Contacts of the helix formed by residues 55 - 70 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D SER* 5.9 4.9 - - - +
35D LYS* 5.9 1.0 + - - -
53D GLU* 4.7 9.8 - - - +
54D GLY* 1.3 74.6 - - - +
56D LYS* 1.3 84.6 + - - +
57D GLU* 3.3 4.3 - - + +
58D ASP* 2.8 23.0 + - - +
59D VAL* 3.0 18.3 + - - +
227D THR* 3.8 31.2 - - - +
228D ALA* 4.6 7.0 - - - +
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Residues in contact with LYS 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ASP* 1.3 85.5 + - - +
57D GLU* 1.3 61.4 + - + +
59D VAL* 3.2 4.0 + - - +
60D ASP* 2.9 29.2 + - + +
227D THR 4.8 1.7 + - - +
231D ALA* 3.8 27.2 - - + +
234D SER* 6.0 1.8 - - - -
235D HIS* 5.8 1.2 - - + -
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 3.4 34.5 - - + +
55D ASP* 3.3 3.5 - - + +
56D LYS* 1.3 81.0 - - + +
58D ASP* 1.3 62.1 - - - +
60D ASP* 3.5 8.6 + - - +
61D LYS* 3.2 28.1 + - + +
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Residues in contact with ASP 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 4.5 11.6 - - + +
24D ILE* 3.9 5.6 - - + +
30D ASP 4.1 2.6 - - - +
31D ALA* 3.4 12.4 - - - +
32D VAL* 2.9 38.0 + - - +
33D SER* 5.2 0.7 + - - -
53D GLU 4.1 0.3 - - - +
54D GLY* 3.4 13.4 - - - -
55D ASP* 2.8 35.6 + - - +
57D GLU* 1.3 75.3 - - - +
59D VAL* 1.3 66.4 + - - +
61D LYS* 3.2 14.9 + - - +
62D ALA* 3.0 20.8 + - - +
221D VAL* 4.2 10.6 - - + +
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Residues in contact with VAL 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ASP 3.0 16.2 + - - +
56D LYS 3.4 8.1 - - - +
58D ASP* 1.3 76.7 - - - +
60D ASP* 1.3 56.8 + - - +
62D ALA* 3.1 8.3 + - - +
63D VAL* 2.8 46.7 + - + +
190D VAL* 4.8 1.1 - - + -
221D VAL* 4.1 15.7 - - + -
228D ALA* 3.7 27.8 - - + +
231D ALA* 3.8 14.6 - - + +
232D ILE* 3.7 35.4 - - + +
235D HIS* 4.6 4.0 - - + -
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Residues in contact with ASP 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LYS* 2.9 19.0 + - + +
57D GLU* 3.6 9.9 - - - +
58D ASP 3.2 0.2 - - - -
59D VAL* 1.3 77.2 - - - +
61D LYS* 1.3 61.3 + - - +
63D VAL* 3.5 1.0 + - - +
64D LYS* 3.0 58.9 + - - +
235D HIS* 2.8 37.4 + - + +
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Residues in contact with LYS 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 6.1 0.2 - - - +
24D ILE* 3.9 20.7 - - + +
29D HIS* 3.8 33.1 + - - +
30D ASP 4.6 5.7 + - - -
32D VAL* 3.9 26.4 - - + +
57D GLU* 3.2 15.2 + - + +
58D ASP* 3.2 13.9 + - - +
59D VAL 3.2 0.4 - - - -
60D ASP* 1.3 77.6 - - + +
62D ALA* 1.3 58.2 + - - +
64D LYS* 3.4 10.5 + - + +
65D ALA* 3.0 28.1 + - - +
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 3.9 15.7 - - + +
58D ASP 3.0 13.1 + - - +
59D VAL 3.1 8.3 + - - +
61D LYS* 1.3 74.9 - - - +
63D VAL* 1.3 59.1 + - - +
65D ALA* 3.2 4.4 + - - +
66D ALA* 2.9 24.6 + - - +
190D VAL* 3.9 16.2 - - + -
219D ASN* 3.4 20.5 + - + -
221D VAL* 3.8 21.8 - - + -
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Residues in contact with VAL 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D VAL* 2.8 30.5 + - + +
