Contacts of the helix formed by residues 63 - 77 (chain B) in PDB entry 2HUE
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 ARG 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B LEU 4.2 0.8 + - - -
62B ILE* 1.3 76.2 - - - +
64B LYS* 1.3 68.2 + - - +
65B LEU* 3.6 3.6 - - + +
66B PRO* 3.5 33.8 - - + +
67B PHE* 3.5 15.8 + - - +
93B GLN* 4.2 0.4 - - - -
401B SO4 2.9 47.3 + - - +
28C GLY 4.6 0.7 - - - +
30C THR* 3.5 20.1 - - + +
33C ALA* 5.4 1.4 - - - +
36C ARG* 5.0 2.0 - - - +
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Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B ILE 3.8 1.8 + - - -
63B ARG* 1.3 78.2 - - - +
65B LEU* 1.3 77.3 + - + +
67B PHE* 3.2 3.3 + - - +
68B GLN* 2.8 66.1 + - - +
86B SER* 5.6 9.4 - - - +
89B VAL* 4.5 17.9 - - + -
90B MET* 6.0 3.4 - - + +
93B GLN* 3.6 23.6 - - - +
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Residues in contact with LEU 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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63B ARG* 4.7 3.4 - - + +
64B LYS* 1.3 95.7 - - + +
66B PRO* 1.4 70.4 - - + +
68B GLN* 3.3 22.8 + - - +
69B ARG* 3.0 22.0 + - - +
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Residues in contact with PRO 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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63B ARG* 3.5 49.4 - - + +
65B LEU* 1.4 95.2 - - + +
67B PHE* 1.3 62.1 - - - +
69B ARG* 3.2 8.4 + - + +
70B LEU 3.1 17.8 + - - -
27C GLN 3.6 20.6 - - - +
28C GLY* 3.7 10.4 - - - +
30C THR* 5.2 7.9 - - + -
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Residues in contact with PHE 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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62B ILE* 3.9 17.7 - - + -
63B ARG 3.5 12.3 - - - +
64B LYS* 3.2 8.7 + - - +
65B LEU 3.1 0.4 - - - -
66B PRO* 1.3 77.8 - - - +
68B GLN* 1.3 65.4 + - - +
70B LEU* 3.2 4.6 + - + +
71B VAL* 3.0 45.7 + - + +
89B VAL* 4.0 14.1 - - + -
92B LEU* 3.7 3.8 - - + -
93B GLN* 3.5 38.4 - - + +
96B SER* 3.4 33.2 - - - -
28C GLY* 3.5 25.2 + - - +
29C ILE* 4.9 1.6 - - + -
58C LEU* 4.7 4.5 - - + -
62C LEU* 4.0 20.6 - - + -
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Residues in contact with GLN 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 LYS* 2.8 47.9 + - - +
65B LEU* 3.3 16.9 + - - +
67B PHE* 1.3 75.6 - - - +
69B ARG* 1.3 61.2 + - - +
71B VAL* 3.3 4.0 + - - +
72B ARG* 3.0 65.3 + - + +
84B PHE* 5.1 4.0 + - - +
86B SER* 6.0 2.2 - - - +
89B VAL* 3.9 35.1 - - + +
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Residues in contact with ARG 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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65B LEU 3.0 13.2 + - - +
66B PRO* 3.6 10.8 - - + +
67B PHE 3.2 0.6 - - - -
68B GLN* 1.3 73.2 - - - +
70B LEU* 1.3 67.2 + - - +
72B ARG* 3.3 15.8 + - - +
73B GLU* 2.4 67.5 + - + +
26C ILE* 4.2 19.9 - - + +
27C GLN 5.8 0.2 - - - +
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Residues in contact with LEU 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 PRO 3.1 6.8 + - - +
67B PHE* 3.6 8.5 - - + +
