Contacts of the helix formed by residues 55 - 70 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A SER* 6.0 3.4 - - - +
53A GLU* 4.0 14.5 - - - +
54A GLY* 1.3 73.4 - - - +
56A LYS* 1.3 85.0 + - - +
57A GLU* 3.3 4.9 - - + +
58A ASP* 2.7 13.4 + - - +
59A VAL* 3.0 26.9 + - - +
227A THR* 3.7 34.4 - - - +
228A ALA* 4.5 6.1 - - - +
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASP* 1.3 88.3 + - - +
57A GLU* 1.3 61.8 + - + +
59A VAL* 3.3 2.6 + - - +
60A ASP* 2.9 29.6 + - + +
231A ALA* 3.8 26.3 - - + +
234A SER* 5.8 3.4 - - - -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL* 3.1 38.8 - - + +
55A ASP* 3.3 3.6 - - + +
56A LYS* 1.3 79.9 - - + +
58A ASP* 1.3 63.1 + - - +
60A ASP* 3.5 8.2 + - - +
61A LYS* 3.2 26.6 + - + +
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Residues in contact with ASP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 3.5 28.4 - - + +
24A ILE* 3.6 7.9 - - - +
30A ASP 4.3 1.2 - - - +
31A ALA* 3.4 12.0 - - - +
32A VAL* 2.9 35.3 + - - +
33A SER* 5.2 0.7 + - - -
53A GLU 3.9 0.5 - - - +
54A GLY* 3.2 6.3 - - - -
55A ASP* 2.7 33.1 + - - +
57A GLU* 1.3 74.4 + - - +
59A VAL* 1.3 66.1 + - - +
61A LYS* 3.1 14.5 + - - +
62A ALA* 3.0 18.7 + - - +
221A VAL* 4.2 6.9 - - + +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASP 3.0 15.8 + - - +
56A LYS 3.6 7.9 - - - +
58A ASP* 1.3 76.8 - - - +
60A ASP* 1.3 56.9 - - - +
62A ALA* 2.9 9.5 + - - +
63A VAL* 2.8 39.5 + - + +
190A VAL* 5.0 1.1 - - + -
221A VAL* 4.2 16.4 - - + -
228A ALA* 3.6 28.0 - - + +
231A ALA* 3.9 12.8 - - + +
232A ILE* 3.7 37.7 - - + +
235A HIS* 4.4 5.6 - - + -
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Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LYS* 2.9 20.3 + - + +
57A GLU* 3.6 9.8 - - - +
58A ASP 3.2 0.2 - - - -
59A VAL* 1.3 77.4 - - - +
61A LYS* 1.3 63.3 + - - +
63A VAL* 3.5 1.4 + - - +
64A LYS* 2.9 55.9 + - - +
235A HIS* 3.6 28.3 + - + +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.8 19.2 - - + +
29A HIS* 4.2 32.2 + - - +
30A ASP 4.5 6.9 + - - -
32A VAL* 4.0 26.1 - - + +
57A GLU 3.2 15.3 + - - +
58A ASP* 3.1 12.5 + - - +
60A ASP* 1.3 78.7 - - - +
62A ALA* 1.3 63.1 + - - +
64A LYS* 3.3 10.3 + - - +
65A ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.5 19.9 - - + +
58A ASP 3.0 11.4 + - - +
59A VAL 2.9 8.9 + - - +
61A LYS* 1.3 76.7 - - - +
63A VAL* 1.3 56.5 + - - +
65A ALA* 3.2 4.4 + - - +
66A ALA* 2.9 28.6 + - - +
190A VAL* 4.0 15.7 - - + -
219A ASN* 3.8 11.6 + - + -
221A VAL* 3.8 23.3 - - + -
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A VAL* 2.8 29.7 + - + +
60A ASP 4.0 0.7 - - - +
62A ALA* 1.3 72.3 - - - +
64A LYS* 1.3 57.4 + - + +
66A ALA* 3.4 1.4 + - - +
67A ARG* 2.9 27.7 + - - +
