Contacts of the helix formed by residues 295 - 300 (chain F) in PDB entry 6MZL
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 GLU 295 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291F MET 3.8 8.7 - - - +
292F LYS* 3.6 21.1 - - - +
293F GLY 3.3 5.0 + - - +
294F ASN* 1.3 68.7 - - - +
296F THR* 1.3 59.3 + - - +
297F MET 3.1 2.0 - - - -
298F LEU* 3.0 13.4 + - + +
299F ASP* 2.9 36.6 + - - +
607F ARG* 4.2 21.7 + - - +
627F LEU* 5.3 2.7 - - + +
85L SER* 5.0 2.5 - - - -
86L PRO 2.9 29.7 - - - +
87L PRO* 3.3 11.3 - - - +
88L PRO* 3.2 25.9 - - + +
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Residues in contact with THR 296 (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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278F ASP* 4.9 12.1 - - - +
281F VAL* 6.2 4.3 - - + -
294F ASN* 4.7 13.4 + - - +
295F GLU* 1.3 76.1 + - - +
297F MET* 1.3 57.0 + - - +
298F LEU 3.0 3.5 + - - -
299F ASP 4.2 1.3 - - - +
300F PHE* 2.7 47.0 + - + +
301F ARG* 3.3 16.4 + - - +
627F LEU* 3.3 37.9 + - + +
628F ALA* 5.0 3.5 - - - +
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Residues in contact with MET 297 (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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249F LEU* 3.3 37.2 - - + +
252F VAL* 4.1 15.5 - - + -
281F VAL* 5.4 4.7 - - + -
285F LEU* 3.6 43.1 - - + -
290F HIS* 3.4 33.2 - - + +
291F MET* 3.7 25.1 - - + +
294F ASN* 3.6 16.6 - - + +
296F THR* 1.3 74.6 - - - +
298F LEU* 1.3 58.7 + - - +
301F ARG* 3.3 34.2 - - - +
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Residues in contact with LEU 298 (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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249F LEU* 4.9 9.0 - - + -
291F MET* 3.8 42.8 - - + +
295F GLU* 3.0 12.8 + - + +
297F MET* 1.3 84.7 - - + +
299F ASP* 1.3 61.3 + - - +
300F PHE 3.4 0.9 - - - -
301F ARG* 2.9 17.5 + - - -
302F THR* 2.3 28.1 + - - +
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Residues in contact with ASP 299 (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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295F GLU* 2.9 22.8 + - - +
296F THR 4.5 0.2 - - - +
298F LEU* 1.3 80.9 - - - +
300F PHE* 1.3 62.7 + - - +
301F ARG 3.6 0.2 + - - -
302F THR* 3.7 16.9 + - - +
304F LYS* 4.7 7.1 - - - +
626F HIS 5.6 0.3 - - - +
627F LEU* 3.7 34.8 - - + +
88L PRO* 3.6 27.6 - - - +
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Residues in contact with PHE 300 (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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241F TYR* 4.7 19.7 - + - -
242F PRO* 5.4 9.9 - - + -
245F VAL* 4.6 14.4 - - + -
278F ASP* 5.0 15.0 - - - -
296F THR* 2.7 36.6 + - + +
299F ASP* 1.3 73.0 - - - +
301F ARG* 1.3 76.3 + - + +
302F THR 3.4 2.4 + - - -
304F LYS* 3.5 68.1 + - + +
305F PHE* 5.7 1.7 - - - -
627F LEU* 4.0 9.0 - - + +
648F ASP* 6.0 1.3 - - + -
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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