Contacts of the helix formed by residues 65 - 79 (chain B) in PDB entry 3HUU
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 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LYS 5.2 4.0 - - - -
63B SER* 3.5 0.8 - - - -
64B GLU* 1.3 86.9 - - - +
66B SER* 1.3 59.2 + - - +
67B GLY* 3.3 6.3 + - - +
68B ASP* 2.8 53.0 + - - +
69B LEU* 3.0 27.4 + - - +
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Residues in contact with SER 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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28B LYS 5.1 5.6 + - - -
65B ASN* 1.3 73.1 - - - +
67B GLY* 1.3 63.7 + - - +
69B LEU* 3.6 13.7 - - - +
70B TYR* 3.0 24.4 + - - +
91B LEU* 5.8 4.0 - - - +
95B PRO* 6.2 5.6 - - - -
96B ILE* 5.0 2.3 - - - +
154B TYR* 5.1 6.4 + - - -
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Residues in contact with GLY 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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65B ASN* 3.3 6.7 + - - +
66B SER* 1.3 79.8 - - - +
68B ASP* 1.3 63.2 + - - +
70B TYR* 3.5 5.4 + - - +
71B HIS* 3.1 32.5 + - - -
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Residues in contact with ASP 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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63B SER* 3.2 20.0 - - - +
64B GLU 5.2 1.2 + - - -
65B ASN* 2.8 36.4 + - - +
67B GLY* 1.3 74.2 - - - +
69B LEU* 1.3 55.9 + - - +
71B HIS* 3.2 6.8 + - - +
72B GLU* 2.7 36.9 + - - +
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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
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26B ILE* 4.0 9.9 - - + -
27B GLN 3.6 19.7 - - - +
28B LYS* 4.1 13.5 - - - +
61B THR* 3.6 39.5 - - + +
63B SER* 3.2 15.2 + - - +
65B ASN 3.0 17.0 + - - +
66B SER* 3.6 11.2 - - - +
68B ASP* 1.3 77.3 - - - +
70B TYR* 1.3 57.1 + - - +
72B GLU* 3.6 5.3 - - - +
73B VAL* 2.8 38.4 + - + +
89B TYR* 4.0 7.2 - - + +
96B ILE* 4.0 23.1 - - + -
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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 SER 3.0 13.3 + - - +
67B GLY* 3.6 9.9 - - - +
69B LEU* 1.3 76.7 - - - +
71B HIS* 1.3 84.0 + + + +
74B LYS* 2.9 42.7 + - + +
95B PRO* 3.8 31.6 - - + -
96B ILE* 3.5 13.6 - - + +
98B HIS* 6.0 0.2 - - + -
99B LEU* 3.6 46.9 - - + +
102B GLU* 3.9 11.4 + - - -
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Residues in contact with HIS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY* 3.1 22.5 + - - +
68B ASP* 3.2 9.2 + - - +
70B TYR* 1.3 96.5 - + + +
72B GLU* 1.3 59.1 + - - +
74B LYS* 3.8 15.0 - - + +
75B THR* 2.8 33.3 + - - +
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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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52A ASN* 4.2 4.3 + - - +
61B THR* 3.5 17.6 - - + -
62B VAL* 2.7 37.6 + - - +
63B SER* 2.5 39.7 + - - +
68B ASP 2.7 20.4 + - - +
69B LEU* 3.6 3.9 - - - +
71B HIS* 1.3 73.2 - - - +
73B VAL* 1.3 58.4 + - - +
75B THR* 3.2 7.8 + - - -
76B MET* 2.9 44.2 + - + +
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Residues in contact with VAL 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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26B ILE* 4.1 20.2 - - + -
61B THR* 4.0 25.1 - - + -
69B LEU* 2.8 31.4 + - + +
70B TYR 3.9 2.9 - - - +
72B GLU* 1.3 71.9 - - - +
74B LYS* 1.3 65.3 - - - +
76B MET* 3.2 9.5 + - - +
77B ILE* 3.0 24.4 + - + +
85B PHE* 4.3 7.2 - - + -
96B ILE* 4.4 6.5 - - + -
99B LEU* 3.8 17.3 - - + -
100B LEU* 4.0 22.7 - - + -
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Residues in contact with LYS 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* 2.9 38.6 + - + +
71B HIS* 3.8 15.5 - - + +
72B GLU 3.2 0.2 - - - -
73B VAL* 1.3 77.8 - - - +
75B THR* 1.3 62.5 + - - +
77B ILE* 3.0 7.4 + - + +
78B GLN* 3.0 54.6 + - + +
99B LEU* 3.8 19.5 - - + +
103B PHE* 4.3 18.2 - - + -
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Residues in contact with THR 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 HIS* 2.8 22.8 + - - +
72B GLU* 3.2 8.0 + - - -
74B LYS* 1.3 76.2 - - - +
76B MET* 1.3 57.9 + - + +
78B GLN* 4.6 8.2 + - - -
79B SER* 2.8 47.5 + - - +
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Residues in contact with MET 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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52A ASN* 3.9 18.8 - - - +
24B GLY* 5.5 2.2 - - - -
59B ARG* 4.0 19.1 - - + +
61B THR* 3.7 33.2 - - + +
72B GLU* 2.9 36.3 + - + +
73B VAL* 3.3 12.1 - - - +
74B LYS 3.1 0.2 - - - -
75B THR* 1.3 77.9 - - + +
77B ILE* 1.3 62.5 + - - +
79B SER* 4.8 0.4 - - - -
80B LYS* 3.1 17.0 + - - -
81B SER* 3.3 29.6 + - - +
82B VAL* 4.4 6.3 + - + +
85B PHE* 3.9 29.8 - - + -
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Residues in contact with ILE 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 VAL* 3.0 15.6 + - + +
74B LYS* 3.0 7.6 + - + +
76B MET* 1.3 77.9 - - - +
78B GLN* 1.3 59.8 + - + +
80B LYS* 3.4 19.9 + - - +
82B VAL 6.1 0.4 - - - -
85B PHE* 3.9 19.3 - - + -
99B LEU* 4.1 20.6 - - + -
100B LEU* 3.7 27.6 - - + -
103B PHE* 3.9 29.6 - - + +
105B VAL* 3.7 27.4 - - + -
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Residues in contact with GLN 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 LYS* 3.0 51.8 + - + +
75B THR* 4.3 6.5 + - - +
77B ILE* 1.3 72.3 - - + +
79B SER* 1.3 61.9 + - - +
80B LYS* 3.0 13.9 + - - +
103B PHE* 4.5 19.9 - - + -
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Residues in contact with SER 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 THR* 2.8 34.3 + - - +
76B MET* 4.2 2.2 - - - -
78B GLN* 1.3 75.7 - - - +
80B LYS* 1.3 70.1 + - - +
81B SER* 3.1 11.9 + - - -
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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