Contacts of the helix formed by residues 61 - 81 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.4 23.0 + - + +
60A CYS* 1.3 79.8 - - - +
62A LYS* 1.3 70.7 + - - +
63A SER* 3.3 4.9 - - - +
64A CYS* 2.9 15.5 + - - +
65A THR* 3.2 6.9 + - - +
261A PHE* 4.1 28.3 - - + -
262A ASN* 3.8 10.3 - - - +
32B ILE* 6.1 8.7 - - + -
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 1.3 74.0 - - - +
63A SER* 1.3 55.7 + - - +
65A THR* 2.7 42.1 + - + +
66A LEU* 3.4 15.6 + - + +
69A LEU* 4.2 18.8 - - - -
86A PRO 5.0 2.7 - - - -
87A ARG* 3.8 22.4 + - - +
90A ALA 4.5 4.2 + - - -
91A LEU* 4.1 21.8 - - + +
253A GLU* 3.3 35.3 + - - +
262A ASN* 4.1 4.3 - - - +
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.2 3.2 + - - +
62A LYS* 1.3 76.7 - - - +
64A CYS* 1.3 63.0 + - - +
66A LEU* 3.0 34.9 + - - +
67A PRO* 3.9 2.8 - - - +
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Residues in contact with CYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR 5.1 0.7 - - - +
60A CYS* 2.0 54.9 - - - -
61A LEU* 2.9 10.3 + - - +
63A SER* 1.3 79.4 - - - +
65A THR* 1.3 57.7 + - - +
67A PRO* 3.8 10.5 - - - +
68A PHE 5.5 0.2 + - - -
265A ALA* 3.8 17.7 - - - -
268A LEU* 4.7 6.0 - - - +
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A CYS* 3.9 10.8 - - - -
61A LEU 3.4 14.6 - - - +
62A LYS* 2.7 31.4 + - - +
64A CYS* 1.3 73.9 - - - +
66A LEU* 1.3 62.7 + - - -
67A PRO* 3.5 1.1 - - - -
68A PHE* 3.2 8.0 + - - +
69A LEU* 3.1 34.9 + - - +
92A ALA* 4.0 22.2 + - + +
262A ASN* 3.9 26.5 - - + +
268A LEU* 4.3 13.2 - - + -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 3.4 26.9 + - + +
63A SER* 3.0 28.2 + - - +
65A THR* 1.3 76.0 - - - +
67A PRO* 1.3 72.2 - - + +
69A LEU* 2.9 6.9 + - + +
70A GLU* 2.7 44.0 + - + +
86A PRO* 4.5 13.5 - - + +
87A ARG* 3.2 46.7 - - + +
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Residues in contact with PRO 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER 3.9 3.6 - - - +
64A CYS* 3.8 12.3 - - - +
65A THR 3.7 2.7 - - - -
66A LEU* 1.3 94.6 - - + +
68A PHE* 1.3 56.0 + - - +
70A GLU* 3.4 17.2 + - - +
71A GLU* 3.0 27.7 + - - +
74A ARG* 4.8 2.3 + - - -
272A VAL* 3.8 16.4 - - + +
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Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A CYS 5.5 0.2 + - - -
65A THR 3.2 8.2 + - - +
66A LEU 3.1 0.8 - - - -
67A PRO* 1.3 78.1 - - - +
69A LEU* 1.3 71.3 + - + +
71A GLU* 3.2 3.3 + - - +
72A ALA* 2.8 26.6 + - + +
92A ALA* 4.4 3.4 - - + -
228A LEU* 4.4 7.2 - - + -
239A LEU* 3.7 21.3 - - + -
240A GLY 3.6 19.5 - - - -
241A PHE* 3.7 31.0 - + + -
268A LEU* 3.6 31.0 - - + +
271A GLY* 3.6 39.7 - - - -
272A VAL* 3.5 14.7 - - + +
275A LEU* 3.9 14.6 - - + -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 4.2 11.7 - - - -
65A THR* 3.1 29.7 + - - +
66A LEU* 2.9 10.8 + - + +
68A PHE* 1.3 80.7 - - + +
70A GLU* 1.3 61.1 + - - +
72A ALA* 3.3 4.4 - - + +
73A ALA* 2.8 31.5 + - - +
86A PRO* 3.8 24.7 - - + +
90A ALA* 3.6 31.3 - - + +
91A LEU* 3.7 11.7 - - - +
92A ALA* 3.4 31.0 - - - +
241A PHE* 4.5 8.5 - - + -
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 2.7 33.2 + - + +
67A PRO* 3.4 18.7 - - - +
69A LEU* 1.3 74.3 - - - +
71A GLU* 1.3 60.7 + - - +
73A ALA* 3.3 3.3 + - - +
74A ARG* 3.0 44.1 + - - +
86A PRO* 4.0 24.8 - - + +
87A ARG* 4.0 20.6 + - - -
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO 3.0 14.4 + - - +
68A PHE* 3.2 8.0 + - - +
70A GLU* 1.3 76.9 - - - +
72A ALA* 1.3 53.1 + - - +
74A ARG* 2.6 47.6 + - - +
75A TRP* 2.7 35.2 + - - +
