Contacts of the helix formed by residues 71 - 87 (chain D) in PDB entry 5BMU
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 ASN 71 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D SER* 1.3 98.5 + - - +
72D LEU* 1.3 65.2 + - - +
73D MET* 3.0 33.9 - - + +
74D GLU* 3.2 21.6 + - - +
75D HIS* 2.9 33.1 + - - -
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Residues in contact with LEU 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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71D ASN* 1.3 76.2 - - - +
73D MET* 1.3 67.0 - - + +
75D HIS* 3.3 25.5 - - + +
76D THR* 3.2 15.9 + - - -
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Residues in contact with MET 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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71D ASN* 3.5 24.9 - - + +
72D LEU* 1.3 79.6 - - + +
74D GLU* 1.3 60.4 + - + +
75D HIS 3.2 0.2 - - - -
76D THR* 2.7 29.9 + - - -
77D GLU* 3.1 21.8 + - - +
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Residues in contact with GLU 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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68D TYR 3.8 6.1 - - - +
69D GLY* 3.5 9.9 - - - -
70D SER* 3.4 29.9 + - - +
71D ASN* 3.2 28.0 + - - +
73D MET* 1.3 81.1 - - + +
75D HIS* 1.3 59.6 + - - +
76D THR 3.3 0.2 - - - -
77D GLU* 4.1 17.5 - - - +
78D ILE* 3.1 26.7 + - - +
113D VAL* 3.6 33.4 - - + +
115D ASN* 5.5 5.2 + - - +
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Residues in contact with HIS 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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68D TYR* 3.1 49.4 + + + +
69D GLY 4.5 3.8 - - - -
70D SER 4.0 7.1 + - - -
71D ASN* 2.9 37.7 + - - -
72D LEU* 3.3 29.2 + - + +
74D GLU* 1.3 77.2 - - - +
76D THR* 1.3 58.7 + - - +
78D ILE* 2.7 19.6 - - - +
79D ASP* 2.8 16.8 - - - +
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Residues in contact with THR 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 LEU 3.2 13.7 + - - -
73D MET* 2.7 17.0 + - - -
75D HIS* 1.3 72.0 - - - +
77D GLU* 1.3 52.7 - - - -
79D ASP* 3.0 10.7 + - + +
80D HIS* 2.7 38.5 + - + +
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Residues in contact with GLU 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 MET* 3.1 19.1 + - - +
74D GLU* 4.2 21.3 - - - +
76D THR* 1.3 76.2 - - - +
78D ILE* 1.3 52.5 + - - +
80D HIS* 3.0 11.6 - - + +
81D TRP* 2.7 52.2 + - + +
109D ARG* 4.0 22.5 + - - -
112D LEU 3.5 20.0 - - - +
113D VAL* 4.5 8.7 - - - -
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Residues in contact with ILE 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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67D LEU 3.2 16.2 - - - +
68D TYR* 3.4 36.6 - - + +
74D GLU 3.1 16.1 + - - +
75D HIS* 2.7 30.3 - - - +
77D GLU* 1.3 77.6 - - - +
79D ASP* 1.3 56.2 + - - +
81D TRP* 3.2 2.3 + - - +
82D LEU* 2.8 38.2 + - + +
113D VAL* 6.4 0.7 - - + -
118D SER* 4.3 4.9 - - - +
119D LEU* 3.1 34.1 - - + +
120D ALA* 3.5 25.5 - - + +
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Residues in contact with ASP 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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56D ARG* 2.7 45.8 + - - +
60D ARG* 5.1 3.2 + - - -
68D TYR* 2.9 20.6 + - - -
75D HIS 2.8 18.8 - - - +
76D THR* 3.0 11.4 + - + +
78D ILE* 1.3 73.2 - - - +
80D HIS* 1.3 66.0 + - - +
82D LEU* 3.1 3.4 + - - +
83D GLU* 3.0 31.4 + - + +
