Contacts of the helix formed by residues 61 - 81 (chain B) in PDB entry 2DOU
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 LEU 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ILE* 6.4 4.7 - - + -
59B TYR* 3.3 21.4 + - + +
60B CYS* 1.3 76.1 - - - +
62B LYS* 1.3 70.0 + - + +
63B SER* 3.4 4.7 - - - +
64B CYS* 2.8 22.0 + - + +
65B THR* 3.2 4.7 + - - +
261B PHE* 4.6 22.9 - - + -
262B ASN* 3.7 8.7 - - - +
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 1.3 75.2 - - - +
63B SER* 1.3 55.9 + - - +
65B THR* 2.5 42.5 + - - +
66B LEU* 3.5 12.7 + - + +
69B LEU* 4.0 19.5 - - - -
86B PRO 5.0 3.6 - - - -
87B ARG* 4.3 15.7 + - - +
88B ARG* 5.9 0.6 - - - +
90B ALA 4.4 4.8 + - - -
91B LEU* 4.0 19.6 - - + +
253B GLU* 2.9 40.8 + - - +
262B ASN* 4.0 5.6 - - - +
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Residues in contact with SER 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 6.1 2.2 - - - -
61B LEU* 3.4 4.1 - - - +
62B LYS* 1.3 78.6 - - - +
64B CYS* 1.3 66.5 + - - +
66B LEU* 3.1 35.1 + - - +
67B PRO* 3.9 4.0 - - - +
87B ARG* 5.8 3.6 - - - +
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Residues in contact with CYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR 5.2 0.2 - - - +
60B CYS* 2.0 46.4 - - - -
61B LEU* 2.8 22.1 + - + +
63B SER* 1.3 82.7 + - - +
65B THR* 1.3 56.8 + - - +
66B LEU 3.4 0.6 + - - -
67B PRO* 3.7 10.7 - - - +
68B PHE* 5.4 0.3 + - - +
265B ALA* 3.9 14.6 - - - -
268B LEU* 4.9 5.6 - - - +
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Residues in contact with THR 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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60B CYS* 3.9 13.9 - - - -
61B LEU 3.7 11.4 - - - +
62B LYS* 2.5 33.1 + - - +
64B CYS* 1.3 72.6 - - - +
66B LEU* 1.3 62.8 + - - -
67B PRO 3.5 0.7 - - - -
68B PHE* 3.1 7.8 + - - +
69B LEU* 3.0 33.1 + - - +
92B ALA* 4.0 29.2 + - + +
262B ASN* 4.2 19.5 - - + +
268B LEU* 4.0 14.6 - - + -
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS* 3.5 13.4 + - + +
63B SER* 3.1 24.7 + - - +
65B THR* 1.3 73.9 - - - +
67B PRO* 1.3 64.1 - - + +
69B LEU* 2.8 11.5 + - + +
70B GLU* 2.6 54.4 + - - +
86B PRO* 4.5 15.0 - - + +
87B ARG* 3.9 52.3 - - + +
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Residues in contact with PRO 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER 3.9 4.0 - - - +
64B CYS* 3.7 12.6 - - - +
65B THR 3.6 3.4 - - - -
66B LEU* 1.3 93.4 - - + +
68B PHE* 1.3 55.6 + - - +
70B GLU* 3.6 16.4 - - - +
71B GLU* 3.0 27.5 + - - +
74B ARG* 4.7 2.1 + - - -
272B VAL* 4.0 15.0 - - + +
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Residues in contact with PHE 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 CYS 5.4 0.2 + - - -
65B THR 3.1 8.1 + - - +
66B LEU 3.0 0.8 - - - -
67B PRO* 1.3 78.2 - - - +
69B LEU* 1.3 69.6 + - + +
71B GLU* 3.3 2.3 + - - +
72B ALA* 2.8 26.9 + - + +
92B ALA* 4.4 4.3 - - + -
228B LEU* 4.3 7.9 - - + -
239B LEU* 3.8 20.4 - - + -
240B GLY 3.5 19.7 - - - -
241B PHE* 3.7 30.3 - + + -
268B LEU* 3.5 36.3 - - + +
271B GLY* 3.6 43.1 - - - -
272B VAL* 3.6 7.7 - - + +
275B LEU* 3.8 14.4 - - + -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS* 4.0 13.9 - - + -
65B THR* 3.0 31.5 + - - +
66B LEU* 2.8 13.9 + - + +
68B PHE* 1.3 76.2 - - + +
70B GLU* 1.3 60.4 + - - +
72B ALA* 3.2 6.2 + - + +
73B ALA* 2.8 29.6 + - - +
86B PRO* 3.9 21.5 - - + +
90B ALA* 3.4 28.3 - - + +
91B LEU 3.6 12.8 - - - +
92B ALA* 3.4 31.6 - - + +
241B PHE* 4.7 7.6 - - + -
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 2.6 50.0 + - + +
67B PRO* 3.6 12.9 - - - +
69B LEU* 1.3 72.4 - - - +
71B GLU* 1.3 62.9 + - - +
73B ALA* 3.0 5.0 + - - +
74B ARG* 3.0 47.9 + - - +
86B PRO* 3.8 25.5 - - + +
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Residues in contact with GLU 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 PRO 3.0 17.8 + - - +
68B PHE* 3.6 5.2 - - - +
70B GLU* 1.3 76.4 - - - +
72B ALA* 1.3 57.4 + - - +
74B ARG* 2.6 44.0 + - - +
75B TRP* 2.9 28.2 + - - +
272B VAL* 4.1 18.9 - - + +
275B LEU* 3.7 29.5 - - + +
276B LYS* 3.6 32.6 + - - +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 2.8 15.2 + - + +
69B LEU* 3.3 13.9 - - + +
70B GLU 3.1 0.2 - - - -
71B GLU* 1.3 77.8 - - - +
