Contacts of the strand formed by residues 27 - 36 (chain F) in PDB entry 1M06
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 ARG 27 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24F MET* 3.7 13.7 - - + +
25F LEU 2.6 16.3 + - - +
26F GLY* 1.3 76.5 - - - +
28F LEU* 1.3 60.1 + - - +
29F LYS* 3.6 4.5 + - - +
153F ASN* 4.9 1.6 + - - +
155F ASP* 3.5 30.3 + - - +
156F ASP* 3.4 19.8 + - - +
159F TYR* 3.4 34.9 - - + +
160F GLY 3.0 17.6 + - - +
161F PHE 3.0 13.5 - - - +
162F ARG* 3.2 33.0 - - + +
288F ALA 4.2 2.1 - - - +
289F LEU* 3.7 8.5 - - - +
390F VAL 4.5 3.8 + - - +
392F HIS* 2.9 37.5 + - + +
393F GLN* 5.1 1.6 + - - +
407F TRP* 4.8 4.0 + - - -
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Residues in contact with LEU 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F GLY 3.9 1.6 + - - -
27F ARG* 1.3 68.7 - - - +
29F LYS* 1.3 59.2 + - - +
68F PHE* 4.7 1.8 - - + -
128F TYR* 2.5 42.5 + - + +
131F ILE* 4.7 3.1 - - + -
132F TYR* 4.7 7.4 - - + -
136F PHE* 3.5 54.3 - - + -
159F TYR 4.2 0.9 - - - -
160F GLY* 3.4 5.9 - - - -
161F PHE 2.9 9.0 + - - +
163F CYS* 3.6 16.6 - - - -
287F LEU* 3.7 33.7 - - + -
288F ALA 3.3 22.4 - - - +
289F LEU* 4.0 6.3 - - + +
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Residues in contact with LYS 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ASP* 2.8 42.0 + - - +
22F CYS 3.7 16.6 - - - +
23F GLY* 4.9 2.2 - - - -
27F ARG 3.6 2.5 + - - +
28F LEU* 1.3 73.9 - - - +
30F THR* 1.3 74.8 + - - +
31F VAL* 3.7 1.8 - - + +
108F GLY* 3.3 31.2 + - - +
109F TYR* 4.5 2.5 - - - +
111F GLY* 4.0 8.3 - - - -
158F ARG 4.5 8.7 - - - +
159F TYR* 3.9 15.3 - - - +
160F GLY* 5.0 0.2 - - - -
287F LEU* 3.1 5.4 - - - +
288F ALA 2.7 39.5 + - - +
407F TRP* 4.4 19.1 - - + -
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Residues in contact with THR 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ASP* 3.4 0.2 - - - +
28F LEU 4.3 0.2 + - - -
29F LYS* 1.3 100.2 + - - +
31F VAL* 1.3 62.6 + - - +
32F SER 3.9 16.6 - - - +
33F TRP* 4.5 2.9 - - + -
109F TYR 2.5 25.5 + - - -
110F VAL* 3.5 10.5 - - - +
111F GLY* 3.4 12.2 - - - +
128F TYR* 3.8 1.4 - - - -
285F MET* 3.3 34.5 - - + +
286F THR 3.7 10.5 - - - +
287F LEU* 3.7 13.7 - - + +
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Residues in contact with VAL 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ALA* 4.1 12.7 - - + +
21F ASP* 3.5 22.1 - - + +
29F LYS 3.7 11.2 - - - +
30F THR* 1.3 78.0 - - - +
32F SER* 1.3 61.4 + - - +
67F PHE* 4.8 3.1 - - + -
111F GLY* 5.6 3.6 - - - -
286F THR* 2.7 15.7 + - + +
287F LEU 4.1 1.1 - - - -
288F ALA* 3.7 26.7 - - + +
407F TRP* 5.3 3.8 - - + -
409F LYS* 2.8 42.0 - - - +
413F TYR* 3.4 9.4 - - + +
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Residues in contact with SER 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F HIS* 3.0 32.3 + - - -
19F ALA* 5.3 0.9 - - - -
30F THR* 3.7 3.9 - - - +
31F VAL* 1.3 82.1 - - - +
33F TRP* 1.3 67.9 + - - +
34F THR* 4.6 2.5 + - - -
111F GLY* 5.7 1.1 - - - -
284F MET 3.8 1.6 - - - +
285F MET* 3.7 0.3 - - - -
286F THR* 2.9 32.3 + - - -
413F TYR* 3.7 28.7 - - - -
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Residues in contact with TRP 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F HIS* 5.6 0.9 + - - -
30F THR* 4.5 6.1 - - + -
32F SER* 1.3 78.9 + - - +
34F THR* 1.3 67.0 + - - +
35F PRO* 3.7 27.8 - - + +
110F VAL 3.7 19.8 + - - -
111F GLY 3.5 21.2 + - - -
112F THR* 4.3 10.3 - - - -
121F PRO* 5.3 3.4 - - + -
123F PHE* 4.1 20.0 - + - -
124F LEU* 3.7 32.4 - - + +
283F VAL* 3.9 9.4 - - + -
284F MET 3.2 6.1 - - - -
285F MET* 3.7 24.5 - - + -
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Residues in contact with THR 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 3.8 30.6 - - + +
17F HIS* 4.8 9.9 - - - -
32F SER* 4.6 6.2 + - - -
33F TRP* 1.3 78.6 + - - +
35F PRO* 1.3 82.3 - - + +
36F VAL* 3.5 3.3 + - + +
42F PHE* 4.2 26.1 - - + -
283F VAL* 3.5 3.7 - - - +
284F MET* 2.9 33.7 + - - +
415F VAL* 5.0 4.9 - - + +
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Residues in contact with PRO 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 5.2 0.3 - - - +
33F TRP* 3.7 25.8 - - + +
34F THR* 1.3 94.9 - - + +
36F VAL* 1.3 63.4 + - - +
37F ILE* 5.5 0.6 - - - +
74F HIS* 5.5 4.5 - - + -
123F PHE* 5.2 9.6 - - + -
282F GLY 3.5 9.2 - - - +
283F VAL* 4.4 3.1 - - + -
419F ARG* 3.7 11.3 + - - -
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Residues in contact with VAL 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F THR* 3.8 4.0 - - + +
35F PRO* 1.3 80.1 - - - +
37F ILE* 1.3 66.9 + - - +
40F ASP* 3.7 11.4 - - + +
42F PHE* 4.1 15.5 - - + -
71F TYR* 4.3 6.1 - - + -
74F HIS* 4.6 2.6 - - - -
278F VAL* 3.3 35.0 - - + -
281F HIS* 3.6 3.8 - - - +
282F GLY* 2.7 47.2 + - - +
283F VAL 4.3 0.7 - - - +
284F MET* 3.4 29.2 - - + -
417F VAL* 5.8 0.7 - - + -
419F ARG* 4.1 3.1 - - - +
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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