Contacts of the helix formed by residues 55 - 70 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33L SER* 5.8 4.3 - - - +
53L GLU* 4.3 13.1 - - - +
54L GLY* 1.3 73.3 - - - +
56L LYS* 1.3 84.5 + - - +
57L GLU* 3.3 3.4 - - + +
58L ASP* 3.0 14.4 + - - +
59L VAL* 3.0 26.2 + - - +
227L THR* 3.3 32.6 + - - +
228L ALA* 4.5 7.2 - - - +
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Residues in contact with LYS 56 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55L ASP* 1.3 88.4 + - - +
57L GLU* 1.3 60.7 + - + +
59L VAL* 3.2 4.2 + - - +
60L ASP* 2.9 28.8 + - + +
227L THR 4.8 1.8 + - - +
231L ALA* 3.8 27.1 - - + +
234L SER* 6.1 0.7 - - - -
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Residues in contact with GLU 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L VAL* 3.4 35.4 - - + +
55L ASP* 3.3 3.3 - - + +
56L LYS* 1.3 80.6 - - + +
58L ASP* 1.3 62.7 + - - +
60L ASP* 3.3 8.9 + - - +
61L LYS* 3.2 26.5 + - - +
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Residues in contact with ASP 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L ILE* 4.1 13.1 - - + +
24L ILE* 3.7 8.8 - - - +
29L HIS* 6.0 0.2 - - - +
30L ASP 4.0 3.1 - - - +
31L ALA* 3.1 13.1 - - - +
32L VAL* 3.0 40.1 + - - +
33L SER* 5.0 1.2 + - - -
54L GLY* 3.7 13.8 - - - -
55L ASP* 3.0 32.3 + - - +
57L GLU* 1.3 77.1 - - - +
59L VAL* 1.3 62.6 + - - +
61L LYS* 3.3 11.4 + - - +
62L ALA* 3.1 18.4 + - - +
221L VAL* 4.2 10.2 - - + +
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Residues in contact with VAL 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L ASP 3.0 14.6 + - - +
56L LYS 3.4 8.1 - - - +
58L ASP* 1.3 73.8 - - - +
60L ASP* 1.3 60.4 + - - +
62L ALA* 3.1 8.1 + - - +
63L VAL* 2.9 39.8 + - + +
190L VAL* 4.9 1.8 - - + -
221L VAL* 4.1 18.2 - - + -
228L ALA* 3.7 28.0 - - + +
231L ALA* 4.0 20.0 - - + +
232L ILE* 3.9 27.6 - - + +
235L HIS* 4.5 4.3 - - + -
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Residues in contact with ASP 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L LYS* 2.9 14.5 + - + +
57L GLU* 3.6 11.9 - - - +
59L VAL* 1.3 78.2 - - - +
61L LYS* 1.3 60.1 + - + +
63L VAL* 3.4 1.4 + - - +
64L LYS* 2.9 56.5 + - - +
235L HIS* 3.0 34.9 + - + +
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Residues in contact with LYS 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L ILE* 3.9 16.7 - - + +
29L HIS* 4.3 27.0 + - - +
30L ASP 5.2 3.8 + - - -
32L VAL* 4.1 23.6 - - + +
57L GLU* 3.2 16.5 + - + +
58L ASP* 3.6 11.0 + - - +
59L VAL 3.2 0.2 - - - -
60L ASP* 1.3 77.9 - - + +
62L ALA* 1.3 61.8 + - - +
64L LYS* 3.4 9.5 + - - +
65L ALA* 3.1 22.9 + - - +
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Residues in contact with ALA 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L ILE* 3.6 15.2 - - + +
58L ASP 3.1 12.2 + - - +
59L VAL 3.1 8.6 + - - +
61L LYS* 1.3 74.8 - - - +
63L VAL* 1.3 60.2 + - - +
65L ALA* 3.3 3.8 + - - +
66L ALA* 3.0 27.5 + - - +
190L VAL* 3.9 11.2 - - + -
219L ASN* 3.6 21.4 + - + -
221L VAL* 3.8 21.5 - - + -
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Residues in contact with VAL 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L VAL* 2.9 27.2 + - + +
60L ASP 3.9 1.1 - - - +
61L LYS 3.4 0.2 - - - -
