Contacts of the helix formed by residues 64 - 81 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B SER* 1.3 85.4 - - - +
65B ALA* 1.3 65.6 + - - +
66B GLU* 3.7 7.6 + - - +
67B GLU* 3.2 22.1 + - + +
68B LYS* 2.9 29.3 + - - +
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Residues in contact with ALA 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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64B THR* 1.3 74.0 - - - +
66B GLU* 1.3 62.7 + - + +
68B LYS* 3.7 11.2 + - - +
69B ALA* 3.2 22.3 + - - +
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 4.4 17.1 - - + +
64B THR* 3.2 7.4 + - - +
65B ALA* 1.3 79.3 - - + +
67B GLU* 1.3 60.6 + - - +
69B ALA* 3.4 8.0 + - - +
70B MSE 3.1 27.8 + - + +
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Residues in contact with GLU 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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59B TYR 4.5 1.9 - - - +
62B GLY* 3.4 10.8 - - - -
63B SER* 3.1 31.6 + - - +
64B THR* 3.2 21.0 + - - +
66B GLU* 1.3 72.9 - - - +
68B LYS* 1.3 61.1 + - - +
70B MSE 3.2 6.5 + - - +
71B VAL* 2.9 28.8 + - - +
109B THR* 4.0 20.2 + - - +
111B TYR* 4.6 7.1 + - - +
112B ASN* 2.7 46.5 + - - +
114B THR* 4.4 8.1 - - + +
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.3 25.6 - - + +
62B GLY* 3.5 19.7 - - - +
63B SER 3.6 17.1 + - - -
64B THR 2.9 20.7 + - - +
65B ALA* 4.0 7.8 - - - +
67B GLU* 1.3 74.8 - - - +
69B ALA* 1.3 56.5 + - - +
71B VAL* 3.4 2.9 + - - +
72B GLN* 3.0 37.3 + - + +
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA 3.2 11.7 + - - +
66B GLU* 3.4 12.1 - - - +
68B LYS* 1.3 75.4 - - - +
70B MSE 1.3 60.8 + - + +
72B GLN* 3.5 16.0 + - - +
73B GLN* 3.0 27.9 + - - +
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Residues in contact with MSE 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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168A ARG 4.1 15.7 - - - +
169A LEU* 4.4 18.4 - - + -
66B GLU* 3.1 17.9 + - + +
67B GLU* 3.2 9.4 + - - +
69B ALA* 1.3 73.1 - - + +
71B VAL* 1.3 66.4 + - - +
73B GLN* 3.2 36.3 + - - +
74B TRP* 3.0 38.1 + - + +
101B TYR* 3.2 26.2 - - - +
109B THR* 3.7 29.4 - - - +
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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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60B LEU 4.2 8.7 - - - +
61B LEU* 3.5 38.8 - - + +
62B GLY* 4.1 1.1 - - - +
67B GLU* 2.9 18.4 + - + +
68B LYS 3.6 2.9 - - - +
70B MSE 1.3 74.6 - - - +
72B GLN* 1.3 64.6 + - + +
74B TRP* 3.2 3.1 + - - +
75B LEU* 2.9 45.6 + - + +
109B THR* 3.9 10.5 - - + +
114B THR* 3.8 29.4 - - + +
115B LEU* 4.8 0.7 - - + -
116B ALA* 4.3 8.5 - - - +
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Residues in contact with GLN 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 LYS* 3.0 20.0 + - + +
69B ALA* 3.5 17.4 - - - +
71B VAL* 1.3 76.2 - - + +
73B GLN* 1.3 58.7 + - - +
75B LEU* 3.4 10.3 + - + +
76B GLU* 3.0 31.5 + - - +
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG* 4.9 12.0 + - - +
69B ALA 3.0 15.0 + - - +
70B MSE 3.2 43.9 - - - +
72B GLN* 1.3 75.1 - - - +
74B TRP* 1.3 77.0 + - + +
76B GLU* 3.4 10.4 + - - +
77B TYR* 2.9 26.9 + - + +
101B TYR* 5.3 0.8 - - - -
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Residues in contact with TRP 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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168A ARG* 4.0 20.9 - - - -
