Contacts of the helix formed by residues 67 - 79 (chain B) in PDB entry 2POZ
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 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B LYS* 3.4 20.4 - - - +
64B ASP* 3.1 48.7 + - - +
65B PRO 3.2 1.2 - - - -
66B SER* 1.3 83.2 - - - +
68B ILE* 1.3 58.7 + - - +
69B GLU 3.5 2.2 - - - -
70B GLU* 2.5 55.4 + - + +
71B LEU* 3.0 46.6 + - - +
117F GLY 3.9 3.4 - - - -
118F GLY* 4.3 3.8 - - - -
119F LYS* 3.7 24.2 - - + +
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Residues in contact with ILE 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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65B PRO 3.5 16.4 - - - +
66B SER 3.9 5.2 - - - +
67B ARG* 1.3 68.9 - - - +
69B GLU* 1.3 64.4 + - - +
71B LEU* 3.2 6.4 + - - +
72B TRP* 2.9 29.5 + - + +
97B GLU* 4.1 18.2 - - + -
100B LEU* 3.7 37.4 - - + +
101B TRP* 3.5 47.8 - - + +
104B LYS* 3.5 20.2 - - - -
117F GLY* 3.0 12.2 + - - +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 1.3 79.2 - - - +
70B GLU* 1.3 56.7 + - - +
72B TRP* 3.7 10.5 - - - +
73B SER* 2.9 30.1 + - - -
101B TRP* 5.6 1.1 - - - -
288B MSE 4.1 11.7 - - - +
292B LYS* 2.9 25.5 + - - -
116F PHE 3.7 7.4 - - - +
117F GLY* 3.0 15.0 + - - +
118F GLY 4.8 0.2 - - - +
120F ILE* 3.9 21.6 - - + +
291F LYS* 2.7 28.5 + - - -
324F ASN* 3.5 26.0 - - - +
326F THR* 4.7 8.9 + - - +
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Residues in contact with GLU 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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67B ARG* 2.5 52.7 + - + +
68B ILE 3.3 0.2 - - - -
69B GLU* 1.3 75.6 - - - +
71B LEU* 1.3 57.8 + - - +
73B SER* 3.3 4.5 + - - -
74B THR* 2.7 45.4 + - - +
118F GLY 6.2 0.2 - - - -
119F LYS 4.4 1.4 - - - +
120F ILE* 3.8 38.6 - - + +
174H ARG* 4.4 19.7 + - - +
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Residues in contact with LEU 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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5B ILE* 5.0 3.8 - - + -
59B PHE* 4.2 4.3 - - + +
60B LEU* 4.1 16.8 - - + -
63B LYS* 3.5 40.2 - - + +
64B ASP 3.8 18.4 - - - +
65B PRO* 4.2 2.2 - - + -
67B ARG* 3.0 34.4 + - - +
68B ILE 3.6 4.0 - - - +
70B GLU* 1.3 77.6 - - + +
72B TRP* 1.3 62.4 + - - +
74B THR* 3.2 4.8 + - - +
75B MSE 3.0 34.1 + - + +
100B LEU* 3.8 34.3 - - + -
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Residues in contact with TRP 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 ILE* 2.9 18.1 + - + +
69B GLU* 3.7 14.1 - - - +
71B LEU* 1.3 75.2 - - - +
73B SER* 1.3 65.2 + - - +
75B MSE 3.3 13.5 + - + +
76B TYR* 3.0 56.9 + + + -
90B PHE* 4.2 20.9 - + - -
93B ILE* 3.3 22.0 - - + +
97B GLU* 4.0 22.0 - - + -
100B LEU* 5.8 0.2 - - - +
261B THR* 4.5 4.9 - - + -
262B ARG* 4.0 17.5 - - - -
263B PHE* 4.7 6.5 - + - -
285B GLY* 2.9 25.2 + - - -
289B GLU* 3.7 36.5 - - + +
298F GLU* 6.0 0.4 - - - -
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Residues in contact with SER 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 GLU 2.9 19.1 + - - -
70B GLU* 3.5 8.7 - - - -