62L ALA* 1.3 75.9 - - - +
64L LYS* 1.3 58.0 + - + +
66L ALA* 3.2 2.0 + - - +
67L ARG* 2.8 28.4 + - - +
161L VAL* 4.3 9.0 - - + -
190L VAL* 4.0 18.4 - - + -
235L HIS* 3.6 30.1 - - + +
237L ASP* 3.9 39.5 - - + +
238L VAL* 3.9 15.9 - - + -
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Residues in contact with LYS 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60L ASP* 2.9 45.7 + - - +
61L LYS* 3.5 10.5 - - - +
63L VAL* 1.3 79.6 - - + +
65L ALA* 1.3 56.6 + - - +
67L ARG* 3.5 6.6 + - - +
68L ALA* 3.0 29.3 + - - +
235L HIS* 6.0 0.9 - - + +
237L ASP* 5.8 0.2 - - - -
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Residues in contact with ALA 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L ILE* 3.5 32.1 - - + -
25L ASN* 3.5 27.4 - - - +
61L LYS 3.1 8.0 + - - +
62L ALA 3.5 5.2 - - - +
63L VAL 3.2 0.2 - - - -
64L LYS* 1.3 76.5 - - - +
66L ALA* 1.3 58.4 + - - +
68L ALA* 3.4 6.0 + - - +
69L ALA* 3.0 29.3 + - - +
216L GLY* 3.8 4.8 - - - -
219L ASN* 3.6 6.7 - - - +
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Residues in contact with ALA 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62L ALA 3.0 13.9 + - - +
63L VAL 3.2 7.8 + - - +
65L ALA* 1.3 74.5 - - - +
67L ARG* 1.3 65.9 + - - +
69L ALA* 3.2 3.3 + - - +
70L PHE* 3.0 17.3 + - - +
161L VAL* 4.1 6.3 - - + -
188L VAL* 3.4 30.4 - - + +
189L VAL 4.6 1.3 - - - +
190L VAL* 3.9 15.0 - - + -
216L GLY 3.3 11.8 + - - +
219L ASN* 3.6 11.9 - - - +
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Residues in contact with ARG 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L VAL 2.8 18.5 + - - +
64L LYS* 3.8 6.3 - - - +
66L ALA* 1.3 72.0 - - - +
68L ALA* 1.3 63.0 + - - +
70L PHE* 3.1 35.0 + - - -
71L GLN* 2.8 44.4 + - - +
161L VAL* 3.6 16.7 - - + +
237L ASP* 2.8 61.3 + - - +
239L ASP* 3.0 31.3 + - - -
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Residues in contact with ALA 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L ASN* 6.1 0.4 - - - +
64L LYS 3.0 17.8 + - - +
65L ALA* 3.6 7.9 - - - +
66L ALA 3.2 0.2 - - - -
67L ARG* 1.3 76.9 - - - +
69L ALA* 1.3 62.1 + - - +
71L GLN* 3.1 26.7 + - - +
74L SER* 4.3 5.2 - - - -
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Residues in contact with ALA 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65L ALA 3.0 14.9 + - - +
66L ALA 3.8 3.8 - - - +
68L ALA* 1.3 76.5 - - - +
70L PHE* 1.3 53.6 + - - +
71L GLN 3.4 0.2 - - - -
74L SER* 2.7 26.6 + - - -
76L TRP* 3.8 14.1 - - + +
77L ARG* 4.4 0.2 - - - +
188L VAL* 4.3 6.3 - - + -
214L PRO* 5.7 1.6 - - + -
215L PRO 3.4 25.6 - - - +
216L GLY 3.7 13.9 - - - +
217L VAL* 4.0 8.1 - - + +
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Residues in contact with PHE 70 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66L ALA 3.0 15.5 + - - +
67L ARG* 3.6 27.8 - - - +
68L ALA 3.1 0.6 - - - -
69L ALA* 1.3 77.3 - - - +
71L GLN* 1.3 62.7 + - - +
76L TRP* 4.8 0.7 - + - -
77L ARG* 2.9 65.2 + - - +
158L PRO* 3.5 26.9 - - + -
159L VAL 4.8 2.0 - - - -
160L GLY* 3.6 24.5 - - - -
186L GLY 3.3 24.9 - - - -
187L ASN* 4.2 1.3 - - - -
188L VAL* 3.8 24.9 - - + -
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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