Contacts of the helix formed by residues 60 - 74 (chain J) in PDB entry 4LLL
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 60 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14I HIS* 6.6 0.2 - - + -
54J ALA* 4.5 1.8 - - - -
59J ARG* 1.3 77.2 - - - +
61J GLY* 1.3 64.7 + - - +
62J PRO* 3.3 17.2 - - - +
63J THR* 3.0 23.9 + - - +
64J VAL* 3.1 26.7 + - - +
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Residues in contact with GLY 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J GLN* 5.4 2.6 - - - +
51J ASN* 5.4 10.1 - - - -
54J ALA* 4.8 5.8 - - - +
60J THR* 1.3 76.4 - - - +
62J PRO* 1.3 62.1 - - - +
64J VAL* 3.1 7.6 + - - +
65J SER* 2.9 26.8 + - - -
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Residues in contact with PRO 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J THR* 3.3 15.5 - - - +
61J GLY* 1.3 86.3 - - - +
63J THR* 1.3 63.5 - - - +
65J SER* 2.9 9.8 + - - -
66J ASN* 2.9 28.1 + - - +
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Residues in contact with THR 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J ARG* 4.0 30.6 - - + +
60J THR* 3.0 28.0 + - - +
62J PRO* 1.3 79.2 - - - +
64J VAL* 1.3 61.8 + - + +
66J ASN* 4.4 2.4 - - - +
67J LEU* 3.4 25.0 + - + +
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Residues in contact with VAL 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J GLN* 3.7 20.4 - - + +
53J ILE* 4.8 8.5 - - + +
54J ALA* 3.5 28.5 - - + +
57J LEU* 5.3 6.1 - - + -
59J ARG* 4.0 13.9 - - + -
60J THR 3.1 15.0 + - - +
61J GLY 3.1 7.3 + - - +
62J PRO 3.1 0.2 - - - -
63J THR* 1.3 77.0 - - + +
65J SER* 1.3 55.6 + - - +
67J LEU* 3.8 10.0 - - + +
68J LEU* 2.8 58.6 + - + +
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Residues in contact with SER 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J GLN* 4.0 24.7 + - - +
61J GLY 2.9 13.6 + - - -
62J PRO* 2.9 14.1 + - - -
64J VAL* 1.3 76.0 - - - +
66J ASN* 1.3 57.8 + - - +
68J LEU* 3.9 1.4 - - - +
69J ARG* 3.0 29.6 + - - +
79J ARG* 4.1 4.7 + - - -
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Residues in contact with ASN 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J PRO 2.9 14.1 + - - +
63J THR* 4.4 3.1 - - - +
65J SER* 1.3 73.3 - - - +
67J LEU* 1.3 62.2 + - - +
69J ARG* 3.2 7.8 + - - +
70J ASN* 2.9 35.0 + - - +
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Residues in contact with LEU 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J THR* 5.0 0.7 - - - +
32J GLU* 4.3 11.2 - - + -
33J GLN* 3.5 45.5 - - + +
36J THR* 3.2 36.6 - - + +
57J LEU* 5.1 6.3 - - + -
63J THR* 3.4 20.4 + - + +
64J VAL* 3.3 11.1 + - + +
66J ASN* 1.3 79.6 - - - +
68J LEU* 1.3 64.0 + - + +
70J ASN* 3.4 12.0 - - - +
71J LEU* 3.2 21.9 + - + +
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Residues in contact with LEU 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36J THR* 4.4 22.7 - - + -
40J LEU* 5.7 1.3 - - + -
50J GLN* 3.2 40.4 - - + +
53J ILE* 4.7 6.7 - - + -
64J VAL* 2.8 38.9 + - + +
65J SER 3.9 2.9 - - - +
67J LEU* 1.3 72.9 - - + +
69J ARG* 1.3 53.7 + - - +
71J LEU* 3.0 8.1 + - + +
72J GLU* 2.7 32.4 + - - +
77J ILE* 3.5 25.4 - - + +
79J ARG* 4.1 10.5 - - - +
91J ILE* 3.9 26.7 - - + -
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Residues in contact with ARG 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65J SER 3.0 19.5 + - - +
66J ASN* 3.2 7.8 + - - +
68J LEU* 1.3 75.4 - - - +
70J ASN* 1.3 62.7 - - - +
72J GLU* 3.0 8.8 + - - +
73J ARG* 3.0 29.5 + - + +
79J ARG* 3.9 16.7 - - - +
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Residues in contact with ASN 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J GLN* 4.0 25.0 - - - +
66J ASN* 2.9 19.2 + - - +
67J LEU* 3.4 16.5 - - - +
69J ARG* 1.3 73.6 - - - +
71J LEU* 1.3 64.1 + - - +
73J ARG* 3.0 26.0 + - - +
74J LYS* 3.4 11.3 + - - +
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Residues in contact with LEU 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ILE* 5.1 0.9 - - + -
33J GLN* 3.6 39.9 - - + +
36J THR* 4.4 20.4 - - + -
37J LEU* 3.5 29.4 - - + -
40J LEU* 5.6 0.9 - - + -
67J LEU* 3.2 13.2 + - + +
68J LEU* 3.0 11.9 + - + +
70J ASN* 1.3 79.8 - - - +
72J GLU* 1.3 60.6 + - - +
74J LYS* 3.5 10.7 + - + +
76J LEU* 3.2 45.7 + - + +
77J ILE* 3.6 22.9 + - + -
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Residues in contact with GLU 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J LEU 2.7 16.2 + - - +
69J ARG* 3.0 10.8 + - - +
71J LEU* 1.3 70.9 - - - +
73J ARG* 1.3 66.2 + - + +
75J LYS* 3.1 12.6 + - - +
77J ILE* 3.7 24.8 - - + +
78J TYR* 5.2 0.2 - - - -
79J ARG* 3.3 60.2 + - + +
89J LYS* 5.4 0.9 + - - -
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Residues in contact with ARG 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J ARG* 3.0 23.4 + - + +
70J ASN* 3.2 12.6 - - - +
72J GLU* 1.3 75.2 - - + +
74J LYS* 1.3 59.4 + - + +
75J LYS* 2.9 13.8 + - - +
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Residues in contact with LYS 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J PHE 5.0 1.1 - - - -
28J ASP* 2.7 50.9 + - - +
29J ILE* 4.0 9.0 - - - +
33J GLN* 4.1 9.7 + - - -
70J ASN 3.4 12.4 + - - +
71J LEU* 3.7 7.1 - - + +
72J GLU 3.3 0.4 - - - -
73J ARG* 1.3 76.3 - - + +
75J LYS* 1.3 67.2 + - - +
76J LEU* 3.2 34.7 + - + +
96J SER* 4.5 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