70B MSE 3.0 43.3 + - + +
73B GLN* 1.3 92.2 - - + +
75B LEU* 1.3 60.1 + - - +
77B TYR* 3.5 55.6 - + + +
78B ARG* 3.0 27.2 + - - +
98B LEU* 3.8 26.5 - - + -
101B TYR* 3.4 34.5 + + + -
108B LEU* 3.7 30.1 + - + +
109B THR* 4.2 4.7 - - + -
116B ALA* 3.6 27.6 - - + +
120B LEU* 4.5 3.5 - - + +
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Residues in contact with LEU 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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45B THR* 3.6 32.8 - - + +
49B ALA* 5.3 5.6 - - + -
61B LEU* 5.3 2.5 - - + -
71B VAL* 2.9 33.9 + - + +
72B GLN* 3.8 9.0 - - + +
74B TRP* 1.3 76.0 - - - +
76B GLU* 1.3 62.7 + - - +
78B ARG* 3.2 15.5 + - - +
79B VAL* 3.2 14.7 + - - +
115B LEU* 4.0 26.7 - - + -
116B ALA* 4.0 18.4 - - - +
119B LEU* 3.9 27.1 - - + -
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Residues in contact with GLU 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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45B THR* 5.8 0.4 - - - -
72B GLN 3.0 18.0 + - - +
73B GLN* 3.8 7.4 - - - +
75B LEU* 1.3 73.2 - - - +
77B TYR* 1.3 59.5 + - - +
79B VAL* 3.4 8.8 + - + -
80B THR* 2.6 55.4 + - + +
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Residues in contact with TYR 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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168A ARG* 5.9 2.9 - - - -
73B GLN* 2.9 18.6 + - + +
74B TRP* 3.5 47.1 - + + +
75B LEU 3.2 0.4 - - - -
76B GLU* 1.3 74.2 - - - +
78B ARG* 1.3 62.6 + - - +
80B THR* 3.7 6.1 - - - -
81B GLN* 2.8 64.7 + - + +
82B VAL* 3.4 22.9 + - + -
94B LEU* 3.3 30.9 + - + +
98B LEU* 4.1 16.1 + - - +
120B LEU* 3.8 16.6 - - + -
124B LEU* 5.8 1.7 - - + +
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Residues in contact with ARG 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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6B GLU* 2.4 45.1 + - - -
44B LEU* 3.6 20.2 - - + +
45B THR* 5.1 0.2 - - + -
74B TRP 3.0 14.6 + - - +
75B LEU* 3.4 12.1 - - - +
77B TYR* 1.3 79.5 - - - +
79B VAL* 1.3 58.3 + - + +
82B VAL* 3.4 16.7 - - - +
83B ASP* 2.8 65.3 + - - -
116B ALA 6.1 0.2 - - - +
119B LEU* 2.9 41.7 + - + +
120B LEU* 4.6 9.6 - - + +
123B GLY* 3.6 22.7 - - - +
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Residues in contact with VAL 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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44B LEU* 4.0 18.2 - - + +
45B THR* 3.6 31.2 - - + +
75B LEU 3.6 11.0 - - - +
76B GLU* 3.6 14.8 - - + +
78B ARG* 1.3 77.5 - - + +
80B THR* 1.3 64.2 + - + +
83B ASP* 3.6 33.4 - - + +
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 2.6 43.7 + - + +
77B TYR* 3.7 1.6 - - - -
79B VAL* 1.3 87.4 - - + +
81B GLN* 1.3 78.4 + - - +
82B VAL 3.8 0.2 - - - -
83B ASP 4.0 8.4 - - - +
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Residues in contact with GLN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 2.8 48.6 + - + +
80B THR* 1.3 93.3 + - - +
82B VAL* 1.3 63.6 + - - +
83B ASP 4.5 0.8 - - - +
90B ASP* 5.0 5.4 - - - +
91B ILE* 6.0 0.3 - - - +
94B LEU* 3.9 33.2 - - + +
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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