Contacts of the helix formed by residues 958 - 969 (chain M) in PDB entry 5D4D
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 THR 958 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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956M GLY 5.5 0.4 - - - +
957M LYS* 1.3 72.8 - - - +
959M PRO* 1.3 67.6 - - - +
960M GLU* 3.4 9.4 + - - +
961M GLU* 2.8 59.1 + - - +
962M GLN* 2.9 12.0 + - - +
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Residues in contact with PRO 959 (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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936M VAL* 3.6 34.1 - - + -
941M VAL* 5.4 7.9 - - + -
944M LEU* 3.5 20.8 - - + +
957M LYS 4.0 3.8 - - - +
958M THR* 1.3 86.7 - - - +
960M GLU* 1.3 54.9 + - - +
962M GLN* 4.3 5.8 - - + +
963M LEU* 2.9 36.1 + - - +
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Residues in contact with GLU 960 (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 PHE* 3.6 13.9 - - + -
923M GLU* 5.2 5.0 - - - +
926M PHE* 3.5 43.4 - - + -
927M GLY* 6.1 0.2 - - - -
930M LYS* 3.9 14.9 + - - +
936M VAL* 4.6 2.1 - - + +
958M THR* 3.1 8.3 + - - +
959M PRO* 1.3 75.5 - - - +
961M GLU* 1.3 61.6 + - + +
963M LEU* 3.4 4.4 + - - -
964M LYS* 2.9 29.2 + - + +
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Residues in contact with GLU 961 (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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957M LYS* 3.1 33.5 - - + +
958M THR* 2.8 46.3 + - - +
960M GLU* 1.3 80.0 - - + +
962M GLN* 1.3 55.7 + - - +
964M LYS* 3.3 8.2 + - - +
965M GLU* 2.9 33.0 + - - +
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Residues in contact with GLN 962 (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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944M LEU* 3.6 39.5 - - + +
948M GLU* 3.2 24.1 + - - -
953M VAL* 3.5 21.6 - - + +
954M THR 3.2 20.9 + - - +
955M PRO* 4.3 0.6 - - - +
956M GLY 4.4 0.6 - - - +
957M LYS* 3.9 23.7 + - + +
958M THR 2.9 15.2 + - - +
959M PRO* 3.8 8.5 - - - +
961M GLU* 1.3 73.9 - - - +
963M LEU* 1.3 66.1 + - - +
965M GLU* 3.0 13.4 + - - +
966M LEU* 2.9 25.1 + - - +
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Residues in contact with LEU 963 (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 PHE* 3.8 10.8 - - + -
926M PHE* 3.9 25.1 - - + -
929M ARG* 4.7 0.2 - - - +
936M VAL* 4.9 3.6 - - + -
940M GLU* 3.7 27.8 - - + +
944M LEU* 3.6 29.8 - - + -
959M PRO 2.9 25.5 + - - +
960M GLU 3.7 4.5 - - - +
962M GLN* 1.3 75.5 - - - +
964M LYS* 1.3 58.3 + - - +
966M LEU* 3.3 11.4 + - + +
967M PHE* 2.9 26.3 + - - +
971M LYS 4.9 0.5 - - - +
973M VAL* 3.9 25.1 - - + +
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Residues in contact with LYS 964 (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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919M ALA* 3.6 30.2 - - - +
922M PHE* 3.4 34.3 - - + -
923M GLU* 3.8 18.4 + - - +
960M GLU 2.9 18.2 + - - +
961M GLU* 3.5 8.5 - - - +
963M LEU* 1.3 75.4 - - - +
965M GLU* 1.3 65.6 + - - +
967M PHE* 2.9 1.9 + - - +
968M LEU* 2.9 37.1 + - + +
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Residues in contact with GLU 965 (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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952M LEU 4.5 1.1 - - - +
953M VAL* 3.4 13.4 - - + +
954M THR* 2.5 52.8 + - - +
957M LYS* 3.3 21.6 + - - +
961M GLU 2.9 17.7 + - - +
962M GLN* 3.4 11.4 - - - +
964M LYS* 1.3 77.4 - - + +
966M LEU* 1.3 61.4 + - - +
968M LEU* 3.5 11.6 + - + +
969M GLN* 3.1 34.8 + - - +
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Residues in contact with LEU 966 (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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943M VAL* 5.1 5.4 - - + -
944M LEU* 3.8 24.7 - - + -
947M ALA* 4.2 6.3 - - + -
952M LEU* 3.8 18.4 - - + -
953M VAL* 3.7 18.8 - - + -
962M GLN 2.9 13.2 + - - +
963M LEU* 3.4 17.7 - - + +
965M GLU* 1.3 75.5 - - - +
967M PHE* 1.3 63.3 + - - +
969M GLN* 3.0 17.9 + - - +
971M LYS* 2.9 33.7 + - + +
972M VAL* 5.6 0.4 - - - -
973M VAL* 5.3 3.4 - - + +
986M PRO* 3.7 38.8 - - + -
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Residues in contact with PHE 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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892M LEU* 3.9 10.4 - - + +
896M PHE* 3.7 30.1 - + - -
918M LEU* 3.2 49.7 - - + +
921M ALA* 4.1 2.9 - - + -
922M PHE* 3.6 26.9 - + + -
925M TYR* 3.3 37.5 - + - -
963M LEU 2.9 14.7 + - - +
964M LYS 2.9 7.6 + - - +
966M LEU* 1.3 76.3 - - - +
968M LEU* 1.3 58.5 + - + +
970M GLY* 2.9 19.6 + - - -
971M LYS 3.4 6.3 + - - +
972M VAL* 3.8 24.2 - - + -
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Residues in contact with LEU 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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889M HIS* 5.9 0.5 - - - -
915M LYS* 3.2 49.3 + - + +
918M LEU* 3.3 18.4 - - - +
919M ALA* 3.7 39.7 - - + +
964M LYS* 2.9 34.7 + - + +
965M GLU* 3.7 12.1 - - + +
967M PHE* 1.3 77.6 - - + +
969M GLN* 1.3 59.8 + - + +
970M GLY 3.1 0.9 - - - -
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Residues in contact with GLN 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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889M HIS* 3.7 17.4 + - - -
915M LYS* 4.0 2.5 - - - +
918M LEU* 4.9 0.2 - - - -
952M LEU* 2.7 50.1 + - - +
965M GLU* 3.1 24.2 + - - +
966M LEU* 3.0 15.2 + - - +
968M LEU* 1.3 78.2 - - + +
970M GLY* 1.3 61.0 + - - +
971M LYS* 3.3 21.3 + - + +
950N GLY* 4.6 2.6 - - - -
951N ILE 4.8 0.9 + - - -
952N ASP* 3.8 37.1 + - + +
953N ASP* 5.7 0.5 - - - +
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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