Contacts of the helix formed by residues 65 - 79 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LYS 5.2 4.9 - - - -
29A SER* 5.4 1.1 - - - +
63A SER* 3.5 0.8 - - - -
64A GLU* 1.3 85.5 + - - +
66A SER* 1.3 66.3 + - - +
67A GLY* 3.3 7.8 + - - +
68A ASP* 2.6 51.5 + - - +
69A LEU* 3.0 24.5 + - - +
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Residues in contact with SER 66 (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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28A LYS 5.3 4.4 + - - -
65A ASN* 1.3 73.5 - - - +
67A GLY* 1.3 63.7 + - - +
69A LEU* 3.7 11.3 - - - +
70A TYR* 3.1 23.9 + - - +
91A LEU* 5.7 4.7 - - - +
95A PRO* 6.3 4.3 - - - -
96A ILE* 5.3 1.6 - - - +
154A TYR* 5.2 5.5 + - - -
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASN* 3.3 9.5 - - - +
66A SER* 1.3 80.8 - - - +
68A ASP* 1.3 62.0 + - - +
69A LEU 3.5 0.2 + - - -
70A TYR* 3.5 7.6 + - - +
71A HIS* 3.3 26.7 - - - -
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Residues in contact with ASP 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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63A SER* 3.2 22.2 + - - +
64A GLU 5.0 1.0 + - - -
65A ASN* 2.6 32.0 + - - +
67A GLY* 1.3 77.3 - - - +
69A LEU* 1.3 57.4 + - - +
70A TYR 3.3 0.2 + - - -
71A HIS* 3.4 6.8 + - - +
72A GLU* 2.9 25.6 + - - +
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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
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26A ILE* 4.1 14.6 - - + -
27A GLN 3.7 18.6 - - - +
28A LYS* 3.9 14.4 - - - +
61A THR* 3.5 28.5 - - + +
63A SER* 3.2 15.6 + - - +
65A ASN 3.0 17.5 + - - +
66A SER* 3.7 10.3 - - - +
67A GLY 3.3 0.2 - - - -
68A ASP* 1.3 78.0 - - - +
70A TYR* 1.3 56.7 + - - +
72A GLU* 3.3 19.0 + - - +
73A VAL* 2.8 38.2 + - + +
89A TYR* 4.3 11.7 - - + +
96A ILE* 4.3 12.1 - - + -
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Residues in contact with TYR 70 (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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66A SER 3.1 13.1 + - - +
67A GLY* 3.7 11.2 - - - +
68A ASP 3.3 0.2 - - - -
69A LEU* 1.3 76.1 - - - +
71A HIS* 1.3 84.8 + + + +
73A VAL* 3.2 4.3 + - - +
74A LYS* 2.8 44.4 + - + +
95A PRO* 3.8 31.9 - - + -
96A ILE* 3.5 14.1 - - + +
98A HIS* 6.2 0.2 - - + -
99A LEU* 3.6 44.5 - - + +
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Residues in contact with HIS 71 (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 GLY* 3.3 23.9 + - - -
68A ASP* 3.4 8.1 + - - +
70A TYR* 1.3 97.5 - + - +
72A GLU* 1.3 57.3 + - - +
74A LYS* 3.7 12.2 - - + +
75A THR* 2.6 38.8 + - - +
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Residues in contact with GLU 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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61A THR* 3.3 21.3 - - + -
62A VAL* 2.8 28.8 + - - +
63A SER* 2.6 37.0 + - - +
68A ASP 2.9 18.1 + - - +
69A LEU* 3.5 5.2 - - - +
71A HIS* 1.3 77.0 - - - +
73A VAL* 1.3 57.3 + - - +
75A THR* 3.2 7.5 + - - -
76A MET* 2.9 45.3 + - + +
52B ASN* 4.2 3.3 - - - +
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Residues in contact with VAL 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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26A ILE* 4.3 17.9 - - + -
61A THR* 4.5 13.0 - - + -
69A LEU* 2.8 30.0 + - + +
70A TYR 3.6 3.8 - - - +
72A GLU* 1.3 74.6 - - - +
74A LYS* 1.3 59.6 + - - +
76A MET* 3.2 9.0 + - - +
77A ILE* 2.9 37.4 + - + +
85A PHE* 4.3 11.7 - - + -
96A ILE* 4.0 15.7 - - + -
99A LEU* 3.7 17.7 - - + -
100A LEU* 4.2 14.1 - - + -
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Residues in contact with LYS 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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70A TYR* 2.8 30.9 + - + +
71A HIS* 3.9 13.9 - - + +
73A VAL* 1.3 77.1 - - - +
75A THR* 1.3 57.2 + - - +
77A ILE* 3.1 6.2 + - + +
78A GLN* 2.9 60.0 + - + +
99A LEU* 4.0 25.8 - - + -
103A PHE* 4.2 17.3 - - + -
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Residues in contact with THR 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 HIS* 2.6 26.6 + - - +
72A GLU* 3.5 6.9 - - - -
74A LYS* 1.3 76.0 - - - +
76A MET* 1.3 56.9 + - - +
78A GLN* 3.9 8.8 + - - +
79A SER* 2.7 47.3 + - - +
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Residues in contact with MET 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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24A GLY* 5.4 5.4 - - - -
59A ARG* 5.4 14.8 - - + +
60A MET 4.9 1.8 - - - +
61A THR* 4.0 20.0 - - + +
72A GLU* 2.9 42.6 + - + +
73A VAL* 3.3 11.4 - - - +
75A THR* 1.3 77.4 - - - +
77A ILE* 1.3 63.7 + - - +
79A SER* 3.4 1.0 + - - -
80A LYS* 3.2 16.5 + - - -
81A SER* 3.2 31.4 + - - +
82A VAL* 4.4 6.1 + - + +
85A PHE* 4.0 31.2 - - + -
52B ASN* 4.3 18.2 - - - +
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Residues in contact with ILE 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 VAL* 2.9 20.7 + - + +
74A LYS* 3.5 7.2 - - + +
76A MET* 1.3 77.2 - - - +
78A GLN* 1.3 60.6 + - + +
80A LYS* 3.2 24.5 + - - +
82A VAL* 5.6 1.8 - - - -
85A PHE* 4.0 18.6 - - + -
99A LEU* 4.0 29.4 - - + +
100A LEU* 3.9 25.4 - - + -
103A PHE* 3.8 33.7 - - + +
105A VAL* 4.2 15.9 - - + -
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Residues in contact with GLN 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 LYS* 2.9 52.5 + - + +
75A THR* 4.2 6.1 - - - +
77A ILE* 1.3 72.5 - - + +
79A SER* 1.3 61.2 + - - +
80A LYS* 3.0 16.9 + - - +
103A PHE* 4.5 20.1 - - + -
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Residues in contact with SER 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 THR* 2.7 37.1 + - - +
76A MET* 4.0 3.8 - - - -
77A ILE 3.3 0.2 - - - -
78A GLN* 1.3 74.4 - - - +
80A LYS* 1.3 70.7 + - - +
81A SER* 3.0 15.0 + - - -
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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