Contacts of the helix formed by residues 55 - 70 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K SER* 5.7 5.2 - - - +
35K LYS* 5.2 6.1 + - - +
53K GLU* 4.5 12.1 - - - +
54K GLY* 1.3 73.9 - - - -
56K LYS* 1.3 83.5 + - - +
57K GLU* 3.3 4.7 - - + +
58K ASP* 2.9 14.7 + - - +
59K VAL* 3.0 27.2 + - - +
227K THR* 3.6 31.7 - - - +
228K ALA* 4.5 5.4 - - - +
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Residues in contact with LYS 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K ASP* 1.3 86.2 + - - +
57K GLU* 1.3 61.9 + - + +
59K VAL* 3.3 3.6 + - - +
60K ASP* 2.9 28.9 + - + +
227K THR 4.8 0.9 + - - +
231K ALA* 3.9 26.9 - - + +
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Residues in contact with GLU 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K VAL* 3.4 37.8 - - + +
55K ASP* 3.3 1.9 - - + +
56K LYS* 1.3 78.5 - - + +
58K ASP* 1.3 66.8 + - - +
60K ASP* 3.5 7.9 + - - +
61K LYS* 3.2 27.5 + - - +
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Residues in contact with ASP 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K ILE* 3.3 29.0 - - + +
24K ILE* 3.6 9.1 - - + +
30K ASP 4.0 2.1 - - - +
31K ALA* 3.2 9.4 - - - +
32K VAL* 2.9 38.4 + - - +
33K SER* 5.0 1.7 + - - -
53K GLU 4.2 0.2 - - - +
54K GLY* 3.6 4.1 - - - -
55K ASP* 2.9 32.4 + - - +
57K GLU* 1.3 75.6 + - - +
59K VAL* 1.3 66.4 + - - +
61K LYS* 3.3 13.6 + - - +
62K ALA* 3.1 18.4 + - - +
221K VAL* 4.2 5.8 - - + +
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Residues in contact with VAL 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K ASP 3.0 15.5 + - - +
56K LYS 3.5 7.6 - - - +
58K ASP* 1.3 75.3 - - - +
60K ASP* 1.3 61.2 + - - +
62K ALA* 3.1 7.8 + - - +
63K VAL* 2.9 41.3 + - + +
190K VAL* 4.8 2.2 - - + -
221K VAL* 4.1 17.9 - - + -
228K ALA* 3.7 27.4 - - + +
231K ALA* 3.9 13.2 - - + +
232K ILE* 3.9 33.0 - - + +
235K HIS* 4.5 5.2 - - + -
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Residues in contact with ASP 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K LYS* 2.9 17.9 + - + +
57K GLU* 3.7 9.9 - - - +
58K ASP 3.3 0.4 - - - -
59K VAL* 1.3 78.4 - - - +
61K LYS* 1.3 56.7 + - + +
63K VAL* 3.9 0.9 - - - +
64K LYS* 3.0 61.0 + - - +
235K HIS* 2.8 37.3 + - + +
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Residues in contact with LYS 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K ILE* 3.8 18.6 - - + +
29K HIS* 4.7 24.6 + - - +
30K ASP 5.2 4.0 + - - -
32K VAL* 4.0 24.8 - - + +
57K GLU 3.2 17.5 + - - +
58K ASP* 3.6 11.5 + - - +
59K VAL 3.2 0.4 - - - -
60K ASP* 1.3 77.0 - - + +
62K ALA* 1.3 57.9 + - - +
64K LYS* 3.6 10.3 + - + +
65K ALA* 3.1 27.2 + - - +
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Residues in contact with ALA 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K ILE* 3.6 15.4 - - + +
58K ASP 3.1 12.3 + - - +
59K VAL 3.1 8.4 + - - +
61K LYS* 1.3 75.3 - - - +
63K VAL* 1.3 59.8 + - - +
65K ALA* 3.2 2.1 + - - +
66K ALA* 2.9 24.9 + - - +
190K VAL* 3.8 22.4 - - + -
219K ASN* 3.4 21.6 + - + -
221K VAL* 3.8 15.7 - - + -
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Residues in contact with VAL 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K VAL* 2.9 27.6 + - + +
60K ASP 3.9 0.9 - - - +
62K ALA* 1.3 74.8 - - - +
