Contacts of the helix formed by residues 55 - 70 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B SER* 6.1 4.0 - - - +
35B LYS* 5.2 7.1 + - - -
53B GLU* 4.6 9.9 - - - +
54B GLY* 1.3 74.7 - - - +
56B LYS* 1.3 85.6 + - - +
57B GLU* 3.3 4.5 - - + +
58B ASP* 2.9 22.9 + - - +
59B VAL* 3.1 17.2 + - - +
227B THR* 3.3 33.0 - - - +
228B ALA* 4.5 7.6 - - - +
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP* 1.3 86.3 + - - +
57B GLU* 1.3 67.4 + - + +
59B VAL* 3.3 4.0 + - - +
60B ASP* 2.7 58.5 + - - +
227B THR 5.4 0.2 - - - +
231B ALA* 3.9 28.3 - - + +
235B HIS* 5.0 6.5 - - - -
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL* 3.4 34.9 - - + +
55B ASP* 3.3 3.1 - - + +
56B LYS* 1.3 88.3 - - + +
58B ASP* 1.3 62.4 + - - +
60B ASP* 3.5 8.1 + - - +
61B LYS* 3.2 27.8 + - - +
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Residues in contact with ASP 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.6 22.5 - - + +
24B ILE* 3.8 4.9 - - - +
30B ASP 4.1 1.7 - - - +
31B ALA* 3.4 8.8 - - - +
32B VAL* 2.9 38.8 + - - +
33B SER* 5.0 1.0 + - - -
53B GLU 4.0 0.3 - - - +
54B GLY* 3.4 8.5 - - - -
55B ASP* 2.9 34.4 + - - +
57B GLU* 1.3 76.9 - - - +
59B VAL* 1.3 64.1 + - - +
61B LYS* 3.3 14.2 + - - +
62B ALA* 3.0 21.7 + - - +
221B VAL* 4.3 7.6 - - + +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP 3.1 14.0 + - - +
56B LYS* 3.5 8.5 - - + +
58B ASP* 1.3 71.6 - - - +
60B ASP* 1.3 56.4 + - - +
62B ALA* 2.9 9.6 + - - +
63B VAL* 2.7 51.1 + - + +
190B VAL* 5.0 0.7 - - + -
221B VAL* 4.3 11.0 - - + -
228B ALA* 3.6 32.8 - - + +
231B ALA* 3.9 15.7 - - + +
232B ILE* 3.8 35.7 - - + +
235B HIS* 4.3 5.2 - - + -
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Residues in contact with ASP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LYS* 2.7 44.2 + - - +
57B GLU* 3.5 12.6 - - - +
58B ASP 3.2 0.2 - - - -
59B VAL* 1.3 78.1 - - - +
61B LYS* 1.3 61.3 + - + +
63B VAL* 3.4 1.2 + - - +
64B LYS* 3.0 58.4 + - - +
235B HIS* 3.2 27.2 + - - -
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.9 15.3 - - + +
29B HIS* 3.3 39.0 + - - +
30B ASP 4.7 4.6 + - - -
32B VAL* 3.9 26.8 - - + +
57B GLU 3.2 15.1 + - - +
58B ASP* 3.5 12.3 + - - +
59B VAL 3.2 0.2 - - - -
60B ASP* 1.3 77.8 - - + +
62B ALA* 1.3 63.3 + - - +
64B LYS* 3.4 9.0 + - - +
65B ALA* 3.1 23.7 + - - +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.8 15.0 - - + +
58B ASP 3.0 12.8 + - - +
59B VAL 2.9 8.2 + - - +
61B LYS* 1.3 74.7 - - - +
63B VAL* 1.3 61.1 + - - +
65B ALA* 3.2 3.3 + - - +
66B ALA* 2.9 28.9 + - - +
190B VAL* 3.6 19.3 - - + +
219B ASN* 4.0 12.8 + - + -
221B VAL* 3.8 23.1 - - + -
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B VAL* 2.7 32.4 + - + +
