Contacts of the helix formed by residues 383 - 389 (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 ASN 383 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342F ILE* 3.9 4.9 - - - +
380F THR* 4.3 6.9 + - - +
381F GLY 2.5 15.2 + - - +
382F ASP* 1.3 72.9 - - - +
384F LEU* 1.3 68.7 + - - +
385F GLN* 3.0 22.9 - - - +
386F GLU* 3.2 38.4 + - + +
387F ALA* 3.3 11.6 + - - +
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Residues in contact with LEU 384 (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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140F TRP* 3.9 24.2 - - + -
173F PRO* 4.1 13.9 - - + -
174F LEU 5.9 0.2 - - - +
176F PRO* 4.6 16.2 - - + -
331F TYR* 3.6 23.3 - - - +
342F ILE* 3.9 17.1 - - + +
343F LYS 4.2 14.4 - - - +
344F ILE* 3.9 17.3 - - + -
382F ASP 4.2 1.2 + - - -
383F ASN* 1.3 72.3 - - - +
385F GLN* 1.3 67.6 + - - +
387F ALA* 2.8 14.7 + - - +
388F ILE* 2.9 27.4 + - + +
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Residues in contact with GLN 385 (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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132F TYR* 5.8 0.4 + - - -
140F TRP* 4.2 17.1 - - + -
141F MET* 3.4 34.4 - - + +
142F PRO* 3.0 31.9 + - - +
383F ASN* 3.0 16.0 - - - +
384F LEU* 1.3 74.9 - - - +
386F GLU* 1.3 63.3 + - + +
387F ALA 3.2 0.2 + - - -
388F ILE* 3.2 1.9 + - - +
389F LEU* 3.0 49.1 + - + +
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Residues in contact with GLU 386 (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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162F ARG* 2.9 51.8 + - - +
380F THR* 3.5 41.7 + - - +
383F ASN* 3.2 30.6 + - + +
384F LEU 3.1 0.8 - - - -
385F GLN* 1.3 80.3 + - + +
387F ALA* 1.3 59.6 + - - +
389F LEU* 3.5 5.6 - - - +
391F ARG* 5.4 0.9 - - - +
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Residues in contact with ALA 387 (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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165F HIS* 3.9 12.0 + - - -
170F TRP* 4.2 6.7 - - - -
331F TYR* 3.8 33.4 - - + +
342F ILE* 4.2 4.9 - - + -
376F PRO* 4.2 4.7 - - + +
377F GLY* 3.8 25.3 + - - +
380F THR* 4.2 0.2 + - - -
383F ASN 3.3 8.6 + - - +
384F LEU 2.8 9.7 + - - +
386F GLU* 1.3 76.0 - - - +
388F ILE* 1.3 66.8 + - - +
389F LEU 3.6 6.2 - - - +
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Residues in contact with ILE 388 (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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140F TRP* 3.7 23.6 - - + -
141F MET* 4.0 16.6 - - + -
164F CYS* 4.0 17.9 - - + -
165F HIS* 3.0 33.3 + - - +
170F TRP* 5.0 4.9 - - - -
171F SER* 3.8 35.4 - - - +
173F PRO* 4.2 9.4 - - + -
331F TYR* 4.4 2.5 - - - +
384F LEU* 2.9 43.3 + - + +
385F GLN 3.7 5.6 - - - +
387F ALA* 1.3 75.0 - - - +
389F LEU* 1.3 65.8 + - - +
23J GLN* 5.2 0.9 - - - +
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Residues in contact with LEU 389 (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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132F TYR* 3.9 11.7 - - - +
137F ARG* 5.7 0.7 - - - -
141F MET* 4.1 10.3 - - + -
162F ARG* 2.9 58.6 + - + +
163F CYS* 3.4 24.9 - - - -
164F CYS* 3.9 13.0 - - - +
165F HIS* 4.3 0.7 + - - -
385F GLN* 3.0 48.2 + - + +
386F GLU* 3.5 9.1 - - - +
387F ALA 3.6 4.7 - - - +
388F ILE* 1.3 76.3 - - - +
390F VAL* 1.3 60.9 - - - +
391F ARG* 3.3 2.6 + - - +
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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