Contacts of the helix formed by residues 55 - 70 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I SER* 5.6 5.4 - - - +
35I LYS* 6.0 0.2 + - - -
53I GLU* 3.5 8.6 + - - +
54I GLY* 1.3 73.2 - - - +
56I LYS* 1.3 79.2 + - - +
57I GLU* 3.3 18.3 - - - +
58I ASP* 2.7 12.6 + - - +
59I VAL* 3.0 27.5 + - - +
227I THR* 3.2 33.8 - - - +
228I ALA* 4.5 5.2 - - - +
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Residues in contact with LYS 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ASP* 1.3 85.9 + - - +
57I GLU* 1.3 66.1 + - - +
59I VAL* 3.2 3.8 + - - +
60I ASP* 2.9 29.2 + - + +
227I THR 5.6 0.2 - - - +
231I ALA* 3.8 27.4 - - + +
234I SER* 5.1 11.6 + - - -
235I HIS* 6.6 0.2 - - - -
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Residues in contact with GLU 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I VAL* 3.9 31.0 - - + +
33I SER* 6.0 2.1 - - - -
55I ASP* 3.6 23.4 - - - +
56I LYS* 1.3 82.0 - - + +
58I ASP* 1.3 64.0 + - - +
60I ASP* 3.3 8.0 + - - +
61I LYS* 3.1 26.9 + - - +
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Residues in contact with ASP 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I ILE* 3.6 27.0 - - + +
24I ILE* 3.8 5.4 - - + +
30I ASP 4.2 1.2 - - - +
31I ALA* 3.4 7.2 - - - +
32I VAL* 2.8 41.4 + - - +
33I SER* 5.2 0.9 + - - -
53I GLU 4.2 0.3 - - - +
54I GLY* 3.5 3.4 - - - -
55I ASP* 2.7 35.5 + - - +
57I GLU* 1.3 75.1 - - - +
59I VAL* 1.3 67.0 + - - +
61I LYS* 3.2 15.1 + - + +
62I ALA* 3.0 21.5 + - - +
221I VAL* 4.3 7.4 - - + +
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Residues in contact with VAL 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I ASP 3.0 16.6 + - - +
56I LYS 3.6 7.6 - - - +
58I ASP* 1.3 73.9 - - - +
60I ASP* 1.3 59.7 + - - +
62I ALA* 3.1 7.8 + - - +
63I VAL* 2.8 39.4 + - + +
190I VAL* 4.7 2.2 - - + -
221I VAL* 4.0 22.2 - - + -
228I ALA* 3.7 22.9 - - + +
231I ALA* 4.0 11.7 - - + +
232I ILE* 3.7 37.7 - - + +
235I HIS* 4.8 3.1 - - + -
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Residues in contact with ASP 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I LYS* 2.9 15.6 + - + +
57I GLU* 3.6 11.4 - - - +
58I ASP 3.2 0.2 - - - -
59I VAL* 1.3 77.2 - - - +
61I LYS* 1.3 62.7 + - - +
63I VAL* 3.3 1.6 + - - +
64I LYS* 3.0 56.6 + - - +
235I HIS* 2.7 36.7 + - + +
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Residues in contact with LYS 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I ILE* 3.9 20.1 - - + +
29I HIS* 4.1 31.8 + - - +
30I ASP 4.7 4.8 + - - -
32I VAL* 4.0 25.0 - - + +
57I GLU 3.1 20.2 + - - +
58I ASP* 3.2 12.1 + - - +
60I ASP* 1.3 75.2 - - + +
62I ALA* 1.3 62.9 + - - +
64I LYS* 3.4 9.1 + - - +
65I ALA* 3.0 23.2 + - - +
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Residues in contact with ALA 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I ILE* 3.8 18.5 - - + +
58I ASP 3.0 13.0 + - - +
59I VAL 3.1 8.3 + - - +
61I LYS* 1.3 78.2 - - - +
63I VAL* 1.3 56.6 + - - +
65I ALA* 3.2 5.3 + - - +
66I ALA* 2.9 29.1 + - - +
190I VAL* 3.7 22.9 - - + +
219I ASN* 3.9 11.2 + - + -
221I VAL* 3.9 15.9 - - + -
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Residues in contact with VAL 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I VAL* 2.8 28.1 + - + +
