Contacts of the helix formed by residues 68 - 76 (chain B) in PDB entry 2OZK
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 GLU 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B VAL 3.5 2.2 + - - -
67B PRO* 1.3 77.1 - - - +
69B ILE* 1.3 65.6 + - - +
70B LYS* 3.2 21.9 - - + -
71B ILE* 3.2 35.4 + - + +
72B LEU* 3.2 9.5 + - - +
157B PRO* 5.1 0.2 - - - +
159B GLN* 3.5 25.3 + - - +
160B ALA* 4.8 1.2 - - - +
161B SER* 4.5 17.0 - - - +
166B THR* 3.4 25.7 + - + +
195B THR 5.3 0.2 - - - +
197B SER* 2.5 33.8 + - - -
272B ASP* 4.1 4.7 - - - +
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Residues in contact with ILE 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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67B PRO 5.2 1.1 - - - +
68B GLU* 1.3 73.5 - - - +
70B LYS* 1.3 67.7 + - - +
72B LEU* 3.0 7.6 + - + -
73B ASN* 2.8 51.3 + - - +
85B ILE* 4.8 9.9 - - + -
86B TRP 4.2 6.3 - - - +
87B ASP* 3.5 45.8 - - + +
88B TYR 5.1 0.4 - - - +
94B ALA* 4.6 16.6 - - + -
271B MET* 4.2 13.5 - - - -
272B ASP* 4.1 16.6 + - + +
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Residues in contact with LYS 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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68B GLU* 3.6 19.1 - - + -
69B ILE* 1.3 77.3 - - - +
71B ILE* 1.3 76.0 + - + +
73B ASN* 4.0 2.6 - - - +
74B ASN* 3.0 33.5 + - - +
195B THR* 3.0 21.9 + - - +
196B GLN 3.6 6.3 + - - -
197B SER* 2.8 28.6 + - - +
272B ASP* 3.4 30.2 + - - +
273B SER* 3.8 34.8 + - - +
274B THR* 3.9 6.9 + - - +
323B ASP* 3.5 18.8 - - - +
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Residues in contact with ILE 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 PRO* 4.5 4.3 - - + -
68B GLU* 3.2 39.2 + - + +
70B LYS* 1.3 88.5 - - + +
72B LEU* 1.3 64.1 + - + +
74B ASN* 3.7 6.1 - - - +
75B LEU* 3.1 31.9 + - + +
157B PRO* 3.7 26.9 - - + -
178B TYR* 3.7 37.9 - - + +
194B PHE* 4.8 3.8 - - + -
195B THR* 5.6 1.6 - - - +
323B ASP* 4.5 19.7 - - + +
324B TYR* 4.4 7.4 - - + -
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Residues in contact with LEU 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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67B PRO* 3.8 35.4 - - + +
68B GLU 3.2 10.2 + - - +
69B ILE* 3.0 14.6 + - + +
71B ILE* 1.3 81.2 - - + +
73B ASN* 1.3 65.1 + - - +
75B LEU* 3.3 4.2 + - + +
76B GLY 3.2 4.0 + - - -
77B VAL* 3.2 49.7 + - + +
85B ILE* 4.0 27.8 - - + -
95B HIS* 4.8 9.6 - - + +
122B LEU* 4.0 27.4 - - + -
141B VAL* 5.4 3.8 - - + -
178B TYR* 5.5 2.7 - - + -
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Residues in contact with ASN 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 ILE* 2.8 41.7 + - - +
70B LYS* 4.1 2.7 - - - +
72B LEU* 1.3 72.7 - - - +
74B ASN* 1.3 70.2 + - - +
75B LEU 3.0 1.8 - - - -
76B GLY* 2.9 16.4 + - - +
77B VAL 4.7 10.0 - - - +
94B ALA 5.7 0.5 - - - +
95B HIS* 5.3 3.6 + - - -
271B MET* 3.6 24.4 - - - +
272B ASP 4.4 4.9 + - - -
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Residues in contact with ASN 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 LYS* 3.0 24.7 + - - +
71B ILE 3.7 4.3 - - - +
73B ASN* 1.3 76.4 - - - +
75B LEU* 1.3 63.0 + - - +
76B GLY 3.7 0.2 + - - -
273B SER* 5.9 0.9 - - - -
274B THR* 3.1 27.8 + - - -
323B ASP* 2.6 37.5 + - - +
324B TYR* 4.5 7.8 - - + +
325B ALA* 3.9 22.5 - - + +
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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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71B ILE* 3.1 39.0 + - + +
72B LEU* 3.6 7.0 - - + +
73B ASN 3.0 1.0 - - - -
74B ASN* 1.3 79.0 - - - +
76B GLY* 1.3 56.5 + - - +
77B VAL* 3.5 11.6 + - + -
120B THR* 4.7 2.9 - - - +
141B VAL* 4.3 18.9 - - + +
178B TYR* 3.9 20.9 - - + -
180B LYS* 2.8 44.0 + - + +
189B LEU* 4.6 8.3 - - + -
324B TYR* 3.9 37.7 - - + -
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Residues in contact with GLY 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 LEU 3.2 0.6 + - - -
73B ASN* 2.9 14.1 + - - -
74B ASN 3.5 0.4 + - - -
75B LEU* 1.3 78.0 - - - +
77B VAL* 1.3 68.3 + - - +
78B ASP* 3.1 9.7 + - - +
120B THR* 2.8 22.3 + - - -
180B LYS* 4.9 1.6 - - - -
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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