Contacts of the helix formed by residues 58 - 74 (chain B) in PDB entry 2O3U
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 ARG 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B THR 3.4 0.4 + - - -
57B LYS* 1.3 94.3 - - + +
59B PHE* 1.3 56.0 + - - +
60B PRO* 3.5 4.3 - - - -
61B GLU* 3.1 56.4 + - + +
62B THR* 2.8 38.3 + - - +
170B TYR* 4.2 7.7 - - - -
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Residues in contact with PHE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B THR* 3.4 16.2 - - + -
56B THR* 3.2 21.3 + - - +
57B LYS 4.2 0.7 - - - -
58B ARG* 1.3 75.8 - - - +
60B PRO* 1.4 71.4 - - + +
62B THR* 3.2 5.1 + - - -
63B VAL* 3.0 49.3 + - + +
86B TRP* 3.7 26.7 - + - -
89B PHE* 3.9 11.2 - + - -
93B PHE* 4.0 11.9 - + - -
154B ALA* 5.9 0.2 - - - -
157B LEU* 3.8 22.2 - - + -
158B THR 4.0 9.0 - - - -
159B TRP* 3.4 53.8 - + + -
168B ILE* 4.7 3.4 - - + -
170B TYR* 4.4 0.8 + - + -
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Residues in contact with PRO 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PHE* 1.4 91.2 - - + +
61B GLU* 1.3 74.3 + - + +
63B VAL* 4.1 1.6 - - - +
64B LEU* 3.1 25.7 + - - +
86B TRP* 3.6 43.5 - - + +
168B ILE* 3.7 15.9 - - + -
170B TYR* 3.3 18.2 - - - +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ARG* 3.1 68.5 + - + +
60B PRO* 1.3 86.4 - - + +
62B THR* 1.3 56.8 + - - +
64B LEU* 3.6 6.0 + - - +
65B ALA* 2.9 30.0 + - - +
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Residues in contact with THR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B THR* 5.7 1.7 - - + +
57B LYS 4.1 4.9 + - - -
58B ARG* 2.8 29.1 + - - +
59B PHE* 3.2 6.9 + - - -
61B GLU* 1.3 74.0 - - - +
63B VAL* 1.3 58.5 + - - +
65B ALA* 3.3 5.7 + - - +
66B ARG* 2.9 54.4 + - + +
157B LEU* 3.9 22.9 - - + -
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PHE* 3.0 54.3 + - + +
60B PRO 4.1 0.2 - - - +
62B THR* 1.3 73.9 - - - +
64B LEU* 1.3 58.7 + - - +
66B ARG* 3.4 4.3 + - - -
67B CYS* 3.0 25.4 + - + +
85B VAL* 5.5 1.1 - - + -
86B TRP* 3.8 30.5 - - + +
89B PHE* 3.8 23.8 - - + -
153B LEU* 3.5 25.7 - - + +
157B LEU* 4.0 9.9 - - + -
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PRO 3.1 19.5 + - - +
61B GLU* 3.9 5.4 - - - +
63B VAL* 1.3 78.8 - - - +
65B ALA* 1.3 60.3 + - - +
67B CYS* 3.3 6.2 + - - +
68B VAL* 3.1 32.7 + - + +
82B CYS* 3.6 34.3 - - + +
83B GLN* 4.0 24.7 - - - +
86B TRP* 3.6 21.8 - - + -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLU 2.9 19.1 + - - +
62B THR* 3.8 6.3 - - - +
64B LEU* 1.3 73.4 - - - +
66B ARG* 1.3 60.8 + - + +
68B VAL* 3.5 7.6 + - - +
69B LYS* 2.9 30.6 + - - +
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B THR* 2.9 33.8 + - + +
63B VAL 3.8 4.0 - - - +
64B LEU 3.3 0.2 - - - -