60D ASP 3.8 4.5 - - - +
62D ALA* 1.3 75.5 - - - +
64D LYS* 1.3 59.8 + - + +
66D ALA* 3.3 1.9 + - - +
67D ARG* 2.9 28.2 + - - +
161D VAL* 4.5 4.6 - - + +
190D VAL* 3.9 18.2 - - + -
235D HIS* 3.6 43.7 - - + +
237D ASP* 3.8 27.4 - - + +
238D VAL* 4.0 14.4 - - + -
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Residues in contact with LYS 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ASP* 3.0 48.7 + - - +
61D LYS* 3.7 8.5 - - + +
63D VAL* 1.3 77.0 - - + +
65D ALA* 1.3 62.5 + - - +
67D ARG* 3.4 7.7 + - - +
68D ALA* 3.0 24.3 + - - +
235D HIS* 5.9 1.7 - - + +
237D ASP* 5.6 0.4 - - - -
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 3.7 20.2 - - + -
25D ASN* 3.6 29.0 - - - +
61D LYS 3.0 13.9 + - - +
62D ALA 3.2 7.8 + - - +
64D LYS* 1.3 76.3 - - - +
66D ALA* 1.3 62.8 + - - +
68D ALA* 3.2 8.0 + - - +
69D ALA* 3.0 23.6 + - - +
216D GLY* 4.0 4.1 - - - -
219D ASN* 3.8 8.1 - - - +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ALA 2.9 16.4 + - - +
63D VAL 3.6 5.2 - - - +
64D LYS 3.3 0.2 - - - -
65D ALA* 1.3 75.9 - - - +
67D ARG* 1.3 61.6 + - - +
69D ALA* 3.2 4.0 + - - +
70D PHE 3.1 17.3 + - - -
161D VAL* 3.9 7.4 - - + -
188D VAL* 3.4 29.2 - - + +
189D VAL 4.6 1.6 - - - +
190D VAL* 3.9 15.5 - - + -
216D GLY 3.3 13.2 - - - +
219D ASN* 3.6 11.1 - - - +
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Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D VAL 2.9 17.9 + - - +
64D LYS* 3.6 7.6 - - - +
65D ALA 3.3 0.2 - - - -
66D ALA* 1.3 76.0 - - - +
68D ALA* 1.3 63.5 + - - +
70D PHE* 3.2 33.0 + - - +
71D GLN* 2.9 44.9 + - - +
161D VAL* 3.5 15.2 - - + +
237D ASP* 2.8 58.2 + - - +
239D ASP* 2.9 28.9 + - - -
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Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ASN* 6.1 0.4 - - - +
64D LYS 3.0 14.5 + - - +
65D ALA* 3.2 10.5 + - - +
67D ARG* 1.3 76.7 - - - +
69D ALA* 1.3 61.4 + - - +
70D PHE 3.1 1.4 + - - -
71D GLN* 3.2 25.9 + - - +
74D SER* 4.3 5.4 - - - -
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Residues in contact with ALA 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ALA 3.0 14.8 + - - +
66D ALA 3.2 4.7 + - - +
68D ALA* 1.3 76.0 - - - +
70D PHE* 1.3 56.2 + - - +
71D GLN 3.5 0.4 - - - -
74D SER* 2.9 21.9 + - - -
76D TRP* 3.6 16.7 - - + +
188D VAL* 4.0 6.1 - - + -
214D PRO* 5.8 1.3 - - + -
215D PRO 3.3 25.6 - - - +
216D GLY 3.6 15.0 - - - +
217D VAL* 4.0 7.0 - - + +
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Residues in contact with PHE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ALA 3.1 14.1 + - - +
67D ARG* 3.7 28.5 - - - +
68D ALA 3.1 1.2 - - - -
69D ALA* 1.3 77.8 - - - +
71D GLN* 1.3 58.8 + - - +
76D TRP* 4.9 0.7 - + - -
77D ARG* 2.7 72.8 + - - +
158D PRO* 3.7 26.2 - - + -
159D VAL 4.7 1.8 - - - -
160D GLY* 3.7 28.0 - - - -
161D VAL* 5.2 0.7 - - + -
186D GLY 3.6 20.2 - - - -
187D ASN* 4.6 0.2 - - - -
188D VAL* 3.8 19.7 - - + -
487D LYS* 6.1 2.0 - - - -
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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