Contacts of the helix formed by residues 354 - 361 (chain C) in PDB entry 5M8N
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 SER 354 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339C VAL* 3.8 1.3 - - - -
341C LEU 3.8 3.8 - - - -
342C PHE 3.3 1.1 + - - -
343C ASP* 2.5 37.5 + - - +
344C THR* 3.3 15.3 - - - -
351C SER* 4.0 4.9 - - - -
352C THR* 3.0 1.5 - - - +
353C ASN* 1.3 75.7 - - - +
355C PHE* 1.3 57.8 + - - +
357C ASN* 3.1 28.2 + - - +
358C THR* 2.6 33.7 + - - -
367C GLY 3.9 1.8 + - - -
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Residues in contact with PHE 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C LEU* 3.8 20.0 - - + -
336C CYS* 3.2 20.9 - - + -
337C LEU* 3.8 14.6 - - + -
339C VAL* 3.4 24.6 - - + +
341C LEU 2.8 21.7 + - - +
342C PHE* 3.6 22.9 - + - +
354C SER* 1.3 70.1 - - - +
356C ARG* 1.3 66.2 + - - +
358C THR* 3.0 4.7 + - - -
359C VAL* 2.8 35.7 + - + +
410C VAL* 3.9 24.9 - - + -
411C PHE* 4.1 7.4 - + - -
414C TRP* 3.2 48.0 - + + +
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Residues in contact with ARG 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C GLU* 3.9 1.6 - - - +
217C GLY 3.0 32.0 + - - +
218C PRO* 3.7 19.7 - - + +
220C PHE* 4.2 4.0 - - + -
221C LEU* 4.1 10.8 - - + -
342C PHE* 2.7 33.4 + - + +
343C ASP* 2.6 36.6 + - - +
347C PHE 3.6 0.8 - - - -
348C TYR 2.7 38.2 + - - +
351C SER* 3.9 0.2 + - - -
354C SER* 3.7 0.2 - - - +
355C PHE* 1.3 76.4 - - - +
357C ASN* 1.3 87.0 + - - +
359C VAL* 3.2 10.2 - - - +
360C GLU* 2.7 58.7 + - - +
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Residues in contact with ASN 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C TYR 3.2 11.3 + - - +
349C SER* 2.8 35.6 + - - -
351C SER 3.1 19.7 + - - +
354C SER* 3.1 24.2 + - - +
355C PHE 3.2 0.2 - - - -
356C ARG* 1.3 106.5 + - - +
358C THR* 1.3 57.4 + - - +
360C GLU* 3.7 5.5 - - - +
361C GLY 3.1 6.1 + - - -
362C TYR* 3.0 38.1 + - - +
363C SER* 3.3 12.2 + - - +
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Residues in contact with THR 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C CYS* 3.8 14.1 - - + -
339C VAL* 4.3 1.9 - - + +
354C SER 2.6 24.6 + - - -
355C PHE* 3.5 6.2 - - - -
357C ASN* 1.3 75.0 - - - +
359C VAL* 1.3 66.7 + - - +
361C GLY* 3.3 11.1 + - - -
363C SER* 3.6 8.8 - - - +
364C ASP 3.2 26.7 - - - +
365C PRO* 3.4 25.6 - - + +
367C GLY* 3.3 18.5 - - - +
375C SER* 3.8 1.7 + - - -
376C LEU* 3.2 17.7 - - + +
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Residues in contact with VAL 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C PHE* 4.7 0.2 - - - -
221C LEU* 3.6 32.1 - - + -
336C CYS* 4.7 3.5 - - - +
355C PHE* 2.8 34.8 + - + +
356C ARG 3.2 10.8 - - - +
358C THR* 1.3 74.7 - - - +
360C GLU* 1.3 66.2 + - - +
361C GLY 3.3 0.2 + - - -
376C LEU* 3.5 10.4 - - + +
377C HIS* 3.0 26.5 + - + +
407C THR* 4.1 19.1 - - + +
410C VAL* 3.7 31.9 - - + -
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Residues in contact with GLU 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C HIS* 3.5 14.9 - - - +
216C GLU* 2.8 25.8 + - - -
217C GLY 4.0 0.2 + - - -
220C PHE* 3.5 38.6 - - + -
356C ARG* 2.7 52.5 + - - +
357C ASN* 3.7 5.5 - - - +
359C VAL* 1.3 78.0 - - - +
361C GLY* 1.3 56.7 + - - +
362C TYR* 3.7 22.1 - - + -
377C HIS* 2.9 12.0 + - - +
378C ASN* 2.8 29.2 + - - +
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Residues in contact with GLY 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C ASN 3.1 4.4 + - - -
358C THR 3.7 3.8 - - - -
359C VAL 3.2 1.8 - - - -
360C GLU* 1.3 78.2 - - - +
362C TYR* 1.3 60.0 + - - +
363C SER 3.6 1.6 - - - -
374C ARG* 3.4 10.9 - - - -
375C SER* 3.0 50.0 + - - -
378C ASN* 3.3 14.5 + - - -
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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