Contacts of the helix formed by residues 66 - 81 (chain D) in PDB entry 2BM9
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 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D TYR* 4.1 17.0 - - + -
64D LEU 3.4 3.2 + - - +
65D LYS* 1.3 67.9 - - - +
67D PRO* 1.3 75.9 - - + +
68D ASP* 3.3 14.4 + - - +
69D THR* 2.8 31.2 + - - -
70D GLN* 3.0 29.0 + - - +
221D SER* 4.7 1.4 + - - -
222D SER* 4.2 10.6 + - - -
223D GLN* 3.0 30.3 + - - +
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Residues in contact with PRO 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D TYR* 3.3 43.1 - - + +
66D ASP* 1.3 92.9 - - + +
68D ASP* 1.3 60.0 + - - +
70D GLN* 3.3 15.5 - - - +
71D ALA* 3.0 20.8 + - - +
67E PRO* 3.4 40.9 - - + +
68E ASP* 4.2 10.8 - - - +
71E ALA* 4.0 10.5 - - + -
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ASP* 3.3 16.5 - - - +
67D PRO* 1.3 75.4 - - - +
69D THR* 1.3 67.0 + - - +
71D ALA* 3.0 12.2 - - - +
72D VAL* 3.0 26.1 + - - +
220D ALA 4.5 7.0 - - - +
221D SER* 4.4 14.1 - - - +
222D SER 5.5 1.1 - - - +
56E TYR* 4.6 8.5 + - - -
67E PRO* 4.5 9.4 - - - +
68E ASP* 4.2 16.0 - - - +
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Residues in contact with THR 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LYS* 3.7 22.7 - - + -
66D ASP* 2.8 17.0 + - - -
68D ASP* 1.3 73.3 - - - +
70D GLN* 1.3 65.7 + - - +
72D VAL* 3.2 6.9 + - - +
73D TYR* 3.1 38.7 + - + -
186D GLU* 4.5 2.0 - - - +
221D SER* 2.8 26.7 + - - -
223D GLN* 2.6 31.4 + - + +
224D LEU* 4.2 11.0 - - + -
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Residues in contact with GLN 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D TYR* 4.8 7.9 - - - +
57D GLN 5.0 4.2 + - - +
58D TRP* 5.4 3.1 - - - -
63D MET* 3.3 26.9 - - + +
65D LYS* 2.8 29.0 + - + +
66D ASP* 3.0 22.3 + - - +
67D PRO* 3.3 19.2 - - - +
69D THR* 1.3 74.4 - - - +
71D ALA* 1.3 65.4 + - - +
73D TYR* 3.1 3.0 + - - -
74D HIS* 3.0 18.8 + - - +
98D TRP* 3.3 41.7 + - + -
71E ALA* 5.5 5.4 - - - +
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D PRO 3.0 10.2 + - - +
68D ASP* 3.0 15.0 - - - +
70D GLN* 1.3 78.8 - - - +
72D VAL* 1.3 62.1 + - + +
74D HIS* 3.0 22.6 + - - +
75D ASP* 3.1 16.6 + - - +
56E TYR* 4.6 12.3 - - + -
67E PRO* 3.9 20.9 - - + -
70E GLN* 6.3 0.4 - - - +
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Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ASP 3.0 17.2 + - - +
69D THR 3.2 7.2 + - - +
71D ALA* 1.3 76.5 - - + +
73D TYR* 1.3 59.8 + - - +
75D ASP* 3.4 10.5 + - - +
76D MET* 2.8 32.7 + - + +
217D TYR* 3.7 34.4 - - + +
220D ALA* 3.9 34.1 - - + +
221D SER* 4.4 6.7 - - - -
224D LEU* 3.6 21.8 - - + -
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Residues in contact with TYR 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LYS* 3.9 12.8 - - + -
69D THR* 3.1 36.7 + - + -
70D GLN 3.7 0.2 - - - +
72D VAL* 1.3 73.1 - - - +
74D HIS* 1.3 60.0 + - - +
76D MET* 3.8 21.8 - - + -
77D LEU* 3.0 36.3 + - + +
98D TRP* 3.5 25.6 - + + -
99D PHE* 3.9 24.2 - + + -
156D ILE* 4.8 2.7 - - + -
158D ILE* 3.6 19.3 - - + +
184D ILE* 3.5 42.1 - - + +
186D GLU* 2.8 29.2 + - - -
224D LEU* 3.7 8.6 - - + +
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Residues in contact with HIS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D GLN 3.0 11.6 + - - +