60B ASP 3.8 1.1 - - - +
62B ALA* 1.3 70.3 - - - +
64B LYS* 1.3 60.0 + - + +
66B ALA* 3.2 2.6 + - - +
67B ARG* 2.9 27.6 + - - +
161B VAL* 4.5 4.8 - - + +
190B VAL* 3.8 17.3 - - + -
235B HIS* 3.5 49.6 - - + +
237B ASP* 3.9 25.4 - - + +
238B VAL* 4.0 14.6 - - + -
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Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASP* 3.0 54.6 + - - +
61B LYS* 3.8 8.0 - - - +
63B VAL* 1.3 75.7 - - + +
65B ALA* 1.3 65.3 + - - +
67B ARG* 3.4 7.3 + - - +
68B ALA* 3.0 24.8 + - - +
235B HIS* 5.9 1.1 - - + +
237B ASP* 5.8 0.4 - - - -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.5 14.8 - - + -
25B ASN* 3.4 34.7 - - - +
61B LYS 3.1 17.5 + - - +
62B ALA 3.5 5.2 - - - +
64B LYS* 1.3 77.1 - - - +
66B ALA* 1.3 62.7 + - - +
68B ALA* 3.5 6.2 + - - +
69B ALA* 3.1 23.2 + - - +
216B GLY* 3.8 5.4 - - - -
219B ASN* 3.8 6.3 - - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ALA 2.9 13.1 + - - +
63B VAL 3.4 8.3 - - - +
65B ALA* 1.3 74.9 - - - +
67B ARG* 1.3 66.4 + - - +
69B ALA* 3.1 4.0 + - - +
70B PHE 2.9 18.4 + - - -
161B VAL* 4.1 7.9 - - + -
188B VAL* 3.4 28.0 - - + +
189B VAL 4.6 1.6 - - - +
190B VAL* 3.9 18.2 - - + -
216B GLY 3.4 12.1 + - - -
219B ASN* 3.9 7.2 - - - +
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Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B VAL 2.9 16.8 + - - +
64B LYS* 3.7 8.5 - - - +
66B ALA* 1.3 74.4 - - - +
68B ALA* 1.3 63.3 + - - +
70B PHE* 3.1 33.2 + - - -
71B GLN* 2.9 41.2 + - - +
161B VAL* 3.4 15.0 - - + +
237B ASP* 2.6 59.1 + - - +
239B ASP* 3.0 30.7 + - - -
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASN* 6.0 0.4 - - - +
64B LYS 3.0 17.7 + - - +
65B ALA* 3.7 7.2 - - - +
67B ARG* 1.3 77.7 - - - +
69B ALA* 1.3 63.4 + - - +
71B GLN* 3.2 27.5 + - - +
74B SER* 4.2 5.4 - - - -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ALA 3.1 12.9 + - - +
66B ALA 3.1 8.9 + - - +
68B ALA* 1.3 76.2 - - - +
70B PHE* 1.3 53.4 + - - +
74B SER* 2.6 27.3 + - - -
75B PRO* 6.3 0.2 - - - -
76B TRP* 3.8 13.4 + - + +
188B VAL* 4.1 7.4 - - + -
214B PRO* 5.9 0.9 - - + -
215B PRO 3.5 24.2 - - - +
216B GLY 3.6 15.7 - - - +
217B VAL* 3.9 6.5 - - + +
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ALA 2.9 13.9 + - - +
67B ARG* 3.6 28.9 - - - +
68B ALA 3.1 0.6 - - - -
69B ALA* 1.3 75.4 - - - +
71B GLN* 1.3 60.0 + - - +
77B ARG* 2.7 68.4 + - - +
158B PRO* 3.6 26.7 - - + -
159B VAL 4.8 2.0 - - - -
160B GLY* 3.5 28.9 - - - -
161B VAL* 5.2 0.4 - - + -
186B GLY 3.5 24.5 - - - -
187B ASN* 4.3 0.9 - - - -
188B VAL* 3.9 22.9 - - + -
487B LYS* 6.3 1.1 - - - -
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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