Contacts of the helix formed by residues 55 - 70 (chain C) in PDB entry 1ZUM
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 ASP 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C SER* 6.0 4.3 - - - +
35C LYS* 5.3 6.9 + - - -
53C GLU* 4.6 7.7 - - + +
54C GLY* 1.3 73.0 - - - -
56C LYS* 1.3 86.4 + - - +
57C GLU* 3.2 4.3 - - + +
58C ASP* 2.8 23.5 + - - +
59C VAL* 3.0 16.8 + - - +
227C THR* 3.6 29.6 - - - +
228C ALA* 4.6 6.7 - - - +
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Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASP* 1.3 86.5 + - - +
57C GLU* 1.3 56.2 + - - +
59C VAL* 3.2 3.1 + - - +
60C ASP* 2.9 47.6 + - - +
227C THR 4.9 1.8 + - - +
231C ALA* 3.8 27.5 - - + +
234C SER* 5.9 2.9 - - - -
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Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C VAL* 3.6 41.1 - - + +
55C ASP* 3.0 3.8 + - + +
56C LYS* 1.3 79.4 - - - +
58C ASP* 1.3 63.3 + - - +
60C ASP* 3.5 12.0 + - + +
61C LYS* 3.3 25.8 + - + +
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Residues in contact with ASP 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.4 27.9 - - + +
24C ILE* 3.7 8.7 - - + +
30C ASP 4.1 1.7 - - - +
31C ALA* 3.2 9.2 - - - +
32C VAL* 2.7 40.2 + - - +
33C SER* 5.1 1.0 + - - -
53C GLU 4.2 0.2 - - - +
54C GLY* 3.5 4.7 - - - -
55C ASP* 2.8 34.0 + - - +
57C GLU* 1.3 74.0 + - - +
59C VAL* 1.3 65.7 + - - +
61C LYS* 3.3 13.9 + - + +
62C ALA* 3.1 18.5 + - - +
221C VAL* 4.3 6.6 - - + +
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASP 3.0 13.8 + - - +
56C LYS 3.2 8.9 + - - +
58C ASP* 1.3 76.2 - - - +
60C ASP* 1.3 60.5 + - - +
62C ALA* 3.1 8.0 + - - +
63C VAL* 2.9 39.5 + - + +
190C VAL* 5.0 1.6 - - + -
221C VAL* 4.3 12.8 - - + -
228C ALA* 3.6 32.8 - - + +
231C ALA* 4.0 20.6 - - + +
232C ILE* 3.8 29.2 - - + +
235C HIS* 4.5 5.2 - - + -
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Residues in contact with ASP 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LYS* 2.9 42.6 + - - +
57C GLU* 3.7 11.2 - - + +
58C ASP 3.3 0.2 - - - -
59C VAL* 1.3 78.2 - - - +
61C LYS* 1.3 61.1 + - + +
63C VAL* 3.4 2.1 + - - +
64C LYS* 3.1 38.6 + - + +
231C ALA* 6.0 0.2 - - - +
235C HIS* 2.9 35.1 + - - +
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Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.9 18.3 - - + +
29C HIS* 3.7 34.1 + - - +
30C ASP 4.8 4.8 + - - -
32C VAL* 4.1 23.7 - - + +
57C GLU* 3.3 17.3 + - + +
58C ASP* 3.5 11.5 + - - +
59C VAL 3.2 0.2 - - - -
60C ASP* 1.3 80.1 - - + +
62C ALA* 1.3 62.3 + - - +
64C LYS* 3.4 10.0 + - + +
65C ALA* 3.0 23.4 + - - +
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Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.8 15.4 - - + +
58C ASP 3.1 12.2 + - - +
59C VAL 3.1 8.5 + - - +
61C LYS* 1.3 75.2 - - - +
63C VAL* 1.3 59.3 + - - +
65C ALA* 3.2 3.3 + - - +
66C ALA* 2.9 28.9 + - - +
190C VAL* 3.9 17.3 - - + -
219C ASN* 3.6 25.8 + - + -
221C VAL* 4.0 13.0 - - + -
