3 2.3 + - - +
971M TYR* 2.9 29.3 + - - +
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Residues in contact with ASP 968 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922M PRO* 5.7 4.7 - - + -
923M LYS 4.8 7.6 - - - +
924M LEU* 4.0 21.2 - - + +
928M LEU* 4.9 3.8 - - + -
965M HIS 5.4 0.4 + - - -
966M LEU 3.3 0.4 - - - -
967M MET* 1.3 76.4 - - - +
969M VAL* 1.3 68.6 + - + +
971M TYR* 4.2 10.6 - - - +
972M THR* 2.9 38.2 + - - +
985M MET* 4.7 10.4 - - + +
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Residues in contact with VAL 969 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965M HIS 4.6 2.5 - - - +
966M LEU* 3.3 40.8 + - + +
968M ASP* 1.3 77.5 - - + +
970M VAL* 1.3 62.9 + - + +
972M THR* 2.8 21.3 + - - -
973M TRP* 2.9 16.2 + - + +
982M ILE* 3.5 26.7 - - + +
985M MET* 4.4 18.3 - - + -
986M THR* 4.4 18.4 - - + -
993M ILE* 4.7 16.2 - - + -
997M MET* 6.2 0.7 - - - -
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Residues in contact with VAL 970 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906M THR* 3.8 36.1 - - - +
907M ALA* 4.5 1.8 - - - +
910M SER* 3.9 21.3 - - - +
966M LEU* 2.9 26.8 + - + +
967M MET 3.8 3.6 - - - +
969M VAL* 1.3 75.8 - - + +
971M TYR* 1.3 67.1 + - - +
973M TRP* 3.5 6.6 - - - +
974M ALA* 2.9 24.7 + - + +
996M CYS* 5.1 2.2 - - - -
997M MET* 3.8 30.5 - - + -
1000M LEU* 4.3 6.5 - - + -
1030M ILE* 5.8 1.6 - - + -
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Residues in contact with TYR 971 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903M GLU* 4.2 29.1 - - + +
904M GLN* 5.2 13.7 - - + -
906M THR* 5.6 0.7 - - - -
907M ALA* 5.3 3.1 - - + +
927M GLN* 4.3 22.3 + - - -
928M LEU* 4.0 26.0 - - + -
967M MET 2.9 17.0 + - - +
968M ASP* 3.2 10.1 + - - +
970M VAL* 1.3 77.6 - - - +
972M THR* 1.3 67.9 + - + +
974M ALA* 3.1 7.5 + - - +
975M THR* 2.9 48.0 + - + +
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Residues in contact with THR 972 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968M ASP* 2.9 27.6 + - - +
969M VAL 2.8 19.8 + - - -
971M TYR* 1.3 81.2 - - + +
973M TRP* 1.3 59.5 + - - +
975M THR* 2.2 30.8 + - + -
977M ALA* 3.3 15.6 - - - +
981M HIS* 5.1 3.6 - - + -
982M ILE* 2.9 23.8 - - - +
985M MET* 3.7 23.3 - - + -
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Residues in contact with TRP 973 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969M VAL* 2.9 17.9 + - + +
970M VAL* 3.5 9.2 - - + +
971M TYR 3.2 0.2 - - - -
972M THR* 1.3 76.7 + - - +
974M ALA* 1.3 53.4 + - + +
976M GLY 3.0 5.5 + - - -
977M ALA 4.5 4.3 - - - +
979M PHE* 3.7 43.1 - + + -
982M ILE* 3.8 25.4 - - + -
997M MET* 3.4 26.5 - - + +
1030M ILE* 3.1 40.7 + - + +
1032M ARG* 2.4 70.0 + - + +
1033M ASP* 5.2 4.3 - - + -
1034M ILE* 4.7 8.1 - - + -
1035M VAL* 3.4 31.8 - - + +
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Residues in contact with ALA 974 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903M GLU* 3.3 35.8 - - + +
906M THR* 4.9 6.5 - - + +
970M VAL* 2.9 17.9 + - + +
971M TYR 3.1 2.4 + - - +
973M TRP* 1.3 74.9 - - + +
975M THR* 1.3 56.7 + - - +
976M GLY* 3.0 10.2 + - - -
1026M GLY* 6.5 0.2 - - - -
1029M LYS* 4.0 34.3 + - + +
1030M ILE* 5.5 4.9 - - + +
1032M ARG* 4.2 5.5 + - - +
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Residues in contact with THR 975 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903M GLU* 5.5 5.2 - - + +
971M TYR* 2.9 44.7 + - + +
972M THR* 2.2 35.5 + - + -
974M ALA* 1.3 76.7 - - - +
976M GLY* 1.3 59.6 + - - +
977M ALA* 4.2 4.3 - - - +
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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