69B ARG* 1.3 75.0 - - - +
71B VAL* 1.3 65.0 + - - +
73B GLU* 3.2 1.8 + - - -
74B ILE* 2.9 43.6 + - + +
26C ILE* 3.8 27.4 - - - +
27C GLN* 4.2 4.0 - - - +
28C GLY* 3.5 34.3 - - - +
55C ARG 6.2 0.2 - - - +
58C LEU* 4.4 10.5 - - + -
59C LYS* 5.4 10.1 - - + -
62C LEU* 3.7 24.2 - - + -
502C GOL 4.1 16.4 - - - +
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Residues in contact with VAL 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 PHE* 3.0 49.1 + - + +
68B GLN* 3.6 10.3 - - + +
70B LEU* 1.3 75.0 - - - +
72B ARG* 1.3 54.9 - - + +
74B ILE* 3.2 3.8 + - - +
75B ALA* 2.8 33.8 + - - +
84B PHE* 3.8 38.6 - - + -
89B VAL* 5.0 8.1 - - + -
92B LEU* 3.8 16.6 - - + -
62C LEU* 4.7 6.3 - - + -
66C ILE* 4.0 13.7 - - + +
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Residues in contact with ARG 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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68B GLN* 3.0 57.3 + - + +
69B ARG* 3.6 20.0 - - + +
71B VAL* 1.3 79.4 - - + +
73B GLU* 1.3 58.3 + - + +
75B ALA* 3.4 6.3 + - - +
76B GLN* 3.0 28.2 + - - +
82B LEU 6.1 1.1 - - - +
83B ARG* 5.1 20.2 - - - +
84B PHE* 5.2 15.5 + - + +
89B VAL* 6.4 0.9 - - + -
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Residues in contact with GLU 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 ARG* 2.4 60.4 + - - +
70B LEU 3.7 4.0 - - - +
72B ARG* 1.3 74.0 - - - +
74B ILE* 1.3 67.0 + - - +
76B GLN* 3.3 8.9 + - - +
77B ASP* 3.1 5.7 - - - +
23C ARG* 2.7 57.6 + - - +
26C ILE* 3.7 13.5 - - + -
502C GOL 2.8 30.1 - - - +
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Residues in contact with ILE 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 LEU* 2.9 41.0 + - + +
71B VAL 3.6 3.4 - - - +
73B GLU* 1.3 77.2 - - - +
75B ALA* 1.3 63.0 + - - +
77B ASP* 3.0 20.8 + - + +
78B PHE* 3.5 24.9 - - + -
59C LYS* 4.4 15.3 - - + +
62C LEU* 3.6 29.8 - - + -
63C GLU* 3.9 20.2 - - + -
66C ILE* 3.8 16.8 - - + -
502C GOL 4.1 19.3 - - - +
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Residues in contact with ALA 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 VAL 2.8 16.1 + - - +
72B ARG* 3.9 4.7 - - - +
74B ILE* 1.3 73.9 - - - +
76B GLN* 1.3 57.2 + - - +
78B PHE* 3.1 6.6 + - - +
79B LYS 3.0 29.9 + - - +
82B LEU* 4.4 15.1 - - + +
84B PHE* 3.4 37.9 - - + -
66C ILE* 3.9 14.1 - - + -
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Residues in contact with GLN 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 ARG 3.0 14.6 + - - +
73B GLU* 3.4 17.3 - - - +
74B ILE 3.1 0.2 - - - -
75B ALA* 1.3 77.4 - - - +
77B ASP* 1.3 62.7 + - - +
78B PHE 3.1 1.4 + - - -
79B LYS* 3.4 14.2 + - - +
80B THR* 3.3 41.3 + - - +
81B ASP 4.1 4.9 + - - -
23C ARG* 3.9 13.0 - - - +
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Residues in contact with ASP 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 GLU 3.1 5.1 - - - +
74B ILE* 3.0 9.7 + - + +
76B GLN* 1.3 76.4 - - - +
78B PHE* 1.3 68.6 + - + +
23C ARG* 2.5 40.7 + - - -
502C GOL 3.3 19.9 + - - -
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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