72B TRP* 1.3 86.5 - - - +
74B THR* 1.3 56.4 + - - +
76B TYR* 3.4 2.9 + - - +
77B ASP* 2.9 35.6 + - - +
120F ILE* 5.0 0.2 - - - -
326F THR* 3.6 17.8 - - - +
174H ARG* 3.2 36.9 + - - +
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Residues in contact with THR 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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58B ARG* 5.6 0.9 - - - +
59B PHE* 3.6 27.3 - - + -
63B LYS* 4.0 15.6 + - - +
70B GLU* 2.7 36.3 + - - +
71B LEU* 3.5 8.3 - - - +
73B SER* 1.3 71.5 - - - +
75B MSE 1.3 60.7 + - - +
77B ASP* 4.5 0.9 - - - -
78B HIS* 2.8 48.1 + - + +
174H ARG* 4.9 5.1 + - - +
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Residues in contact with MSE 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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55B LEU* 4.4 12.1 - - + -
59B PHE* 3.7 33.2 - - + -
60B LEU* 4.8 7.2 - - + -
71B LEU* 3.0 31.1 + - + +
72B TRP* 3.8 17.3 - - + +
74B THR* 1.3 74.8 - - - +
76B TYR* 1.3 59.5 + - - +
79B SER* 2.8 32.9 + - - -
82B ALA* 4.0 0.5 - - - +
93B ILE* 4.1 39.8 - - + +
96B ILE* 3.9 45.1 - - + -
97B GLU* 5.2 1.6 - - - +
100B LEU* 5.2 2.5 - - + -
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Residues in contact with TYR 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 TRP* 3.0 42.7 + + + +
73B SER* 3.6 5.4 - - - +
75B MSE 1.3 79.1 - - - +
77B ASP* 1.3 77.3 + - - +
78B HIS 3.5 0.2 + - - -
79B SER* 3.8 2.9 + - - -
80B PHE 4.5 1.7 + - - -
82B ALA* 3.4 41.7 - - + +
83B LYS* 3.7 25.7 - - + +
90B PHE* 3.9 15.7 - + - -
93B ILE* 4.6 3.3 - - + +
263B PHE* 3.7 26.3 - + - -
175H ARG* 4.9 3.8 - - - -
235H ASP* 2.5 39.0 + - - -
237H PHE* 3.3 13.8 - + - -
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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 SER* 2.9 24.3 + - - +
74B THR* 4.5 0.4 - - - -
76B TYR* 1.3 95.0 - - - +
78B HIS* 1.3 81.8 + - + +
79B SER 3.7 0.2 - - - -
80B PHE* 4.5 4.2 + - - -
83B LYS* 4.2 19.7 + - - +
171H HIS* 5.2 7.8 + - - +
172H VAL 4.2 8.4 - - - +
173H THR* 3.5 5.2 - - - +
174H ARG* 2.6 44.6 + - - +
175H ARG 5.5 0.2 - - - -
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Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ARG* 4.7 11.2 + - - +
59B PHE* 3.7 21.4 - + + -
74B THR* 2.8 39.0 + - + +
77B ASP* 1.3 86.0 + - + +
79B SER* 1.3 62.3 + - - +
80B PHE* 3.2 2.5 - - - +
42H GLY* 5.3 1.9 - - - -
43H VAL* 4.1 5.9 + - - +
170H GLN* 3.6 28.4 + - + +
171H HIS 3.5 24.0 + - - -
172H VAL 3.9 9.2 - - - -
173H THR* 3.1 29.0 + - - +
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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
----------------------------------------------------------
55B LEU* 4.5 1.8 - - - -
59B PHE* 4.2 5.6 - - - -
75B MSE 2.8 24.1 + - - -
77B ASP 3.7 0.4 - - - -
78B HIS* 1.3 76.7 - - - +
80B PHE* 1.3 62.1 + - - +
81B TRP* 2.8 15.7 + - - -
82B ALA* 3.2 25.8 + - - +
89B ILE* 4.0 15.8 - - - +
42H GLY* 4.4 0.4 - - - -
43H VAL* 2.9 43.8 + - - -
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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