Contacts of the helix formed by residues 64 - 82 (chain A) in PDB entry 2UZ8
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 THR 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A SER* 1.3 84.5 - - - +
65A ALA* 1.3 59.3 + - - +
66A GLU* 3.6 8.9 + - - +
67A GLU* 3.1 22.0 + - + +
68A LYS* 2.9 35.1 + - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR* 1.3 73.4 - - - +
66A GLU* 1.3 57.9 + - + +
68A LYS* 3.7 12.1 + - - +
69A ALA* 3.1 27.7 + - - +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR* 3.2 8.7 + - - +
65A ALA* 1.3 76.5 - - + +
67A GLU* 1.3 60.0 + - - +
69A ALA* 3.4 6.0 + - - +
70A MSE 3.1 31.8 + - + +
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR 4.8 1.0 - - - +
62A GLY* 3.4 10.5 - - - -
63A SER* 3.1 33.5 + - - +
64A THR* 3.1 20.0 + - - +
66A GLU* 1.3 75.0 - - - +
68A LYS* 1.3 56.0 + - - +
70A MSE 3.2 6.8 + - + +
71A VAL* 2.8 39.9 + - + +
109A THR* 4.0 24.3 + - - +
111A TYR* 4.7 5.7 + - - +
112A ASN* 2.8 37.8 + - - +
114A THR* 4.4 8.4 - - - +
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Residues in contact with LYS 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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58A GLU* 6.3 0.4 - - - +
61A LEU* 3.5 23.5 - - + +
62A GLY 3.4 20.4 - - - +
63A SER 4.4 8.3 - - - -
64A THR 2.9 24.2 + - - +
65A ALA* 3.7 10.1 - - - +
67A GLU* 1.3 75.7 - - - +
69A ALA* 1.3 57.7 + - - +
71A VAL* 3.2 2.9 + - - +
72A GLN* 2.8 37.7 + - + +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA 3.1 19.0 + - - +
66A GLU* 3.8 6.7 - - - +
67A GLU 3.3 0.2 - - - -
68A LYS* 1.3 76.1 - - - +
70A MSE 1.3 59.4 + - + +
72A GLN* 3.4 16.7 + - - +
73A GLN* 2.9 28.9 + - - +
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Residues in contact with MSE 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 GLU* 3.1 19.8 + - + +
67A GLU* 3.2 10.7 + - - +
69A ALA* 1.3 74.3 - - + +
71A VAL* 1.3 65.7 + - - +
73A GLN* 3.2 26.7 + - - +
74A TRP* 3.2 62.7 + - + +
101A TYR* 3.5 15.9 - - + +
109A THR* 3.8 26.5 - - - +
168B ARG 4.7 7.6 - - - +
169B LEU* 4.0 20.4 - - + -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU 4.0 11.7 - - - +
61A LEU* 3.6 33.4 - - + +
62A GLY* 4.1 1.3 - - - +
67A GLU* 2.8 22.5 + - + +
68A LYS 3.7 1.1 - - - +
70A MSE 1.3 70.7 - - - +
72A GLN* 1.3 64.6 + - + +
74A TRP* 3.2 3.3 + - - +
75A LEU* 2.9 44.8 + - + +
109A THR* 3.8 8.7 - - + +
114A THR* 3.7 35.7 - - + +
115A LEU* 4.7 0.7 - - + -
116A ALA* 4.4 12.1 - - - +
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Residues in contact with GLN 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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68A LYS* 2.8 23.5 + - + +
69A ALA* 3.5 16.0 - - - +
71A VAL* 1.3 76.4 - - + +
73A GLN* 1.3 63.4 + - - +
75A LEU* 3.4 10.3 + - + +
76A GLU* 3.0 25.6 + - - +
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Residues in contact with GLN 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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69A ALA 2.9 17.7 + - - +
70A MSE 3.2 26.8 - - - +
72A GLN* 1.3 78.3 - - - +
74A TRP* 1.3 91.8 - - + +
76A GLU* 3.5 8.9 + - - +
77A TYR* 3.0 25.8 + - + +
101A TYR* 5.2 2.8 - - - -
168B ARG* 5.7 4.6 + - - +
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Residues in contact with TRP 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 MSE 3.2 47.8 + - + +
71A VAL 3.2 2.0 + - - -
73A GLN* 1.3 86.9 - - + +