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Residues in contact with HIS 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 THR* 2.7 20.3 + - + +
77D GLU* 3.0 20.6 - - + +
79D ASP* 1.3 73.5 - - - +
81D TRP* 1.3 61.6 + + + +
83D GLU* 3.3 8.6 + - - +
84D PHE* 3.0 32.7 + + - +
101D GLU* 5.6 5.8 - - - -
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Residues in contact with TRP 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 GLU* 2.7 47.4 + - + +
78D ILE 3.6 1.3 - - - +
80D HIS* 1.3 76.9 - + + +
82D LEU* 1.3 64.0 + - - +
84D PHE* 3.7 39.0 - + + +
85D SER* 3.3 16.8 + - - -
101D GLU* 4.9 5.6 - - - -
102D LEU* 3.8 22.7 - - + -
105D SER* 3.6 30.7 - - - -
109D ARG* 6.5 0.7 - - - -
112D LEU* 4.0 27.7 + - + -
120D ALA* 3.6 33.7 - - + -
123D SER* 4.2 1.4 + - - -
124D VAL* 3.5 31.1 - - + +
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Residues in contact with LEU 82 (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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52D ASN* 3.1 48.1 + - + +
55D LEU* 4.1 4.9 - - + -
56D ARG* 3.4 38.6 - - + +
78D ILE* 2.8 36.1 + - + +
79D ASP* 3.1 2.2 + - - +
81D TRP* 1.3 75.8 - - - +
83D GLU* 1.3 64.3 + - - +
85D SER* 3.3 6.3 + - - -
86D ALA 3.3 11.6 + - - -
119D LEU* 3.6 48.9 - - + +
120D ALA 4.0 0.7 - - - +
123D SER* 3.9 8.1 - - - +
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Residues in contact with GLU 83 (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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52D ASN* 4.8 1.1 - - - +
56D ARG* 4.3 11.9 + - - +
79D ASP* 3.0 16.0 + - - +
80D HIS* 3.6 8.2 - - - +
82D LEU* 1.3 75.6 - - - +
84D PHE* 1.3 56.7 + - - +
86D ALA* 2.8 8.7 + - - +
87D THR* 2.7 44.0 + - + +
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Residues in contact with PHE 84 (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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80D HIS* 3.0 25.1 + + - +
81D TRP* 3.7 42.4 - + + +
83D GLU* 1.3 74.8 - - - +
85D SER* 1.3 60.5 + - - +
87D THR* 4.1 4.3 - - - -
88D LYS* 3.0 44.0 + - + +
89D LEU* 3.2 33.5 + - + -
98D THR* 3.4 27.1 - - + -
101D GLU* 3.3 30.5 - - - -
102D LEU* 4.3 18.4 - - + -
124D VAL* 4.3 4.0 - - + -
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Residues in contact with SER 85 (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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52D ASN* 5.1 0.3 + - - -
81D TRP 3.3 7.9 + - - -
82D LEU 3.3 7.1 + - - -
84D PHE* 1.3 79.7 - - - +
86D ALA* 1.3 59.4 + - - +
89D LEU* 3.4 16.9 - - - -
90D SER* 3.2 24.1 + - - -
123D SER* 2.8 29.7 + - - -
124D VAL* 4.0 10.5 - - - -
127D THR* 3.3 32.6 + - - +
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Residues in contact with ALA 86 (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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52D ASN* 3.4 17.7 - - - +
82D LEU 3.3 17.0 + - - +
83D GLU* 2.8 8.9 + - - +
85D SER* 1.3 81.8 + - - +
87D THR* 1.3 61.4 + - + +
90D SER* 3.1 18.0 + - - -
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Residues in contact with THR 87 (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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83D GLU* 2.7 29.3 + - + +
84D PHE* 3.7 4.0 + - - -
86D ALA* 1.3 78.4 - - + +
88D LYS* 1.3 77.9 + - - +
89D LEU 3.2 1.1 - - - -
90D SER* 3.0 21.7 + - - -
91D SER* 3.8 2.9 + - - -
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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