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Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C VAL* 2.9 27.5 + - + +
60C ASP 3.8 4.5 - - - +
61C LYS 3.3 0.2 - - - -
62C ALA* 1.3 75.4 - - - +
64C LYS* 1.3 54.6 + - + +
66C ALA* 3.1 2.0 + - - +
67C ARG* 2.8 33.8 + - - +
161C VAL* 4.4 5.1 - - + +
190C VAL* 3.9 17.0 - - + -
235C HIS* 3.6 40.4 - - + +
237C ASP* 4.0 28.7 - - + +
238C VAL* 4.0 17.5 - - + -
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Residues in contact with LYS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ASP* 3.1 29.0 + - - +
61C LYS* 3.6 9.0 - - + +
63C VAL* 1.3 79.1 - - + +
65C ALA* 1.3 57.5 + - - +
67C ARG* 3.4 6.7 + - - +
68C ALA* 3.0 30.0 + - - +
235C HIS* 6.1 2.2 - - + +
237C ASP* 5.9 0.2 - - - -
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.7 15.7 - - + -
25C ASN* 3.5 34.7 - - - +
61C LYS 3.0 13.6 + - - +
62C ALA 3.6 7.4 - - - +
64C LYS* 1.3 76.6 - - - +
66C ALA* 1.3 62.1 + - - +
68C ALA* 3.5 6.6 + - - +
69C ALA* 3.1 23.9 + - - +
216C GLY* 3.7 4.6 - - - -
219C ASN* 3.9 7.2 - - - +
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ALA 2.9 16.7 + - - +
63C VAL 3.5 4.0 - - - +
65C ALA* 1.3 74.1 - - - +
67C ARG* 1.3 64.7 + - - +
69C ALA* 3.2 3.1 + - - +
70C PHE* 3.1 17.3 + - - +
161C VAL* 4.0 6.7 - - + -
188C VAL* 3.4 27.9 - - + +
189C VAL 4.5 1.3 - - - +
190C VAL* 3.9 14.8 - - + -
216C GLY 3.2 13.9 - - - +
219C ASN* 3.6 12.3 - - - +
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Residues in contact with ARG 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C VAL 2.8 20.3 + - - +
64C LYS* 3.7 7.0 - - - +
66C ALA* 1.3 70.7 - - - +
68C ALA* 1.3 65.3 + - - +
70C PHE* 3.1 37.5 + - - +
71C GLN* 3.2 43.8 + - + +
161C VAL* 3.6 15.4 - - + +
237C ASP* 2.9 54.0 + - - +
239C ASP* 2.7 35.1 + - - -
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ASN* 6.3 0.2 - - - +
64C LYS 3.0 17.7 + - - +
65C ALA* 3.6 7.6 - - - +
67C ARG* 1.3 77.6 - - - +
69C ALA* 1.3 62.5 + - - +
70C PHE 3.1 1.2 + - - -
71C GLN* 3.1 27.1 + - - +
74C SER* 4.3 5.0 - - - -
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Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ALA 3.1 15.2 + - - +
66C ALA 3.2 4.4 + - - +
68C ALA* 1.3 75.8 - - - +
70C PHE* 1.3 55.9 + - - +
74C SER* 2.8 23.5 + - - -
76C TRP* 3.8 15.0 - - + +
77C ARG* 4.4 0.2 - - - +
188C VAL* 4.2 7.2 - - + -
214C PRO* 5.7 1.3 - - + -
215C PRO 3.4 26.0 - - - +
216C GLY 3.6 14.4 - - - +
217C VAL* 4.0 7.4 - - + +
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Residues in contact with PHE 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ALA 3.1 11.0 + - - +
67C ARG* 3.1 33.5 + - - +
68C ALA 3.0 1.0 - - - -
69C ALA* 1.3 78.0 - - - +
71C GLN* 1.3 61.4 + - - +
76C TRP* 4.9 0.9 - + - -
77C ARG* 2.7 71.2 + - - +
158C PRO* 3.7 24.5 - - + -
159C VAL 4.8 2.0 - - - -
160C GLY* 3.6 31.4 - - - -
186C GLY 3.6 23.3 - - - -
187C ASN* 4.5 0.7 - - - -
188C VAL* 4.0 17.7 - - + -
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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