65B ALA* 1.3 74.5 - - + +
67B CYS* 1.3 61.1 + - - +
69B LYS* 4.3 5.4 - - + -
70B TYR* 2.8 32.1 + - - +
152B TYR* 3.2 39.8 + - + +
153B LEU* 2.9 37.8 + - + -
155B ASP* 2.8 30.1 + - - +
156B ASP* 4.9 4.6 + - - +
157B LEU* 3.5 21.1 - - - +
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Residues in contact with CYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B VAL* 3.0 14.0 + - + +
64B LEU* 3.5 10.3 - - - +
65B ALA 3.2 0.4 - - - -
66B ARG* 1.3 78.0 - - - +
68B VAL* 1.3 60.7 + - - +
70B TYR* 3.3 2.3 + - - +
71B THR* 3.1 26.4 + - - +
80B VAL* 4.0 14.4 - - - -
82B CYS* 2.1 53.8 - - + +
85B VAL* 4.4 9.6 - - + -
149B LEU* 4.4 13.5 - - - -
153B LEU* 3.5 13.2 - - + +
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 3.1 21.0 + - + +
65B ALA* 3.8 7.4 - - - +
67B CYS* 1.3 74.8 - - - +
69B LYS* 1.3 60.7 + - - +
71B THR* 3.0 20.3 + - - +
72B GLU* 3.1 36.0 + - + +
82B CYS* 4.0 17.0 - - + -
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ALA 2.9 18.3 + - - +
66B ARG* 3.9 7.2 - - + +
68B VAL* 1.3 77.6 - - - +
70B TYR* 1.3 62.7 + - - +
72B GLU* 3.2 15.6 + - - +
73B ILE* 3.1 46.4 + - + +
152B TYR* 3.5 18.6 + - - +
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ARG 2.8 22.5 + - - +
67B CYS 3.3 4.5 + - - +
69B LYS* 1.3 72.0 - - - +
71B THR* 1.3 54.3 + - + +
73B ILE* 3.2 5.1 + - - -
74B HIS* 2.7 74.5 + + + -
77B MET* 3.8 28.9 - - + -
115B GLN* 2.8 19.2 + - - -
143B PHE* 5.1 0.7 - - - -
147B ASP* 2.7 30.8 + - - -
148B THR 3.8 2.7 - - - -
149B LEU* 3.3 42.5 + - + -
152B TYR* 3.6 34.2 - + + -
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B CYS* 3.1 15.1 + - - +
68B VAL* 3.0 19.6 + - - +
70B TYR* 1.3 77.1 - - + +
72B GLU* 1.3 62.5 + - - +
74B HIS 3.3 14.9 - - - +
77B MET* 3.3 28.0 - - + +
78B ARG* 2.9 42.1 + - - +
80B VAL* 4.4 9.6 - - + +
82B CYS* 4.4 13.9 - - - -
149B LEU* 5.2 2.2 - - + -
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B VAL* 3.1 37.3 + - + +
69B LYS* 3.4 18.9 - - - +
71B THR* 1.3 78.9 - - - +
73B ILE* 1.3 60.1 + - + +
75B PRO* 4.6 1.4 - - - +
78B ARG* 3.0 26.8 + - - +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS* 3.1 43.9 + - + +
70B TYR* 3.7 7.0 - - - +
72B GLU* 1.3 79.5 - - + +
74B HIS* 1.3 81.0 + - + +
75B PRO* 3.2 10.4 - - - +
152B TYR* 4.2 13.7 - - + +
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Residues in contact with HIS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B TYR* 2.7 67.9 + + + +
71B THR* 3.3 10.3 - - - +
73B ILE* 1.3 97.0 - - + +
75B PRO* 1.4 60.9 - - - +
76B GLU* 3.1 27.4 - - - +
77B MET* 2.9 23.0 + - + +
143B PHE* 5.1 11.8 - + - -
147B ASP* 4.4 7.0 + - + +
152B TYR* 6.0 2.0 - + - -
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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