272A VAL* 3.9 17.9 - - + +
275A LEU* 3.7 28.7 - - + +
276A LYS* 3.6 33.4 + - - +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 2.8 15.4 + - + +
69A LEU* 3.1 15.0 + - + +
71A GLU* 1.3 75.4 - - - +
73A ALA* 1.3 63.5 + - - +
75A TRP* 3.1 7.9 + - - +
76A TYR* 2.9 24.3 + - - +
241A PHE* 3.9 34.8 - - + -
243A LEU* 4.8 6.6 - - + +
275A LEU* 3.7 14.5 - - + +
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU 2.8 19.8 + - - +
70A GLU 3.3 2.4 + - - +
72A ALA* 1.3 71.8 - - - +
74A ARG* 1.3 58.5 + - + +
76A TYR* 3.3 7.5 + - - +
77A GLU* 2.8 30.8 + - - +
82A VAL 4.9 0.9 - - - +
84A LEU* 3.7 30.3 + - + +
86A PRO* 3.6 26.0 - - + -
90A ALA* 5.8 0.7 - - + -
243A LEU* 5.1 3.5 - - + +
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PRO 4.8 1.8 + - - -
70A GLU* 3.0 34.6 + - - +
71A GLU* 2.6 48.0 + - - +
73A ALA* 1.3 75.8 - - + +
75A TRP* 1.3 60.3 + - - +
77A GLU* 3.7 6.3 - - - +
78A GLY* 2.8 28.1 + - - -
272A VAL* 5.9 0.8 - - - +
276A LYS* 5.6 1.0 - - - +
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Residues in contact with TRP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLU* 2.7 18.8 + - + +
72A ALA* 3.3 11.0 - - - +
74A ARG* 1.3 73.9 - - - +
76A TYR* 1.3 86.1 + + - +
78A GLY* 3.4 2.0 + - - -
79A ARG* 3.3 76.6 + - + +
80A TYR* 5.2 2.2 - + - -
201A VAL* 4.2 9.9 - - + -
202A ASP* 4.1 12.1 - - - -
226A PHE* 3.7 43.5 - + + -
232A TYR* 4.0 9.9 + - - -
241A PHE* 3.9 20.4 - + - -
275A LEU* 4.1 39.3 - - + +
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Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ALA 2.9 11.9 + - - +
73A ALA 3.6 7.2 - - - +
75A TRP* 1.3 83.3 - + + +
77A GLU* 1.3 66.3 + - - +
79A ARG* 2.8 14.4 + - - +
80A TYR* 2.8 41.0 + + + -
82A VAL* 3.8 34.1 - - + -
84A LEU* 3.6 23.8 - - + -
211A SER* 2.6 27.0 + - - -
213A LEU* 3.2 17.8 - - + +
214A ALA* 3.0 20.6 + - - -
224A GLU* 3.6 11.2 - - - -
226A PHE* 4.1 7.9 - + - -
243A LEU* 3.7 21.8 - - + -
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ALA 2.8 20.8 + - - +
74A ARG* 3.7 7.6 - - - +
76A TYR* 1.3 71.3 - - - +
78A GLY* 1.3 63.0 + - - +
81A GLY* 2.7 45.5 + - - -
82A VAL 3.2 27.1 + - - +
83A GLY* 3.9 10.0 + - - -
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ARG 2.8 16.7 + - - -
75A TRP* 3.8 4.0 - - - -
76A TYR 3.1 0.2 - - - -
77A GLU* 1.3 78.9 + - - +
79A ARG* 1.3 61.9 + - - +
81A GLY 4.8 0.2 - - - -
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TRP* 3.3 52.9 + - + +
76A TYR 2.8 10.2 + - - +
78A GLY* 1.3 83.6 - - - +
80A TYR* 1.3 81.1 + - + +
81A GLY 3.7 0.2 - - - -
201A VAL* 4.6 9.1 + - - +
202A ASP* 2.9 30.7 + - - -
208A GLU* 2.9 44.1 + - - +
232A TYR* 5.6 0.6 + - - -
279A LYS* 5.1 20.5 - - - +
282A VAL* 5.4 4.9 - - - +
283A ARG* 6.4 0.2 - - - +
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TRP* 5.2 6.1 - + - -
76A TYR* 2.8 50.9 + + + +
79A ARG* 1.3 99.6 + - + +
81A GLY* 1.3 67.6 + - - +
82A VAL* 3.0 10.9 - - + +
177A TRP* 3.7 24.0 - + + -
198A ASN* 5.1 0.5 + - - -
201A VAL* 3.7 19.2 - - - +
208A GLU* 3.7 16.9 - - - +
209A ALA 2.7 29.2 + - - -
210A PRO 3.9 2.4 + - - -
211A SER* 3.6 17.1 - - - -
214A ALA* 3.7 19.9 - - + +
226A PHE* 5.2 2.4 - + - -
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLU* 2.7 37.3 + - - -
79A ARG 3.7 1.0 - - - -
80A TYR* 1.3 73.3 - - - +
82A VAL* 1.3 59.8 + - - +
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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
------------------------------------------------------------
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