Contacts of the helix formed by residues 55 - 70 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J SER* 5.7 4.7 - - - +
35J LYS* 5.6 3.1 + - - -
53J GLU* 4.7 10.7 - - - +
54J GLY* 1.3 72.8 - - - -
56J LYS* 1.3 85.6 + - - +
57J GLU* 3.3 3.8 - - + +
58J ASP* 2.7 15.0 + - - +
59J VAL* 3.0 27.4 + - - +
227J THR* 3.6 33.2 - - - +
228J ALA* 4.5 5.2 - - - +
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Residues in contact with LYS 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J ASP* 1.3 86.9 + - - +
57J GLU* 1.3 57.0 + - - +
59J VAL* 3.2 3.6 + - - +
60J ASP* 2.9 29.5 + - + +
227J THR 4.8 0.6 + - - +
231J ALA* 3.8 38.5 + - + +
234J SER* 4.9 10.3 - - - -
235J HIS* 5.6 6.1 - - + +
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Residues in contact with GLU 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J VAL* 3.4 41.9 - - + +
55J ASP* 3.3 2.7 - - + +
56J LYS* 1.3 78.4 - - - +
58J ASP* 1.3 63.3 + - - +
60J ASP* 3.4 8.2 + - + +
61J LYS* 3.3 27.9 + - + +
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Residues in contact with ASP 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J ILE* 4.8 11.4 - - + +
24J ILE* 3.7 8.1 - - + +
30J ASP 4.3 2.4 - - - +
31J ALA* 3.4 10.6 - - - +
32J VAL* 2.8 40.1 + - - +
33J SER* 5.2 1.4 + - - -
54J GLY* 3.4 13.5 - - - -
55J ASP* 2.7 34.4 + - - +
57J GLU* 1.3 74.8 - - - +
59J VAL* 1.3 66.3 + - - +
61J LYS* 3.2 14.0 + - - +
62J ALA* 3.1 18.6 + - - +
221J VAL* 4.3 8.7 - - + +
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Residues in contact with VAL 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J ASP 3.0 17.5 + - - +
56J LYS 3.5 7.2 - - - +
58J ASP* 1.3 74.7 - - - +
60J ASP* 1.3 60.1 + - - +
62J ALA* 3.1 8.3 + - - +
63J VAL* 2.8 45.9 + - + +
190J VAL* 4.6 2.7 - - + -
221J VAL* 4.2 15.7 - - + -
228J ALA* 3.7 26.5 - - + +
231J ALA* 4.0 11.9 - - + +
232J ILE* 3.5 37.5 - - + +
235J HIS* 4.9 3.6 - - + -
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Residues in contact with ASP 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J LYS* 2.9 14.5 + - + +
57J GLU* 3.6 11.9 - - + +
59J VAL* 1.3 78.6 - - - +
61J LYS* 1.3 57.6 + - + +
63J VAL* 3.3 2.1 + - - +
64J LYS* 2.9 63.5 + - - +
235J HIS* 2.9 34.3 + - + +
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Residues in contact with LYS 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J ILE* 3.7 17.6 - - + +
29J HIS* 3.6 35.2 + - - +
30J ASP 4.9 4.2 + - - -
32J VAL* 4.0 24.7 - - + +
57J GLU* 3.3 16.5 + - + +
58J ASP* 3.2 12.1 + - - +
59J VAL 3.2 0.4 - - - -
60J ASP* 1.3 77.7 + - + +
62J ALA* 1.3 56.1 + - - +
64J LYS* 3.3 10.1 + - - +
65J ALA* 3.0 28.4 + - - +
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Residues in contact with ALA 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J ILE* 3.6 16.3 - - + +
58J ASP 3.1 13.2 + - - +
59J VAL 3.1 7.8 + - - +
61J LYS* 1.3 77.2 - - - +
63J VAL* 1.3 57.1 + - - +
65J ALA* 3.2 4.2 + - - +
66J ALA* 2.9 29.1 + - - +
190J VAL* 3.8 22.9 - - + -
219J ASN* 3.6 15.0 + - + -
221J VAL* 3.9 15.5 - - + -
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Residues in contact with VAL 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J VAL* 2.8 29.7 + - + +
60J ASP 3.7 4.7 - - - +
