Contacts of the strand formed by residues 236 - 245 (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 LEU 236 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70F PHE* 3.1 5.8 - - - -
71F TYR* 2.8 53.1 + - + +
135F TYR* 4.5 0.7 - - - +
229F TYR* 3.7 42.8 - - + -
234F ARG* 3.5 2.1 + - - +
235F PRO* 1.3 72.5 - - - +
237F LEU* 1.3 82.0 + - - +
238F VAL* 3.3 6.0 + - + +
276F PHE* 4.3 23.8 - - + -
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Residues in contact with LEU 237 (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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68F PHE* 5.0 1.1 - - + -
69F THR 3.5 7.9 - - - +
70F PHE* 3.3 32.1 - - + -
135F TYR* 4.2 11.0 + - + +
235F PRO 3.7 2.6 + - - -
236F LEU* 1.3 85.5 - - + +
238F VAL* 1.3 66.7 + - - +
239F MET* 3.1 31.2 - - - +
240F HIS* 4.1 20.2 - - + +
24J PHE* 4.2 18.2 - - + -
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Residues in contact with VAL 238 (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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69F THR* 2.7 22.3 + - + +
71F TYR* 4.0 20.9 - - + +
236F LEU* 3.3 14.8 + - + +
237F LEU* 1.3 79.2 - - - +
239F MET* 1.3 65.5 + - - +
273F VAL* 3.4 31.0 - - + -
274F PRO* 5.0 6.2 - - + +
276F PHE* 4.3 29.2 - - + -
284F MET* 4.3 8.3 - - + -
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Residues in contact with MET 239 (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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68F PHE* 3.4 4.5 - - - -
69F THR* 3.1 25.1 + - - -
237F LEU* 3.1 7.0 - - - +
238F VAL* 1.3 85.7 - - - +
240F HIS* 1.3 94.2 + - + +
241F THR* 4.4 8.7 - - - -
271F HIS* 3.7 9.2 - - + -
272F SER 3.4 26.7 - - - +
273F VAL* 3.6 20.2 - - + -
274F PRO* 3.9 15.3 - - + -
10X 3DR 6.3 0.2 - - - -
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Residues in contact with HIS 240 (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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64F LYS* 5.8 0.2 + - - -
66F ASP* 3.1 28.3 + - - -
67F PHE 3.5 4.0 + - - -
68F PHE* 3.3 32.1 - + + +
237F LEU* 4.1 20.6 - - + +
239F MET* 1.3 91.6 - - + +
241F THR* 1.3 75.6 + - - +
242F ASP* 4.4 7.0 - - + +
24J PHE* 4.0 18.2 - + - -
2X 3DR 5.1 4.2 - - - -
10X 3DR 3.4 22.8 - - + +
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Residues in contact with THR 241 (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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66F ASP* 3.3 3.6 - - - -
67F PHE* 2.9 35.2 + - + +
239F MET* 4.4 7.8 - - - -
240F HIS* 1.3 79.5 + - - +
242F ASP* 1.3 64.8 + - - +
243F PHE* 4.5 9.4 - - + -
269F PHE* 6.3 0.4 - - + -
270F LYS 3.9 18.4 - - - +
271F HIS* 2.8 33.6 + - + -
272F SER 4.8 0.7 + - - -
8X 3DR 3.4 11.2 - - + +
10X 3DR 2.6 26.1 + - - +
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Residues in contact with ASP 242 (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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64F LYS* 3.2 25.6 + - - +
65F VAL 3.1 8.5 - - - +
66F ASP* 3.4 21.3 - - - +
240F HIS* 4.4 6.1 - - + +
241F THR* 1.3 73.0 - - - +
243F PHE* 1.3 62.0 + - - +
8X 3DR 1.0 112.1 + - - +
9X 3DR 3.0 16.4 - - - +
10X 3DR 2.0 19.1 + - + +
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Residues in contact with PHE 243 (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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50F LEU* 4.5 6.5 - - + -
64F LYS* 3.6 5.7 - - - +
65F VAL* 2.7 81.0 + - + -
67F PHE* 3.9 14.6 - + - -
241F THR* 4.5 8.3 - - + -
242F ASP* 1.3 73.3 - - - +
244F TRP* 1.3 70.4 + - - +
245F ALA* 4.7 0.9 - - + -
267F GLN* 3.9 25.4 - - + -
268F THR 5.0 0.4 - - - -
269F PHE* 3.7 41.1 - + + -
8X 3DR 2.9 25.8 - + + +
9X 3DR 2.4 22.7 - - - +
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Residues in contact with TRP 244 (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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62F ASP* 3.4 29.2 - - + -
63F SER 3.4 11.9 - - - -
64F LYS* 3.7 38.0 - - + +
243F PHE* 1.3 77.8 - - - +
245F ALA* 1.3 59.5 + - - +
246F SER 3.8 0.4 - - - -
267F GLN* 3.2 26.9 + - - +
293F PRO* 4.5 10.8 - - + -
6J ARG* 3.5 65.6 + - + +
7J SER* 3.5 31.0 - - - -
8J PRO 5.3 0.4 - - - -
9J SER* 5.2 9.2 + - - -
9X 3DR 2.6 45.3 + + - +
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Residues in contact with ALA 245 (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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50F LEU* 4.0 21.5 - - + -
52F LEU* 5.4 0.2 - - + -
62F ASP* 3.4 20.7 - - - +
63F SER* 2.8 31.2 + - - +
65F VAL* 4.1 9.2 - - + -
243F PHE 4.0 0.4 + - - -
244F TRP* 1.3 73.0 - - - +
246F SER* 1.3 59.8 + - - +
265F VAL* 3.5 21.6 - - + +
267F GLN* 3.8 9.6 - - + -
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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