60I ASP 3.3 4.0 + - - +
62I ALA* 1.3 76.8 - - - +
64I LYS* 1.3 57.3 + - + +
66I ALA* 3.2 2.1 + - - +
67I ARG* 2.8 27.5 + - - +
161I VAL* 4.2 5.4 - - + -
190I VAL* 3.9 17.0 - - + -
235I HIS* 3.7 38.1 - - + +
237I ASP* 3.9 25.6 - - + +
238I VAL* 3.8 22.9 - - + -
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Residues in contact with LYS 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60I ASP* 3.0 46.9 + - - +
61I LYS* 3.7 8.5 - - - +
62I ALA 3.3 0.2 - - - -
63I VAL* 1.3 75.9 - - + +
65I ALA* 1.3 57.8 + - - +
67I ARG* 3.4 6.0 + - - +
68I ALA* 2.9 30.8 + - - +
235I HIS* 5.2 5.5 - - + +
237I ASP* 5.6 3.4 - - - +
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Residues in contact with ALA 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I ILE* 3.6 16.2 - - + -
25I ASN* 3.5 35.2 - - - +
61I LYS 3.0 13.5 + - - +
62I ALA 3.4 8.7 - - - +
64I LYS* 1.3 77.2 - - - +
66I ALA* 1.3 61.9 + - - +
68I ALA* 3.4 6.3 + - - +
69I ALA* 3.1 23.0 + - - +
216I GLY* 3.9 4.5 - - - -
219I ASN* 3.7 7.2 - - - +
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Residues in contact with ALA 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I ALA 2.9 16.1 + - - +
63I VAL 3.7 3.8 - - - +
65I ALA* 1.3 74.5 - - - +
67I ARG* 1.3 64.6 + - - +
69I ALA* 3.1 4.0 + - - +
70I PHE* 3.0 23.4 + - - +
161I VAL* 4.2 5.6 - - + -
188I VAL* 3.6 24.6 - - + +
189I VAL 4.5 0.7 - - - +
190I VAL* 3.9 13.2 - - + -
216I GLY 3.4 12.7 + - - +
219I ASN* 3.6 14.1 - - - +
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Residues in contact with ARG 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I VAL 2.8 20.3 + - - +
64I LYS* 3.8 7.2 - - - +
66I ALA* 1.3 72.8 - - - +
68I ALA* 1.3 63.0 + - - +
70I PHE* 3.1 35.2 + - - +
71I GLN* 3.1 42.5 + - - +
161I VAL* 3.4 18.7 - - + +
237I ASP* 2.7 58.7 + - - +
239I ASP* 3.1 32.3 + - - -
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Residues in contact with ALA 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I ASN* 6.0 0.7 - - - +
64I LYS 2.9 17.2 + - - +
65I ALA* 3.6 7.6 - - - +
67I ARG* 1.3 77.1 - - - +
69I ALA* 1.3 56.6 - - - +
71I GLN* 3.0 32.9 + - - +
74I SER* 4.4 4.2 - - - -
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Residues in contact with ALA 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I ALA 3.1 12.6 + - - +
66I ALA 3.1 8.5 + - - +
68I ALA* 1.3 75.5 - - - +
70I PHE* 1.3 56.7 + - - +
71I GLN 3.4 0.2 - - - -
74I SER* 2.9 24.1 + - - -
75I PRO* 6.3 0.4 - - - -
76I TRP* 3.7 14.3 - - + +
188I VAL* 4.2 6.5 - - + -
214I PRO* 5.9 1.1 - - + -
215I PRO 3.5 24.7 - - - +
216I GLY 3.7 13.9 - - - +
217I VAL* 4.0 6.7 - - + +
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Residues in contact with PHE 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I ALA 3.0 14.8 + - - +
67I ARG* 3.6 29.4 - - - +
68I ALA 3.1 0.6 - - - -
69I ALA* 1.3 77.2 - - - +
71I GLN* 1.3 61.6 + - - +
76I TRP* 4.9 0.4 - + - -
77I ARG* 2.8 68.0 + - - +
158I PRO* 3.6 35.4 - - + -
159I VAL 4.8 1.3 - - - -
160I GLY* 3.5 30.3 - - - -
186I GLY 3.6 14.1 - - - -
187I ASN* 4.5 0.9 - - - -
188I VAL* 4.0 18.8 - - + -
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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