71D ALA* 3.0 13.4 + - - +
73D TYR* 1.3 75.7 - - - +
75D ASP* 1.3 69.8 + - - +
76D MET 3.1 0.5 + - - -
77D LEU* 3.1 3.1 + - - +
78D TRP* 2.9 22.6 + - + +
98D TRP* 4.4 0.8 - - + -
102D LEU* 4.6 14.1 - - + -
106D MET* 3.4 29.9 - - + +
57E GLN* 3.2 22.2 + - - -
58E TRP* 3.2 56.6 - + + -
59E ARG* 3.3 16.4 + - - +
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Residues in contact with ASP 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ALA* 3.1 15.5 + - - +
72D VAL* 3.7 6.5 - - - +
74D HIS* 1.3 81.1 + - - +
76D MET* 1.3 62.3 + - - +
78D TRP* 3.5 2.1 + - - +
79D GLU* 3.1 20.1 + - - +
217D TYR* 3.3 27.4 + - + +
24E TYR* 4.6 7.3 + - - +
50E TYR* 5.3 3.8 + - - -
55E PRO* 5.0 4.9 - - - +
56E TYR* 5.6 3.5 - - - -
57E GLN* 3.0 44.0 + - - +
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Residues in contact with MET 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D VAL* 2.8 32.0 + - + +
73D TYR* 3.8 22.2 - - + +
74D HIS 3.0 0.2 - - - -
75D ASP* 1.3 76.5 - - - +
77D LEU* 1.3 59.1 + - + +
79D GLU* 3.2 4.7 + - - +
80D LEU* 3.0 31.9 + - + +
156D ILE* 3.9 26.7 - - + -
182D TYR* 4.1 25.6 - - + -
184D ILE* 3.7 33.0 - - + -
217D TYR* 3.4 28.0 + - + -
224D LEU* 5.2 0.7 - - + -
228D VAL* 4.5 10.3 - - + -
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D TYR* 3.0 31.4 + - + +
74D HIS* 3.7 2.2 - - - +
76D MET* 1.3 79.1 - - + +
78D TRP* 1.3 57.1 + - - +
81D ARG* 2.7 32.4 + - - -
82D PRO* 3.6 18.6 - - + +
85D ILE* 3.9 13.5 - - + -
98D TRP* 5.7 0.2 - - + -
99D PHE* 4.2 19.1 - - + +
102D LEU* 4.4 21.1 - - + -
103D THR* 3.5 28.0 - - + +
106D MET* 3.8 12.1 - - + -
108D ILE* 3.6 5.7 - - + +
156D ILE* 3.8 24.7 - - + -
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Residues in contact with TRP 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D HIS* 2.9 14.0 + - + +
75D ASP 3.7 4.3 - - - +
77D LEU* 1.3 77.3 - - - +
79D GLU* 1.3 63.9 + - - +
81D ARG* 3.7 27.0 + - - +
106D MET* 3.2 45.8 - - + +
108D ILE* 4.9 1.3 - - - -
24E TYR* 5.2 5.8 - + - -
26E PRO* 6.2 2.2 - - + -
57E GLN* 4.0 22.7 - - - +
59E ARG* 3.4 54.3 - - + -
60E GLY* 3.5 15.7 - - - +
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Residues in contact with GLU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ASP 3.1 17.5 + - - +
76D MET 3.7 1.3 - - - +
78D TRP* 1.3 81.9 - - + +
80D LEU* 1.3 66.1 + - - +
81D ARG* 4.7 2.4 - - - +
182D TYR* 3.7 13.0 + - - -
216D LEU* 3.7 7.3 - - - +
217D TYR* 3.2 15.6 + - - +
230D ARG* 4.6 2.9 + - - -
34E ARG* 3.1 41.9 + - - -
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D MET 3.0 17.1 + - - +
79D GLU* 1.3 84.7 - - + +
81D ARG* 1.3 73.7 + - - +
82D PRO* 3.9 23.1 - - + -
154D PRO* 3.6 40.1 - - + +
155D LEU 4.5 2.5 - - - +
156D ILE* 4.0 19.1 - - + -
180D GLY* 4.0 16.8 - - - +
182D TYR* 3.9 24.2 - - + -
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Residues in contact with ARG 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D LEU 2.7 19.0 + - - +
78D TRP* 3.7 33.0 + - - +
79D GLU 4.7 2.2 - - - +
80D LEU* 1.3 78.5 - - - +
82D PRO* 1.3 70.0 - - - +
83D ARG* 3.7 4.0 + - - +
106D MET 3.2 27.5 + - - -
107D GLY* 3.5 16.4 + - - -
108D ILE* 3.4 32.3 - - + +
154D PRO* 3.7 12.0 - - - +
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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