Contacts of the strand formed by residues 282 - 291 (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 GLY 282 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35F PRO* 3.5 3.8 - - - +
36F VAL* 2.7 46.0 + - - +
71F TYR* 4.7 1.1 - - - -
72F ILE 3.3 12.6 - - - -
74F HIS* 3.3 25.6 + - - -
280F GLU 3.6 1.6 + - - -
281F HIS* 1.3 76.2 - - - +
283F VAL* 1.3 55.6 + - - -
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Residues in contact with VAL 283 (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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33F TRP* 3.9 19.1 - - + -
34F THR 3.5 14.1 - - - +
35F PRO* 5.0 2.0 - - + -
36F VAL* 4.3 0.2 - - - +
70F PHE 3.7 0.9 - - - +
71F TYR* 3.5 5.5 - - - -
72F ILE* 2.9 35.4 + - + +
74F HIS* 3.7 9.9 - - + +
123F PHE* 3.3 42.2 - - + +
124F LEU* 4.8 1.8 - - + -
127F SER* 5.0 4.7 - - - +
282F GLY* 1.3 76.7 - - - +
284F MET* 1.3 70.0 + - - +
285F MET* 3.6 27.2 + - + -
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Residues in contact with MET 284 (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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32F SER 3.8 1.0 - - - +
33F TRP* 3.2 3.6 - - - -
34F THR* 2.9 33.5 + - - +
36F VAL* 3.4 27.1 - - + -
42F PHE* 3.5 50.4 - - + -
69F THR* 4.4 12.3 - - + -
70F PHE 3.3 2.7 - - - -
71F TYR* 3.6 34.8 - - + -
238F VAL* 4.3 16.6 - - + -
276F PHE* 3.6 21.8 - - + -
278F VAL* 4.9 0.4 - - - -
283F VAL* 1.3 70.9 - - - +
285F MET* 1.3 61.3 + - - +
286F THR* 4.7 2.1 + - - -
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Residues in contact with MET 285 (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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30F THR* 3.3 35.9 - - + +
32F SER 3.8 2.5 - - - -
33F TRP* 3.7 6.3 - - + -
69F THR* 3.1 2.3 - - - -
70F PHE 2.8 37.8 + - - +
72F ILE* 5.0 2.9 - - + -
110F VAL* 4.6 7.0 - - + -
123F PHE 4.9 0.2 - - - +
124F LEU* 4.3 27.1 - - + +
127F SER* 3.8 30.1 - - - -
128F TYR* 4.5 6.3 - - + +
131F ILE* 4.5 10.1 - - + -
283F VAL* 3.6 23.5 + - + -
284F MET* 1.3 73.3 - - - +
286F THR* 1.3 61.4 - - - +
287F LEU* 3.8 17.2 - - + +
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Residues in contact with THR 286 (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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30F THR* 3.6 2.1 - - - +
31F VAL* 2.7 31.3 + - + -
32F SER* 2.9 20.7 + - - -
42F PHE* 6.0 0.3 - - - -
44F LEU* 4.0 10.5 - - + +
67F PHE* 4.5 10.5 - - + -
68F PHE 3.0 15.0 - - - +
69F THR* 2.9 26.8 + - - +
271F HIS* 4.2 13.9 - - + +
284F MET 4.7 2.1 + - - -
285F MET* 1.3 74.3 - - - +
287F LEU* 1.3 57.7 + - - +
413F TYR* 4.5 20.2 - - + +
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Residues in contact with LEU 287 (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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28F LEU* 3.7 24.9 - - + -
29F LYS 3.1 11.2 - - - +
30F THR* 3.7 24.5 - - + +
31F VAL* 4.0 2.5 - - - +
67F PHE* 3.3 5.9 - - - +
68F PHE* 2.8 34.5 + - + +
70F PHE* 3.9 25.6 - - + -
128F TYR* 4.1 22.7 - - + -
131F ILE* 4.0 17.3 - - + -
285F MET* 3.8 19.5 - - + +
286F THR* 1.3 83.2 - - - +
288F ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 288 (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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27F ARG 4.2 0.5 - - - +
28F LEU* 3.3 6.5 - - - +
29F LYS* 2.7 31.8 + - - +
31F VAL* 3.7 18.6 - - + +
66F ASP 3.2 7.9 - - - +
67F PHE* 4.1 23.8 - - + +
68F PHE* 5.2 0.2 - - - -
287F LEU* 1.3 75.6 - - - +
289F LEU* 1.3 61.9 + - - +
290F ILE* 4.5 10.1 - - + -
407F TRP* 4.7 13.5 - - + -
409F LYS* 5.7 0.7 - - + -
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Residues in contact with LEU 289 (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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25F LEU 4.2 0.2 - - - +
26F GLY 3.6 27.8 - - - +
27F ARG 3.7 18.8 - - - +
28F LEU* 4.0 9.0 - - + +
64F LYS 3.6 3.1 - - - +
65F VAL* 3.6 1.6 - - - -
66F ASP* 2.9 35.5 + - + +
68F PHE* 4.4 7.0 - - + -
136F PHE* 4.3 16.6 - - + -
163F CYS* 4.0 19.7 - - + -
288F ALA* 1.3 79.3 - - - +
290F ILE* 1.3 63.2 + - - +
291F ARG* 3.4 43.9 + - + +
24J PHE* 5.3 1.3 - - - +
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Residues in contact with ILE 290 (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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25F LEU* 3.0 37.0 + - + +
27F ARG 4.9 0.6 + - - -
50F LEU* 3.5 26.9 - - + -
52F LEU* 4.5 13.0 - - + -
63F SER* 4.1 19.5 - - - +
64F LYS 3.7 1.3 - - - -
65F VAL* 3.6 28.3 - - + -
288F ALA* 4.5 6.7 - - + -
289F LEU* 1.3 82.6 - - - +
291F ARG* 1.3 68.4 + - - +
407F TRP* 3.5 44.9 - - + +
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Residues in contact with ARG 291 (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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25F LEU* 4.6 4.0 - - - -
26F GLY* 4.7 8.5 - - - +
63F SER* 3.3 5.5 - - - -
64F LYS* 2.8 39.5 + - + +
66F ASP* 3.3 27.3 + - - -
68F PHE* 5.7 0.2 - - - -
163F CYS* 5.3 1.7 - - - +
164F CYS 3.0 28.0 + - - -
165F HIS* 4.2 2.8 + - + -
166F LEU* 3.7 41.8 - - + +
289F LEU* 3.4 36.9 + - + +
290F ILE* 1.3 82.1 - - - +
292F PHE* 1.3 64.4 + - - +
293F PRO* 4.2 0.9 - - - +
390F VAL* 4.7 12.6 - - + -
24J PHE* 2.9 34.1 + - - +
2X 3DR 4.8 1.8 - - - +
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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