Contacts of the helix formed by residues 287 - 294 (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 LYS 287 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252F VAL* 4.2 17.0 - - - +
255F GLN* 4.2 40.9 + - + +
286F THR* 1.3 97.3 - - + +
288F LYS* 1.3 62.4 + - - +
289F GLU* 3.3 6.7 - - + +
290F HIS* 3.2 28.8 + - + +
291F MET* 3.8 2.4 + - - +
72L ARG* 3.1 44.9 - - - +
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Residues in contact with LYS 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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252F VAL 5.7 1.8 - - - +
253F TYR* 4.0 39.0 + - - -
255F GLN* 3.8 26.4 - - + +
287F LYS* 1.3 74.0 - - - +
289F GLU* 1.3 61.3 + - - +
290F HIS 3.2 1.6 - - - -
291F MET* 3.1 28.2 + - + +
292F LYS* 2.9 35.9 + - + +
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Residues in contact with GLU 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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287F LYS* 3.3 4.6 - - + -
288F LYS* 1.3 76.9 - - - +
290F HIS* 1.3 62.6 + - + +
292F LYS* 3.2 13.1 + - + +
293F GLY 2.9 23.4 + - - -
42H GLU* 5.9 0.5 - - - +
46H ARG* 4.5 5.5 + - - -
75L ILE* 3.0 55.3 - - - +
76L GLN* 2.9 29.2 - - - +
79L ALA* 4.0 13.4 - - + +
83L PHE* 3.2 20.6 - - + -
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Residues in contact with HIS 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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284F SER 3.3 20.8 + - - -
285F LEU* 3.8 19.9 - - + +
286F THR* 3.3 29.5 + - - -
287F LYS* 3.2 22.2 + - + +
288F LYS 3.2 0.4 - - - -
289F GLU* 1.3 83.3 - - + +
291F MET* 1.3 55.6 + - - +
293F GLY* 4.4 0.9 - - - +
294F ASN* 2.8 35.5 + - - +
297F MET* 3.4 6.0 - - + +
45H TYR* 3.5 38.8 - + + -
49H GLU* 3.2 24.7 + - - +
83L PHE* 5.1 2.5 - - - -
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Residues in contact with MET 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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249F LEU* 5.1 7.9 - - + -
252F VAL* 5.3 3.1 - - + -
253F TYR* 4.0 35.0 - - + -
287F LYS 4.4 2.2 - - - +
288F LYS* 3.1 40.8 + - + +
290F HIS* 1.3 78.0 - - - +
292F LYS* 1.3 62.4 + - + +
294F ASN 3.3 16.5 - - - +
295F GLU* 3.8 10.4 - - - +
297F MET* 3.7 27.8 - - + -
298F LEU* 3.8 41.2 - - + +
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Residues in contact with LYS 292 (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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288F LYS* 2.9 23.4 + - + +
289F GLU* 3.2 17.0 + - + +
291F MET* 1.3 78.2 - - - +
293F GLY* 1.3 63.6 + - - +
295F GLU* 3.6 16.6 - - - +
76L GLN* 3.8 26.1 + - - +
79L ALA* 6.1 4.2 - - + +
80L ASP* 4.8 11.2 + - - +
83L PHE* 4.8 5.6 - - + +
85L SER* 4.1 8.9 - - - -
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Residues in contact with GLY 293 (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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289F GLU 2.9 11.7 + - - -
292F LYS* 1.3 80.5 - - - +
294F ASN* 1.3 60.5 + - - +
295F GLU* 3.3 6.4 + - - +
607F ARG* 4.6 7.8 + - - -
83L PHE* 3.6 29.7 - - - -
85L SER* 4.2 17.9 - - - -
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Residues in contact with ASN 294 (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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281F VAL* 3.6 31.5 - - + +
284F SER* 5.3 1.2 + - - -
285F LEU* 5.3 4.6 - - - +
290F HIS* 2.8 24.9 + - - +
291F MET 3.3 6.4 - - - +
293F GLY* 1.3 70.0 - - - +
295F GLU* 1.3 60.1 + - - +
296F THR* 3.1 15.7 + - - +
297F MET* 3.5 25.6 + - + +
607F ARG* 6.0 0.2 - - - +
49H GLU* 3.9 26.4 + - - +
52H GLN* 5.2 2.4 + - - +
83L PHE* 5.1 0.6 - - - -
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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