161A VAL* 4.4 4.6 - - + +
190A VAL* 3.9 21.5 - - + -
235A HIS* 3.7 39.9 - - + +
237A ASP* 3.8 26.2 - - + +
238A VAL* 3.6 23.6 - - + -
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASP* 2.9 49.4 + - - +
61A LYS* 3.5 9.2 - - - +
62A ALA 3.2 0.2 - - - -
63A VAL* 1.3 77.6 - - + +
65A ALA* 1.3 62.7 + - - +
67A ARG* 3.5 5.5 + - - +
68A ALA* 3.0 24.8 + - - +
235A HIS* 5.6 3.8 - - + +
237A ASP* 5.7 0.4 - - - -
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.6 21.3 - - + -
25A ASN* 3.4 35.6 - - - +
61A LYS 3.1 6.5 + - - +
62A ALA 3.5 8.5 - - - +
64A LYS* 1.3 77.7 - - - +
66A ALA* 1.3 59.8 + - - +
68A ALA* 3.3 7.4 + - - +
69A ALA* 3.0 24.1 + - - +
216A GLY* 4.0 4.7 - - - -
219A ASN* 3.9 7.4 - - - +
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA 2.9 16.1 + - - +
63A VAL 3.7 4.3 - - - +
65A ALA* 1.3 76.3 - - - +
67A ARG* 1.3 62.7 + - - +
69A ALA* 3.1 4.5 + - - +
70A PHE 3.0 17.0 + - - -
161A VAL* 4.1 7.0 - - + -
188A VAL* 3.4 28.5 - - + +
189A VAL 4.6 1.1 - - - +
190A VAL* 3.9 16.2 - - + -
216A GLY 3.4 11.6 + - - +
219A ASN* 3.7 11.9 - - - +
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Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A VAL 2.9 18.5 + - - +
64A LYS* 3.8 5.8 - - - +
66A ALA* 1.3 75.6 - - - +
68A ALA* 1.3 61.7 + - - +
70A PHE* 3.2 37.1 + - - -
71A GLN* 2.9 45.4 + - - +
161A VAL* 3.5 16.7 - - + +
237A ASP* 2.9 57.4 + - - +
239A ASP* 2.9 30.1 + - - -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LYS 3.0 17.7 + - - +
65A ALA* 3.6 7.9 - - - +
66A ALA 3.2 0.4 - - - -
67A ARG* 1.3 76.9 - - - +
69A ALA* 1.3 61.6 + - - +
71A GLN* 3.2 27.4 + - - +
74A SER* 4.3 4.9 - - - -
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA 3.0 11.9 + - - +
66A ALA 3.1 8.5 + - - +
68A ALA* 1.3 76.0 - - - +
70A PHE* 1.3 55.0 + - - +
71A GLN 3.4 0.2 - - - -
74A SER* 2.7 27.1 + - - -
75A PRO* 6.2 0.4 - - - -
76A TRP* 3.7 13.4 - - + +
77A ARG* 4.3 0.2 - - - +
188A VAL* 4.2 7.0 - - + -
214A PRO* 5.9 0.9 - - + -
215A PRO 3.4 25.6 - - - +
216A GLY 3.7 14.4 - - - +
217A VAL* 4.0 6.5 - - + +
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Residues in contact with PHE 70 (chain A).
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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66A ALA 3.0 14.4 + - - +
67A ARG* 3.2 31.4 + - - +
68A ALA 3.1 0.8 - - - -
69A ALA* 1.3 75.7 - - - +
71A GLN* 1.3 62.6 + - - +
77A ARG* 2.9 57.1 + - - -
158A PRO* 3.6 26.2 - - + -
159A VAL 4.8 1.3 - - - -
160A GLY* 3.5 30.7 - - - -
186A GLY 3.5 24.9 - - - -
187A ASN* 4.3 1.1 - - - -
188A VAL* 3.9 19.5 - - + -
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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