75A LEU* 1.3 61.2 + - - +
77A TYR* 3.4 54.5 + + + +
78A ARG* 3.0 26.5 + - - +
98A LEU* 4.3 10.8 - - + -
101A TYR* 3.3 48.1 + + + -
108A LEU* 3.7 35.2 + - + +
109A THR* 4.2 5.6 - - + -
116A ALA* 3.5 25.8 - - + +
120A LEU* 4.7 2.6 - - + +
168B ARG* 5.6 4.7 - - - -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 3.6 39.9 - - + +
49A ALA* 5.2 2.9 - - + -
61A LEU* 5.1 4.9 - - + -
71A VAL* 2.9 28.3 + - + +
72A GLN* 3.7 8.5 - - + +
74A TRP* 1.3 75.7 - - - +
76A GLU* 1.3 61.8 + - - +
78A ARG* 3.2 16.2 + - - +
79A VAL* 3.3 9.7 + - - +
115A LEU* 4.1 21.3 - - + -
116A ALA* 3.9 28.5 - - - +
119A LEU* 4.0 23.3 - - + -
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 5.9 0.2 - - - -
72A GLN 3.0 16.8 + - - +
73A GLN* 3.7 7.8 - - - +
75A LEU* 1.3 71.2 - - - +
77A TYR* 1.3 64.9 + - - +
79A VAL* 3.3 9.0 + - + +
80A THR* 2.7 48.3 + - + +
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Residues in contact with TYR 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 GLN* 3.0 16.2 + - + +
74A TRP* 3.5 49.1 - + + +
75A LEU 3.3 0.2 - - - -
76A GLU* 1.3 76.2 - - - +
78A ARG* 1.3 59.4 + - - +
80A THR* 3.8 5.6 - - - -
81A GLN* 2.8 72.9 + - + +
82A VAL* 3.3 20.3 + - + -
94A LEU* 3.3 31.2 + - + +
98A LEU* 3.9 18.5 + - + +
120A LEU* 3.8 18.4 - - + -
124A LEU* 6.0 0.9 - - + +
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Residues in contact with ARG 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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3A ALA* 6.3 0.6 - - - +
6A GLU* 2.4 44.6 + - - -
44A LEU* 3.5 16.1 - - + +
45A THR* 5.1 1.3 - - + -
74A TRP 3.0 12.6 + - - +
75A LEU* 3.2 13.0 + - - +
77A TYR* 1.3 84.3 - - - +
79A VAL* 1.3 65.6 + - + +
82A VAL* 3.3 15.4 + - - +
83A ASP* 2.8 60.7 + - - -
119A LEU* 3.0 39.4 + - + +
120A LEU* 4.5 9.0 - - + +
123A GLY* 3.6 21.5 - - - +
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Residues in contact with VAL 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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44A LEU* 4.2 19.3 - - + +
45A THR* 3.5 33.9 - - + +
75A LEU 3.3 6.5 + - - +
76A GLU* 3.6 17.9 - - + +
78A ARG* 1.3 78.6 - - + +
80A THR* 1.3 67.0 + - + +
83A ASP* 3.7 31.2 - - - +
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Residues in contact with THR 80 (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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76A GLU* 2.7 43.5 + - + +
77A TYR* 3.7 4.3 + - - -
79A VAL* 1.3 87.1 - - + +
81A GLN* 1.3 73.5 + - - +
83A ASP 4.1 7.7 - - - +
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Residues in contact with GLN 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 2.8 51.7 + - + +
80A THR* 1.3 85.9 + - - +
82A VAL* 1.3 65.0 + - - +
83A ASP 4.5 1.5 - - - +
91A ILE* 5.1 1.7 - - - +
94A LEU* 3.5 37.7 - - + +
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Residues in contact with VAL 82 (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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77A TYR* 3.7 30.5 - - + -
78A ARG* 3.3 14.3 + - - +
81A GLN* 1.3 81.1 - - - +
83A ASP* 1.3 71.9 + - - +
84A GLY 3.7 1.0 + - - -
91A ILE* 4.8 8.4 - - - +
94A LEU* 4.0 13.7 - - + -
120A LEU* 3.7 15.9 - - + -
123A GLY* 3.7 33.2 - - - +
124A LEU* 4.0 13.2 - - + -
126A ARG* 5.2 2.3 + - - -
127A PHE* 4.3 14.3 - - + -
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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