Contacts of the helix formed by residues 60 - 74 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59O ARG* 1.3 77.9 - - - +
61O GLY* 1.3 68.9 + - - +
62O PRO* 4.1 11.0 - - - +
63O THR* 2.5 32.1 + - - -
64O VAL* 3.1 15.2 + - - +
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Residues in contact with GLY 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O ASN* 6.4 1.1 - - - -
54O ALA* 4.9 6.8 - - - +
59O ARG 3.8 1.0 + - - -
60O THR* 1.3 68.9 - - - +
62O PRO* 1.3 62.7 - - - +
64O VAL* 2.8 29.8 + - - +
65O SER* 2.9 12.5 + - - -
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Residues in contact with PRO 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O THR* 3.6 11.2 - - - +
61O GLY* 1.3 86.0 - - - +
63O THR* 1.3 59.4 + - - +
65O SER* 3.6 10.6 - - - -
66O ASN* 2.8 40.6 + - - +
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Residues in contact with THR 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O GLU* 5.8 5.6 - - + -
59O ARG* 4.1 17.3 - - + -
60O THR* 2.5 32.1 + - - -
61O GLY 3.1 0.2 - - - -
62O PRO* 1.3 81.2 - - - +
64O VAL* 1.3 63.8 + - - +
65O SER 3.3 0.3 + - - -
66O ASN* 3.3 8.3 + - - +
67O LEU* 3.1 28.0 + - + +
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Residues in contact with VAL 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50O GLN* 3.6 18.4 - - + +
53O ILE* 4.2 17.9 - - + -
54O ALA* 3.7 26.9 - - + +
57O LEU* 6.0 0.7 - - + -
59O ARG* 3.8 13.5 - - + +
60O THR 3.1 16.2 - - - +
61O GLY* 2.8 10.4 + - - +
63O THR* 1.3 69.2 - - - +
65O SER* 1.3 59.9 + - - +
67O LEU* 3.2 14.6 + - + +
68O LEU* 2.8 53.8 + - + +
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Residues in contact with SER 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50O GLN* 6.5 0.9 - - - -
61O GLY 2.9 11.0 + - - -
62O PRO* 3.6 15.9 - - - -
64O VAL* 1.3 77.3 - - - +
66O ASN* 1.3 60.2 + - - +
68O LEU* 3.9 6.6 - - - +
69O ARG* 2.9 30.6 + - - +
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Residues in contact with ASN 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62O PRO* 2.8 22.8 + - - +
63O THR* 3.8 8.1 + - - +
65O SER* 1.3 75.0 + - - +
67O LEU* 1.3 60.2 - - - +
69O ARG* 3.7 7.0 - - - +
70O ASN* 3.0 31.2 + - - +
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Residues in contact with LEU 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O THR* 4.7 0.4 - - - +
32O GLU* 4.0 21.5 - - + -
33O GLN* 3.6 43.1 - - + +
36O THR* 3.8 28.9 - - + +
57O LEU* 4.6 8.7 - - + -
59O ARG* 5.8 3.1 - - + -
63O THR* 3.1 18.3 + - + +
64O VAL* 3.2 26.0 - - + +
66O ASN* 1.3 75.8 - - - +
68O LEU* 1.3 58.5 + - + +
70O ASN* 3.1 8.5 + - - +
71O LEU* 3.0 30.3 + - + +
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Residues in contact with LEU 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O THR* 5.3 6.5 - - + -
40O LEU* 5.6 0.9 - - + -
50O GLN* 4.3 22.9 - - + +
53O ILE* 5.2 7.4 - - + -
64O VAL* 2.8 42.0 + - + +
65O SER* 3.9 5.8 - - - +
67O LEU* 1.3 71.0 - - + +
69O ARG* 1.3 56.5 + - - +
70O ASN 3.0 1.6 - - - -
71O LEU* 4.2 10.1 - - + +
72O GLU* 2.7 40.1 + - - +
77O ILE* 3.4 26.5 - - + +
79O ARG* 6.1 4.3 - - - +
91O ILE* 4.0 32.5 - - + -
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Residues in contact with ARG 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65O SER* 2.9 19.4 + - - +
66O ASN* 3.7 8.5 - - - +
67O LEU 3.3 0.2 - - - -
68O LEU* 1.3 75.5 - - - +
70O ASN* 1.3 57.8 + - - +
72O GLU* 3.7 9.0 - - - +
73O ARG* 3.0 32.4 + - - +
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Residues in contact with ASN 70 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O GLN* 2.9 30.2 + - - +
66O ASN 3.0 14.6 + - - +
67O LEU* 3.3 7.9 - - - +
68O LEU 3.0 0.2 - - - -
69O ARG* 1.3 76.3 - - - +
71O LEU* 1.3 60.1 + - - +
73O ARG* 3.3 16.7 - - - +
74O LYS* 2.9 48.7 + - - +
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Residues in contact with LEU 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O ILE* 5.0 0.4 - - + -
33O GLN* 3.5 38.8 - - + +
36O THR* 4.1 31.0 - - + -
37O LEU* 4.1 12.3 - - + -
40O LEU* 5.3 0.2 - - + -
67O LEU* 3.0 20.0 + - + +
68O LEU* 3.1 10.1 + - + +
70O ASN* 1.3 74.4 - - - +
72O GLU* 1.3 58.7 + - - +
74O LYS* 3.2 5.6 + - + +
75O LYS 2.9 7.8 + - - -
76O LEU* 2.9 47.1 + - + -
77O ILE* 3.4 34.3 - - + +
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Residues in contact with GLU 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68O LEU* 2.7 22.7 + - - +
69O ARG* 3.7 9.4 - - - +
71O LEU* 1.3 73.3 - - - +
73O ARG* 1.3 55.2 + - - +
75O LYS* 2.7 32.1 + - - +
77O ILE* 3.3 25.8 - - + +
78O TYR* 5.0 2.1 - - - -
79O ARG* 3.7 41.2 + - - +
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Residues in contact with ARG 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69O ARG 3.0 20.0 + - - +
70O ASN* 3.3 22.9 - - - +
72O GLU* 1.3 79.0 - - - +
74O LYS* 1.3 58.5 + - + +
75O LYS* 3.1 22.3 + - - +
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Residues in contact with LYS 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27O PHE 5.3 2.2 - - - +
28O ASP* 3.0 40.9 + - - +
29O ILE* 4.3 2.2 - - + +
30O THR* 5.4 2.4 - - - +
33O GLN* 3.7 21.5 + - - +
70O ASN* 2.9 40.4 + - - +
71O LEU* 3.5 5.6 - - - +
72O GLU 3.0 0.2 - - - -
73O ARG* 1.3 78.8 - - + +
75O LYS* 1.3 71.1 + - - +
76O LEU* 3.2 30.8 + - + +
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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