Contacts of the helix formed by residues 351 - 359 (chain N) in PDB entry 6CET
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 TYR 351 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176N VAL* 5.4 5.0 - - - +
177N PHE 4.6 6.2 + - - -
178N THR* 3.7 20.8 + - - -
179N LYS 5.1 1.4 + - - -
180N ASP* 4.8 14.0 + - - -
260N LEU* 3.6 26.2 - - + -
348N CYS 5.0 2.1 + - - +
349N HIS* 4.5 0.2 - - - +
350N SER* 1.3 98.7 + - - +
352N ASP* 1.3 59.9 + - - +
354N ILE* 3.3 10.7 - - + +
355N CYS* 2.9 44.3 + - - +
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Residues in contact with ASP 352 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345N TYR* 5.0 8.1 - - - -
349N HIS* 3.4 29.1 + - + +
350N SER 4.0 0.6 - - - +
351N TYR* 1.3 77.4 - - - +
353N GLU* 1.3 63.7 + - - +
355N CYS* 3.9 1.3 - - - +
356N CYS* 3.0 47.0 + - - -
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Residues in contact with GLU 353 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283N GLN* 5.1 10.5 + - - +
287N SER* 3.1 33.0 + - - -
345N TYR* 4.7 10.4 + - - -
349N HIS* 3.4 32.9 + - + +
352N ASP* 1.3 85.2 - - + +
354N ILE* 1.3 60.1 + - + +
356N CYS* 3.4 7.2 + - - +
357N LYS* 2.9 38.5 + - + +
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Residues in contact with ILE 354 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257N ASP* 5.5 2.9 - - - +
260N LEU* 3.6 33.2 - - + -
261N GLN* 4.3 15.9 - - - +
279N ARG* 5.8 0.9 - - - +
283N GLN* 4.5 14.6 - - - +
349N HIS* 5.5 0.4 - - + -
350N SER 3.3 21.3 - - - +
351N TYR* 3.3 21.8 - - + +
353N GLU* 1.3 79.9 - - + +
355N CYS* 1.3 76.8 + - - +
357N LYS* 3.5 7.1 + - - +
358N THR* 2.3 42.7 + - - +
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Residues in contact with CYS 355 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351N TYR* 2.9 36.4 + - - +
352N ASP* 3.9 2.2 - - - +
354N ILE* 1.3 87.1 - - - +
356N CYS* 1.3 66.8 + - - +
358N THR* 3.0 19.1 + - - -
359N GLY* 3.0 13.3 + - - -
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Residues in contact with CYS 356 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352N ASP* 3.0 39.6 + - - +
353N GLU* 3.8 7.9 - - - +
355N CYS* 1.3 76.1 - - - +
357N LYS* 1.3 64.5 + - - +
359N GLY* 4.3 2.6 + - - -
360N MET* 4.8 9.2 + - - +
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Residues in contact with LYS 357 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282N PHE* 6.5 0.7 - - - -
283N GLN* 5.0 15.3 - - - +
286N CYS* 3.3 35.1 + - - +
287N SER* 4.8 9.4 + - - +
353N GLU* 2.9 24.4 + - - +
354N ILE* 3.5 9.4 - - - +
356N CYS* 1.3 78.1 - - - +
358N THR* 1.3 50.7 + - - +
359N GLY 2.8 1.4 + - - -
360N MET* 2.5 35.2 + - - +
362N TYR* 3.5 24.9 + - + +
363N HIS* 3.0 38.1 - - + +
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Residues in contact with THR 358 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264N CYS* 5.0 14.4 - - - -
354N ILE* 2.3 33.5 + - - +
355N CYS* 3.0 11.8 + - - -
357N LYS* 1.3 71.3 - - - +
359N GLY* 1.3 61.2 + - - +
360N MET 3.1 9.1 - - - +
363N HIS* 3.7 4.1 + - - -
364N GLU* 3.3 26.1 + - - +
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Residues in contact with GLY 359 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355N CYS 3.0 12.5 + - - -
356N CYS 4.8 2.7 - - - -
357N LYS 2.8 6.2 + - - -
358N THR* 1.3 72.6 - - - +
360N MET* 1.3 60.3 + - - +
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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