62J ALA* 1.3 75.0 - - - +
64J LYS* 1.3 54.6 + - + +
66J ALA* 3.2 1.8 + - - +
67J ARG* 2.8 34.0 + - - +
161J VAL* 4.4 5.6 - - + -
190J VAL* 4.0 15.7 - - + -
235J HIS* 3.6 46.4 - - + +
237J ASP* 3.8 25.1 - - + +
238J VAL* 4.0 14.6 - - + -
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Residues in contact with LYS 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J ASP* 2.9 50.8 + - - +
61J LYS* 3.5 9.9 - - - +
63J VAL* 1.3 78.0 - - + +
65J ALA* 1.3 61.6 + - - +
67J ARG* 3.7 5.6 - - - +
68J ALA* 3.0 24.9 + - - +
235J HIS* 5.7 3.7 - - + +
237J ASP* 5.8 0.9 - - - +
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Residues in contact with ALA 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J ILE* 3.6 22.9 - - + -
25J ASN* 3.7 26.3 - - - +
61J LYS 3.0 13.8 + - - +
62J ALA 3.5 8.1 - - - +
64J LYS* 1.3 75.3 - - - +
66J ALA* 1.3 62.4 + - - +
68J ALA* 3.4 7.2 + - - +
69J ALA* 3.0 23.7 + - - +
216J GLY* 3.8 4.9 - - - -
219J ASN* 3.9 8.1 - - - +
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Residues in contact with ALA 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J ALA 2.9 16.5 + - - +
63J VAL 3.5 4.5 - - - +
65J ALA* 1.3 73.6 - - - +
67J ARG* 1.3 66.8 + - - +
69J ALA* 3.0 4.7 + - - +
70J PHE* 3.0 22.7 + - - +
161J VAL* 4.0 7.2 - - + -
188J VAL* 3.7 23.2 - - + +
189J VAL 4.6 0.9 - - - +
190J VAL* 3.9 14.8 - - + -
216J GLY 3.4 12.1 - - - +
219J ASN* 3.7 11.4 - - - +
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Residues in contact with ARG 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63J VAL 2.8 20.6 + - - +
64J LYS* 3.7 7.0 - - - +
65J ALA 3.4 0.2 - - - -
66J ALA* 1.3 72.1 - - - +
68J ALA* 1.3 62.2 - - - +
70J PHE* 3.2 36.4 + - - -
71J GLN* 3.0 43.4 + - - +
161J VAL* 3.4 15.1 - - + +
237J ASP* 2.8 59.0 + - - +
239J ASP* 2.8 31.7 + - - -
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Residues in contact with ALA 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64J LYS 3.0 17.2 + - - +
65J ALA* 3.7 6.7 - - - +
66J ALA 3.2 0.2 - - - -
67J ARG* 1.3 76.2 - - - +
69J ALA* 1.3 63.4 + - - +
71J GLN* 3.2 27.2 + - - +
74J SER* 4.2 5.2 - - - -
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Residues in contact with ALA 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65J ALA 3.0 15.8 + - - +
66J ALA 3.6 4.0 - - - +
68J ALA* 1.3 76.3 - - - +
70J PHE* 1.3 55.9 + - - +
71J GLN 3.4 0.2 - - - -
74J SER* 2.8 26.6 + - - -
75J PRO* 6.4 0.2 - - - -
76J TRP* 3.8 14.4 - - + +
77J ARG* 4.3 0.3 - - - +
188J VAL* 4.3 6.7 - - + -
214J PRO* 5.8 1.1 - - + -
215J PRO 3.4 25.6 - - - +
216J GLY 3.7 14.1 - - - -
217J VAL* 3.9 7.2 - - + +
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Residues in contact with PHE 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66J ALA 3.0 14.1 + - - +
67J ARG* 3.7 30.3 - - - +
68J ALA 3.1 0.6 - - - -
69J ALA* 1.3 77.5 - - - +
71J GLN* 1.3 60.6 + - - +
76J TRP* 4.9 0.4 - + - -
77J ARG* 2.8 65.5 + - - +
158J PRO* 3.6 26.5 - - + -
159J VAL 4.7 2.2 - - - -
160J GLY* 3.6 28.7 - - - -
186J GLY 3.6 22.7 - - - -
187J ASN* 4.5 0.4 - - - -
188J VAL* 3.9 20.2 - - + -
487J LYS* 5.6 4.0 - - - -
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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