73B ALA* 1.3 56.5 + - - +
75B TRP* 3.1 8.1 + - - +
76B TYR* 2.9 30.2 + - - +
241B PHE* 4.1 32.1 - - + -
243B LEU* 4.5 9.6 - - + +
275B LEU* 3.6 16.3 - - + +
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Residues in contact with ALA 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 LEU 2.8 14.4 + - - +
70B GLU* 3.0 12.3 + - - +
72B ALA* 1.3 75.9 - - - +
74B ARG* 1.3 62.8 + - + +
76B TYR* 3.1 7.8 + - - +
77B GLU* 2.9 25.9 + - - +
82B VAL 5.2 0.3 - - - +
84B LEU* 3.8 36.7 + - + +
86B PRO* 4.4 11.7 - - + -
243B LEU* 5.1 2.7 - - + +
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Residues in contact with ARG 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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67B PRO 4.7 1.8 + - - -
70B GLU* 3.0 35.4 + - - +
71B GLU* 2.6 50.9 + - - +
73B ALA* 1.3 77.9 - - + +
75B TRP* 1.3 58.2 + - - +
77B GLU* 3.8 7.7 - - - +
78B GLY* 2.8 28.2 + - - -
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Residues in contact with TRP 75 (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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71B GLU* 2.9 14.5 + - - +
72B ALA 3.1 10.1 + - - +
74B ARG* 1.3 77.1 - - - +
76B TYR* 1.3 86.1 + + + +
78B GLY* 3.2 10.2 + - - -
79B ARG* 3.3 60.4 + - + +
80B TYR* 5.3 1.1 - + - -
201B VAL* 4.1 9.0 - - + -
202B ASP* 4.1 14.1 + - - -
226B PHE* 3.6 41.3 - + - -
232B TYR* 4.0 12.1 + - - -
241B PHE* 3.7 27.8 - + - -
275B LEU* 3.7 39.7 - - + +
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Residues in contact with TYR 76 (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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72B ALA 2.9 12.6 + - - +
73B ALA 3.6 6.7 - - - +
75B TRP* 1.3 85.8 - + + +
77B GLU* 1.3 60.5 + - - +
79B ARG* 3.2 3.8 + - - -
80B TYR* 3.0 55.0 + + + -
82B VAL* 3.6 28.9 - - + -
84B LEU* 3.6 15.0 - - + -
211B SER* 2.7 26.4 + - - -
213B LEU* 3.0 22.5 - - + +
214B ALA* 3.0 21.3 + - - -
224B GLU* 3.6 11.4 - - - -
226B PHE* 4.1 8.5 - + - -
243B LEU* 3.7 26.9 - - + -
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Residues in contact with GLU 77 (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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73B ALA 2.9 16.5 + - - +
74B ARG* 4.0 7.5 - - - +
76B TYR* 1.3 77.4 - - - +
78B GLY* 1.3 58.3 + - - +
79B ARG 3.0 1.7 + - - -
81B GLY* 2.8 33.9 + - - +
82B VAL 3.5 24.7 - - - +
83B GLY* 3.9 20.4 + - - -
84B LEU 5.1 0.5 + - - -
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Residues in contact with GLY 78 (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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74B ARG 2.8 18.8 + - - -
75B TRP* 3.6 4.3 - - - -
76B TYR 3.2 0.8 - - - -
77B GLU* 1.3 77.3 - - - +
79B ARG* 1.3 58.2 + - - +
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Residues in contact with ARG 79 (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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75B TRP* 3.3 59.2 - - - +
76B TYR* 3.6 7.0 - - - +
78B GLY* 1.3 78.5 - - - +
80B TYR* 1.3 90.5 + - + +
81B GLY 3.7 1.1 - - - -
201B VAL* 4.1 17.4 + - - +
202B ASP* 2.9 30.6 + - - +
208B GLU* 4.3 20.1 + - - +
209B ALA 5.8 2.0 - - - +
283B ARG* 6.1 0.2 - - - +
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Residues in contact with TYR 80 (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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75B TRP* 5.3 1.3 - + - -
76B TYR* 3.0 47.4 + + + +
79B ARG* 1.3 107.0 + - + +
81B GLY* 1.3 61.7 + - - +
82B VAL* 3.1 12.8 + - - +
177B TRP* 3.9 22.2 - + - -
198B ASN* 4.7 0.9 + - - -
201B VAL* 3.7 19.7 - - + +
208B GLU* 5.9 4.0 - - + -
209B ALA 2.5 31.1 + - - -
210B PRO* 4.0 1.3 + - + -
211B SER* 3.5 28.7 - - - -
214B ALA* 3.8 18.5 - - + +
226B PHE* 5.1 5.4 - + - -
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Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU* 2.8 27.4 + - - +
79B ARG 3.7 0.8 - - - -
80B TYR* 1.3 77.1 - - - +
82B VAL* 1.3 59.8 + - - +
83B GLY 4.0 1.2 + - - -
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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
------------------------------------------------------------
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