Contacts of the helix formed by residues 62 - 72 (chain G) in PDB entry 6WNX
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 ASP 62 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58G MET* 2.7 26.1 + - - +
59G VAL 3.6 3.9 - - - +
61G THR* 1.3 73.3 + - - +
63G PRO* 1.4 67.8 - - - +
64G LEU* 3.1 25.1 + - - +
65G TRP* 3.0 41.8 + - + -
66G LYS 3.1 9.0 + - - -
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Residues in contact with PRO 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G THR 3.4 10.5 - - - +
62G ASP* 1.4 85.2 - - - +
64G LEU* 1.3 56.4 + - + +
66G LYS* 3.3 16.2 - - + +
67G GLY* 2.7 31.2 + - - -
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Residues in contact with LEU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G ASP* 3.1 21.6 + - - +
63G PRO* 1.3 79.4 - - + +
65G TRP* 1.3 57.9 + - + +
67G GLY* 3.2 2.5 + - - -
68G LEU* 2.9 43.4 + - + +
103G ILE* 4.1 38.8 - - + -
106G ILE* 5.7 11.0 - - + -
107G GLU* 5.8 3.6 - - - +
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Residues in contact with TRP 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G ILE* 4.3 10.5 - - + -
58G MET* 3.4 43.0 - - + +
59G VAL* 3.9 4.7 - - + -
62G ASP* 3.0 35.8 + - + +
64G LEU* 1.3 77.3 - - + +
66G LYS* 1.3 56.5 + - - +
68G LEU* 3.5 5.5 + - - -
69G SER* 2.9 36.0 + - - -
74G TRP* 3.6 13.0 - + - -
96G TYR* 3.5 43.3 - + - -
99G ILE* 3.6 43.5 - - + -
100G ILE* 3.6 24.7 - - + +
103G ILE* 3.5 21.3 - - + +
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Residues in contact with LYS 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G VAL* 3.7 31.2 - - + +
60G ARG 6.2 0.2 - - - -
62G ASP 3.1 4.9 + - - -
63G PRO* 3.3 20.0 - - + +
65G TRP* 1.3 73.9 - - - +
67G GLY* 1.3 64.8 + - - +
69G SER* 2.5 26.5 + - - +
70G GLU* 3.3 31.0 + - - +
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Residues in contact with GLY 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G PRO 2.7 19.7 + - - -
64G LEU* 3.5 1.8 - - - -
66G LYS* 1.3 70.0 - - - +
68G LEU* 1.3 53.4 + - - +
70G GLU* 2.9 30.8 + - - +
71G ARG* 3.0 38.3 + - - +
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Residues in contact with LEU 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G LEU* 2.9 30.2 + - + +
65G TRP* 3.8 5.2 - - - +
67G GLY* 1.3 70.5 - - - -
69G SER* 1.3 56.6 + - - +
71G ARG* 4.5 8.0 - - + +
72G ARG* 2.9 53.9 + - + +
74G TRP* 3.9 11.4 - - + +
99G ILE* 4.4 8.5 - - + -
102G ASP* 3.8 35.9 - - + +
103G ILE* 3.6 35.4 - - + +
106G ILE* 5.4 7.6 - - + -
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Residues in contact with SER 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G VAL* 4.1 12.6 - - - +
65G TRP 2.9 14.4 + - - -
66G LYS* 2.5 23.3 + - - +
68G LEU* 1.3 71.5 - - - +
70G GLU* 1.3 59.8 + - - +
73G GLY* 3.0 16.6 + - - -
74G TRP* 3.0 36.3 + - - -
75G ASP* 2.9 38.3 + - - +
78G LEU* 4.7 1.3 - - - -
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Residues in contact with GLU 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G LYS* 3.3 43.5 + - - +
67G GLY* 2.9 14.1 + - - +
69G SER* 1.3 81.3 + - - +
71G ARG* 1.3 77.6 + - + +
72G ARG 3.2 1.6 - - - -
73G GLY* 3.0 14.7 + - - -
75G ASP* 3.5 20.3 - - + +
137G ASP* 5.6 1.2 - - - +
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Residues in contact with ARG 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G GLY* 3.0 36.5 + - - +
68G LEU* 4.5 8.3 - - + +
70G GLU* 1.3 88.8 + - + +
72G ARG* 1.3 67.2 + - - +
137G ASP* 3.8 27.7 + - - -
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Residues in contact with ARG 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G LEU* 2.9 33.3 + - + +
71G ARG* 1.3 82.3 + - - +
73G GLY* 1.3 60.8 + - - +
74G TRP* 3.4 25.3 - - + +
102G ASP* 3.0 42.1 + - - +
106G ILE* 5.1 7.3 - - - +
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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