64K LYS* 1.3 59.7 + - + +
66K ALA* 3.2 1.9 + - - +
67K ARG* 2.8 27.9 + - - +
161K VAL* 4.4 5.3 - - + +
190K VAL* 3.9 18.2 - - + -
232K ILE* 5.9 0.2 - - - -
235K HIS* 3.6 43.7 - - + +
237K ASP* 3.8 27.1 - - + +
238K VAL* 3.9 17.3 - - + -
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Residues in contact with LYS 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60K ASP* 3.0 50.0 + - - +
61K LYS* 3.8 9.2 - - + +
62K ALA 3.3 0.2 - - - -
63K VAL* 1.3 78.9 - - + +
65K ALA* 1.3 60.6 + - - +
67K ARG* 3.8 6.2 - - - +
68K ALA* 3.1 24.1 + - - +
235K HIS* 5.5 2.8 + - + +
237K ASP* 5.6 0.4 - - - -
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Residues in contact with ALA 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K ILE* 3.6 14.6 - - + -
25K ASN* 3.3 34.5 - - - +
61K LYS 3.1 17.1 + - - +
62K ALA 3.2 4.9 + - - +
64K LYS* 1.3 75.2 - - - +
66K ALA* 1.3 62.7 + - - +
68K ALA* 3.3 7.0 + - - +
69K ALA* 3.0 23.7 + - - +
216K GLY* 3.9 3.6 - - - -
219K ASN* 3.9 6.5 - - - +
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Residues in contact with ALA 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62K ALA 2.9 16.0 + - - +
63K VAL 3.2 4.9 + - - +
65K ALA* 1.3 75.1 - - - +
67K ARG* 1.3 65.2 + - - +
69K ALA* 3.2 3.6 + - - +
70K PHE 3.0 17.8 + - - -
161K VAL* 4.0 15.5 - - + -
188K VAL* 3.5 29.1 - - + +
189K VAL 4.6 1.6 - - - +
190K VAL* 4.0 6.1 - - + -
216K GLY 3.4 12.3 - - - +
219K ASN* 3.6 11.6 - - - +
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Residues in contact with ARG 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63K VAL 2.8 19.6 + - - +
64K LYS* 3.8 7.2 - - - +
65K ALA 3.4 0.2 - - - -
66K ALA* 1.3 72.7 - - - +
68K ALA* 1.3 62.2 + - - +
70K PHE* 3.1 36.0 + - - -
71K GLN* 3.0 46.2 + - - +
161K VAL* 3.6 13.6 - - + +
237K ASP* 2.8 52.9 + - - +
239K ASP* 2.7 34.7 + - - -
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Residues in contact with ALA 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K ASN* 6.0 0.7 - - - +
64K LYS 3.1 17.5 + - - +
65K ALA* 3.5 8.1 - - - +
66K ALA 3.2 0.2 - - - -
67K ARG* 1.3 78.6 - - - +
69K ALA* 1.3 61.1 + - - +
71K GLN* 3.1 27.9 + - - +
74K SER* 4.3 4.9 - - - -
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Residues in contact with ALA 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65K ALA 3.0 14.7 + - - +
66K ALA 3.2 3.8 + - - +
68K ALA* 1.3 75.6 - - - +
70K PHE* 1.3 56.8 + - - +
71K GLN 3.4 0.2 - - - -
74K SER* 2.8 23.1 + - - -
75K PRO* 6.3 0.4 - - - -
76K TRP* 3.8 15.2 - - + +
77K ARG* 4.2 0.3 - - - +
188K VAL* 4.3 6.5 - - + -
214K PRO* 5.7 1.3 - - + -
215K PRO 3.3 26.5 - - - +
216K GLY 3.7 14.4 - - - +
217K VAL* 4.0 7.6 - - + +
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Residues in contact with PHE 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K ALA 3.0 14.4 + - - +
67K ARG* 3.1 31.2 + - - +
68K ALA 3.1 0.6 - - - -
69K ALA* 1.3 76.6 - - - +
71K GLN* 1.3 57.7 + - - +
76K TRP* 5.1 0.4 - + - -
77K ARG* 2.7 67.8 + - - +
158K PRO* 3.7 30.3 - - + -
159K VAL 4.8 1.6 - - - -
160K GLY* 3.5 34.8 - - - -
161K VAL* 5.1 0.2 - - + -
186K GLY 3.7 12.6 - - - -
188K VAL* 3.9 18.6 - - + -
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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