Contacts of the helix formed by residues 55 - 70 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H SER* 5.9 5.2 - - - +
35H LYS* 5.4 6.1 + - - -
53H GLU* 4.7 9.3 - - - +
54H GLY* 1.3 73.5 - - - +
56H LYS* 1.3 86.9 + - - +
57H GLU* 3.2 4.3 - - + +
58H ASP* 2.7 23.8 + - - +
59H VAL* 3.1 16.9 + - - +
227H THR* 3.9 29.3 - - - +
228H ALA* 4.5 6.3 - - - +
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Residues in contact with LYS 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ASP* 1.3 87.8 + - - +
57H GLU* 1.3 61.1 + - + +
59H VAL* 3.3 2.8 + - - +
60H ASP* 3.0 43.2 + - - +
227H THR 4.7 1.9 + - - +
231H ALA* 3.8 29.0 - - + +
235H HIS* 6.4 0.4 - - - -
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Residues in contact with GLU 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H VAL* 3.4 37.0 - - + +
55H ASP* 3.1 3.5 + - + +
56H LYS* 1.3 80.5 - - + +
58H ASP* 1.3 63.9 + - - +
60H ASP* 3.3 14.7 + - - +
61H LYS* 3.2 24.8 + - + +
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Residues in contact with ASP 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H ILE* 4.6 12.3 - - + +
24H ILE* 3.7 7.6 - - - +
30H ASP 4.1 2.3 - - - +
31H ALA* 3.2 15.1 - - - +
32H VAL* 2.9 34.9 + - - +
33H SER 5.4 0.5 + - - -
54H GLY* 3.4 8.4 - - - -
55H ASP* 2.7 35.3 + - - +
57H GLU* 1.3 74.2 + - - +
59H VAL* 1.3 66.9 + - - +
61H LYS* 3.2 15.3 + - - +
62H ALA* 3.0 18.2 + - - +
221H VAL* 4.1 15.6 - - + +
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Residues in contact with VAL 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ASP 3.1 11.5 + - - +
56H LYS 3.6 7.9 - - - +
58H ASP* 1.3 76.7 - - - +
60H ASP* 1.3 57.5 + - - +
62H ALA* 3.0 7.4 + - - +
63H VAL* 2.8 42.3 + - + +
190H VAL* 4.8 1.6 - - + -
221H VAL* 4.0 19.7 - - + -
228H ALA* 3.8 24.7 - - + +
231H ALA* 4.0 13.7 - - + +
232H ILE* 3.7 36.6 - - + +
235H HIS* 4.5 4.9 - - + -
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Residues in contact with ASP 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H LYS* 3.0 36.1 + - - +
57H GLU* 3.4 18.3 - - - +
58H ASP 3.2 0.2 - - - -
59H VAL* 1.3 76.6 - - - +
61H LYS* 1.3 62.4 + - + +
63H VAL* 3.5 1.6 + - - +
64H LYS* 3.0 34.6 + - + +
235H HIS* 3.2 32.4 + - - +
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Residues in contact with LYS 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H ILE* 3.7 18.2 - - + +
29H HIS* 3.9 34.8 + - - +
30H ASP 4.6 5.1 + - - -
32H VAL* 4.1 25.4 - - + +
57H GLU 3.2 15.2 + - - +
58H ASP* 3.2 13.0 + - - +
60H ASP* 1.3 79.3 - - + +
62H ALA* 1.3 58.0 + - - +
64H LYS* 3.4 8.7 + - - +
65H ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H ILE* 3.4 18.8 - - + +
58H ASP 3.0 12.2 + - - +
59H VAL 3.0 8.5 + - - +
61H LYS* 1.3 75.5 - - - +
63H VAL* 1.3 59.2 + - - +
65H ALA* 3.1 3.9 + - - +
66H ALA* 2.9 29.5 + - - +
190H VAL* 3.8 24.4 - - + +
219H ASN* 3.8 13.2 + - + -
221H VAL* 3.9 12.1 - - + -
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Residues in contact with VAL 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H VAL* 2.8 31.3 + - + +
60H ASP 3.9 0.7 - - - +
62H ALA* 1.3 71.4 - - - +
64H LYS* 1.3 58.7 + - + +
