Contacts of the helix formed by residues 63 - 76 (chain K) in PDB entry 3J8B
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 63 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61K PHE 4.1 2.8 + - - -
62K GLN* 1.3 71.6 - - - +
64K THR* 1.3 59.3 + - - +
66K THR* 3.4 4.8 + - - -
67K ALA* 2.9 30.2 + - - +
97K ARG 5.3 9.2 - - - -
98K PRO 5.8 1.8 - - - -
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Residues in contact with THR 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62K GLN* 3.4 1.0 - - - +
63K THR* 1.3 78.1 - - - +
65K VAL* 1.3 59.0 + - - +
67K ALA* 3.2 6.8 + - - +
68K GLN* 2.9 30.1 + - - +
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Residues in contact with VAL 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K GLU* 4.9 18.2 - - + +
33K VAL* 5.2 14.2 - - + +
62K GLN* 3.6 21.4 + - + +
63K THR 3.4 0.4 - - - -
64K THR* 1.3 78.6 - - - +
66K THR* 1.3 57.8 + - - +
68K GLN* 3.3 7.0 + - - +
69K ILE* 2.9 29.7 + - - +
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Residues in contact with THR 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62K GLN 3.0 20.3 + - - -
63K THR* 3.7 5.4 - - - -
65K VAL* 1.3 76.2 - - - +
67K ALA* 1.3 63.5 + - - +
69K ILE* 3.3 7.6 + - - +
70K LEU* 3.0 23.6 + - - +
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Residues in contact with ALA 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63K THR 2.9 17.9 + - - +
64K THR* 3.2 7.4 + - - +
66K THR* 1.3 77.4 - - - +
68K GLN* 1.3 56.9 + - - +
70K LEU* 3.4 6.5 + - - +
71K LEU* 2.9 29.8 + - - +
98K PRO* 5.8 10.8 - - + -
99K ILE* 5.9 4.5 - - - +
102K ILE* 5.5 12.3 - - + +
127K LEU* 5.2 15.3 - - + -
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Residues in contact with GLN 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K VAL* 5.6 9.9 - - + +
37K ALA* 5.3 13.5 - - + -
64K THR 2.9 16.3 + - - +
65K VAL* 3.7 7.9 - - - +
67K ALA* 1.3 73.6 - - - +
69K ILE* 1.3 61.1 + - - +
71K LEU* 3.8 6.0 - - - +
72K LYS* 2.9 31.7 + - - +
127K LEU* 6.1 1.8 - - - +
131K ILE* 6.5 1.3 - - + -
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Residues in contact with ILE 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K VAL* 6.1 1.5 - - - +
47K ASN* 4.5 27.7 - - + +
50K VAL* 6.3 1.3 - - + -
51K LEU* 6.3 2.2 - - + -
65K VAL 2.9 17.7 + - - +
66K THR* 3.5 8.1 - - - +
68K GLN* 1.3 78.2 - - - +
70K LEU* 1.3 57.8 + - - +
72K LYS* 3.8 4.4 - - - +
73K ALA* 2.9 29.7 + - - +
85K CYS* 5.7 4.3 - - + -
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Residues in contact with LEU 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K THR 3.0 17.4 + - - +
67K ALA* 3.7 6.7 - - - +
68K GLN 3.3 0.2 - - - -
69K ILE* 1.3 78.1 - - - +
71K LEU* 1.3 62.1 + - - +
73K ALA* 3.2 8.8 + - - +
74K LEU* 3.0 21.5 + - - +
82K PHE* 5.3 1.7 - - - +
85K CYS* 5.2 9.4 - - + +
102K ILE* 5.1 13.0 - - + -
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Residues in contact with LEU 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67K ALA 2.9 18.7 + - - +
68K GLN* 3.9 6.5 - - - +
70K LEU* 1.3 75.7 - - - +
72K LYS* 1.3 62.9 + - - +
74K LEU* 3.2 10.9 + - - +
75K THR* 3.1 18.0 + - - -
102K ILE* 6.0 2.9 - - + +
131K ILE* 5.6 10.3 - - + -
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Residues in contact with LYS 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K GLN* 6.1 4.9 - - + -
37K ALA* 6.5 0.7 - - - -
42K TYR* 6.2 4.5 - - + -
68K GLN 2.9 19.0 + - - +
69K ILE* 3.8 5.2 - - - +
71K LEU* 1.3 72.7 - - - +
73K ALA* 1.3 66.9 + - - +
75K THR* 3.0 19.7 + - - +
76K ASN* 3.3 10.4 + - - +
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Residues in contact with ALA 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69K ILE 2.9 15.3 + - - +
70K LEU* 3.3 13.0 - - - +
71K LEU 3.2 0.2 - - - -
72K LYS* 1.3 76.6 - - - +
74K LEU* 1.3 57.9 + - - +
76K ASN* 2.9 25.3 + - - +
77K LEU* 3.7 3.3 + - - -
79K HIS 5.4 0.2 - - - +
81K ASP* 3.8 19.8 - - + +
82K PHE* 3.7 31.0 + - - +
85K CYS* 4.8 6.3 - - + -
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Residues in contact with LEU 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K LEU 3.0 12.7 + - - +
71K LEU* 3.2 12.3 + - - +
73K ALA* 1.3 72.5 - - - +
75K THR* 1.3 60.4 + - - +
76K ASN 2.9 6.4 + - - -
77K LEU* 3.1 21.5 + - - +
82K PHE* 4.5 10.5 - - + +
106K GLY* 5.5 11.2 - - - -
138K VAL* 5.8 2.1 - - - -
141K PHE* 5.4 2.6 - - - +
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Residues in contact with THR 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71K LEU 3.1 11.0 + - - -
72K LYS* 3.0 15.9 + - - -
74K LEU* 1.3 75.4 - - - +
76K ASN* 1.3 58.0 + - - +
77K LEU 3.4 5.2 + - - +
134K PHE* 5.2 7.2 - - - -
137K SER* 3.5 41.3 - - - +
138K VAL* 5.2 2.2 - - - +
141K PHE* 5.9 0.2 - - - +
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Residues in contact with ASN 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K LYS 3.3 7.5 + - - +
73K ALA* 2.9 14.4 + - - +
75K THR* 1.3 77.9 - - - +
77K LEU* 1.3 65.1 + - - +
79K HIS* 3.0 25.3 + - + +
81K ASP* 4.3 13.9 - - + -
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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