Contacts of the helix formed by residues 344 - 355 (chain W) in PDB entry 6NE3
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 LEU 344 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340W LEU* 5.0 1.8 - - - -
343W ASN* 1.3 100.0 - - + +
345W HIS* 1.3 62.1 + - - +
346W GLU* 3.2 3.6 + - - +
347W LEU* 3.4 6.0 + - - -
348W TRP* 2.9 26.1 + - - +
362W ALA 5.4 0.7 - - - +
365W PHE* 3.7 34.3 - - + -
366W ASP* 3.9 24.7 - - + +
369W PHE* 3.8 28.0 - - + -
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Residues in contact with HIS 345 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314W LYS* 4.3 22.2 + - + +
315W ASN* 5.8 2.2 - - + -
316W GLU* 5.3 1.1 - - - +
317W LYS* 6.3 0.7 - - - +
342W ASN* 3.5 41.1 + - + +
343W ASN* 3.9 11.4 - - + +
344W LEU* 1.3 80.3 + - - +
346W GLU* 1.3 65.0 + - + +
348W TRP* 3.4 17.9 - - + +
349W SER* 2.8 30.3 + - - -
362W ALA* 6.1 4.0 - - + -
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Residues in contact with GLU 346 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313W ILE 5.2 1.4 - - - +
314W LYS* 4.0 18.6 - - + +
339W PRO 4.1 5.2 - - - +
340W LEU* 4.8 2.2 - - + -
341W GLN* 3.7 47.8 - - + +
342W ASN 4.7 2.9 - - - +
343W ASN 5.5 0.2 - - - -
344W LEU 3.2 1.2 - - - +
345W HIS* 1.3 81.2 + - + +
347W LEU* 1.3 61.9 + - + +
349W SER* 3.1 5.2 + - - -
350W LEU* 3.0 27.9 + - - +
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Residues in contact with LEU 347 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202W ILE* 5.2 13.7 - - + -
339W PRO* 3.5 34.1 - - + +
340W LEU* 3.7 28.9 - - + +
344W LEU* 3.4 6.1 + - - +
346W GLU* 1.3 78.2 - - - +
348W TRP* 1.3 57.3 + - - +
350W LEU* 3.9 4.7 - - + +
351W LEU* 2.9 32.1 + - - +
365W PHE* 3.6 23.9 - - + -
387W VAL* 4.5 24.0 - - + -
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Residues in contact with TRP 348 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316W GLU* 2.7 42.5 + - - -
344W LEU* 2.9 16.3 + - + +
345W HIS* 3.4 18.8 - - + +
346W GLU 3.2 0.2 - - - -
347W LEU* 1.3 77.6 - - - +
349W SER* 1.3 57.8 + - - +
351W LEU* 3.4 1.3 + - - +
352W ASN* 2.9 34.4 + - + +
359W PHE* 3.5 32.8 - + + -
360W ASN 3.4 20.2 - - - -
361W SER* 3.2 43.7 - - - -
362W ALA* 3.9 19.6 - - + +
364W ASP* 5.4 1.1 - - + -
365W PHE* 4.1 32.5 - + + -
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Residues in contact with SER 349 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313W ILE* 4.0 16.0 + - - +
314W LYS 3.6 17.6 + - - -
315W ASN 4.6 0.4 - - - -
316W GLU* 3.4 39.9 - - - -
325W ARG* 3.3 11.5 + - - -
345W HIS 2.8 18.1 + - - -
346W GLU 3.1 9.5 + - - -
348W TRP* 1.3 70.4 - - - +
350W LEU* 1.3 63.2 + - - +
352W ASN* 3.3 1.4 + - - -
353W PHE* 2.9 24.1 + - - +
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Residues in contact with LEU 350 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202W ILE* 4.2 24.7 - - + -
313W ILE* 5.5 9.9 - - + +
334W LEU* 5.2 6.0 - - + +
339W PRO 6.1 0.9 - - - +
346W GLU 3.0 13.4 + - - +
347W LEU* 3.9 8.7 - - + +
348W TRP 3.3 0.2 - - - -
349W SER* 1.3 83.5 + - - +
351W LEU* 1.3 57.2 + - - +
353W PHE* 3.2 9.3 + - - +
354W LEU* 2.9 32.2 + - - +
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Residues in contact with LEU 351 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347W LEU 2.9 19.6 + - - +
348W TRP* 3.8 4.5 - - - +
350W LEU* 1.3 77.0 - - - +
352W ASN* 1.3 60.0 + - - +
354W LEU* 4.6 1.1 - - - +
355W LEU 2.9 32.7 + - - +
359W PHE* 3.6 38.0 - - + -
365W PHE* 4.9 4.0 - - + -
391W PHE* 4.2 15.3 - - + -
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Residues in contact with ASN 352 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316W GLU* 4.3 12.1 - - - +
325W ARG* 3.4 18.2 + - - +
348W TRP* 2.9 35.3 + - + +
349W SER 3.3 4.5 + - - +
351W LEU* 1.3 76.3 - - - +
353W PHE* 1.3 57.7 + - - +
356W PRO* 3.3 28.8 - - + +
359W PHE* 4.5 8.2 - - + +
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Residues in contact with PHE 353 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305W LEU* 3.9 2.7 - - + -
307W ILE* 3.9 17.5 - - + -
313W ILE* 4.3 16.4 - - + -
324W VAL* 3.3 56.5 - - + -
325W ARG* 3.3 26.4 - - + +
332W ARG* 3.6 35.1 + - + -
333W LEU 5.4 0.7 - - - -
334W LEU* 3.8 28.5 - - + -
349W SER 2.9 11.8 + - - +
350W LEU* 3.6 6.3 - - - +
352W ASN* 1.3 78.5 - - - +
354W LEU* 1.3 69.4 + - - +
355W LEU 3.7 0.2 - - - -
356W PRO* 3.4 12.2 - - - +
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Residues in contact with LEU 354 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200W ASN* 3.1 47.9 + - + +
201W GLY 4.5 4.3 - - - +
202W ILE* 6.0 1.3 - - + -
332W ARG* 3.3 8.4 + - - -
334W LEU* 4.0 20.6 - - + -
350W LEU 2.9 16.9 + - - +
351W LEU* 4.7 2.0 - - - +
353W PHE* 1.3 86.2 - - - +
355W LEU* 1.3 59.0 + - + +
356W PRO* 3.3 5.7 - - - +
391W PHE* 5.7 4.5 - - + -
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Residues in contact with LEU 355 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199W ILE* 3.8 29.8 - - + -
200W ASN* 4.4 7.6 - - - +
351W LEU* 2.9 15.7 + - - +
354W LEU* 1.3 76.8 - - + +
356W PRO* 1.3 65.5 - - - +
357W ASP* 3.2 5.1 + - - -
358W VAL* 3.7 6.0 + - + -
359W PHE* 3.2 21.9 - - + -
391W PHE* 5.0 7.2 - - + -
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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