66H ALA* 3.3 2.2 + - - +
67H ARG* 2.9 27.9 + - - +
161H VAL* 4.5 3.8 - - + -
190H VAL* 3.8 17.7 - - + -
235H HIS* 3.5 46.0 - - + +
237H ASP* 3.9 26.0 - - + +
238H VAL* 3.8 19.3 - - + -
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Residues in contact with LYS 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H ASP* 3.0 25.9 + - + +
61H LYS* 3.8 7.6 - - - +
63H VAL* 1.3 75.0 - - + +
65H ALA* 1.3 65.1 + - - +
67H ARG* 3.9 6.8 - - - +
68H ALA* 3.1 23.7 + - - +
235H HIS* 5.8 3.8 - - + +
237H ASP* 5.7 0.7 - - - -
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Residues in contact with ALA 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H ILE* 3.6 15.5 - - + -
25H ASN* 3.6 33.7 - - - +
61H LYS 3.0 14.3 + - - +
62H ALA 3.5 7.6 - - - +
64H LYS* 1.3 73.9 - - - +
66H ALA* 1.3 64.4 + - - +
68H ALA* 3.3 6.2 + - - +
69H ALA* 3.0 23.2 + - - +
216H GLY* 3.9 4.7 - - - -
219H ASN* 3.9 6.7 - - - +
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Residues in contact with ALA 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62H ALA 2.9 16.1 + - - +
63H VAL 3.6 4.7 - - - +
65H ALA* 1.3 78.0 - - - +
67H ARG* 1.3 62.4 + - - +
69H ALA* 3.1 3.8 + - - +
70H PHE 3.1 17.2 + - - -
161H VAL* 4.0 6.5 - - + -
188H VAL* 3.4 30.2 - - + +
189H VAL 4.6 1.3 - - - +
190H VAL* 3.8 14.1 - - + -
216H GLY 3.3 12.9 + - - +
219H ASN* 3.7 12.1 - - - +
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Residues in contact with ARG 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H VAL 2.9 18.3 + - - +
64H LYS* 3.9 6.5 - - - +
65H ALA 3.4 0.2 - - - -
66H ALA* 1.3 75.3 - - - +
68H ALA* 1.3 63.3 + - - +
70H PHE* 3.1 34.3 + - - -
71H GLN* 2.8 43.5 + - - +
161H VAL* 3.5 16.0 - - + +
237H ASP* 2.8 54.2 + - - +
239H ASP* 2.8 35.5 + - - -
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Residues in contact with ALA 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H LYS 3.1 19.1 + - - +
65H ALA* 3.7 6.1 - - - +
66H ALA 3.2 0.2 - - - -
67H ARG* 1.3 76.7 - - - +
69H ALA* 1.3 63.3 + - - +
70H PHE 3.1 0.7 + - - -
71H GLN* 3.2 26.5 + - + +
74H SER* 4.3 4.9 - - - -
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Residues in contact with ALA 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H ALA 3.0 8.0 + - - +
66H ALA 3.1 8.5 + - - +
68H ALA* 1.3 76.7 - - - +
70H PHE* 1.3 54.5 + - - +
74H SER* 2.8 27.5 + - - -
75H PRO* 6.3 0.4 - - - -
76H TRP* 3.8 12.7 - - + +
188H VAL* 4.2 7.9 - - + -
214H PRO* 5.8 1.3 - - + -
215H PRO 3.5 24.5 - - - +
216H GLY 3.6 19.1 - - - +
217H VAL* 3.9 7.9 - - + +
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Residues in contact with PHE 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H ALA 3.1 13.9 + - - +
67H ARG* 3.7 29.2 - - - +
68H ALA 3.1 0.8 - - - -
69H ALA* 1.3 76.9 - - - +
71H GLN* 1.3 61.4 + - - +
76H TRP* 4.9 0.4 - + - -
77H ARG* 2.9 64.4 + - - +
158H PRO* 3.5 29.2 - - + -
159H VAL 4.7 2.5 - - - -
160H GLY* 3.6 29.6 - - - -
161H VAL* 5.1 0.7 - - + -
186H GLY 3.5 23.6 - - - -
187H ASN* 4.4 0.4 - - - -
188H VAL* 4.0 19.5 - - + -
487H LYS* 5.9 2.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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