Contacts of the helix formed by residues 326 - 334 (chain D) in PDB entry 2NYM
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 ILE 326 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284D VAL* 3.9 25.1 - - + +
287D PHE* 4.3 11.7 - - + -
288D GLN* 5.6 0.4 - - + -
291D MSE 4.3 21.8 - - + -
306D VAL* 4.7 3.8 - - + -
309D PHE* 4.4 12.6 - - + -
310D CYS* 4.6 17.0 - - - -
313D LEU* 5.1 0.9 - - + -
321D VAL* 3.1 23.9 + - + +
322D ILE* 3.8 14.8 - - + +
325D GLN* 1.3 78.2 - - - +
327D LEU* 1.3 67.6 + - - +
328D PRO* 3.1 4.2 - - - -
329D CYS* 3.2 13.7 + - - +
330D ILE* 3.2 32.2 + - + +
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Residues in contact with LEU 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D ILE* 2.8 25.9 + - + +
323D MSE 3.8 23.6 - - - +
326D ILE* 1.3 73.2 - - - +
328D PRO* 1.3 67.9 - - + +
330D ILE* 3.8 16.2 - - + -
331D LYS* 3.2 43.4 + - + +
352D LEU* 5.8 0.4 - - + -
356D LEU* 5.4 2.5 - - + -
364D HIS* 3.6 36.8 - - + +
365D LEU* 3.7 29.8 - - + -
368D LEU* 4.8 2.5 - - + -
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Residues in contact with PRO 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D GLN* 5.9 0.9 - - - +
292D LYS* 5.5 1.1 - - - -
323D MSE 3.8 9.9 - - - +
324D SER* 3.6 16.8 - - - +
325D GLN 3.7 14.6 - - - +
326D ILE 3.2 4.9 - - - -
327D LEU* 1.3 95.4 - - + +
329D CYS* 1.3 65.2 + - - +
330D ILE 3.3 0.3 + - - -
331D LYS* 3.4 17.3 + - + +
332D GLU* 3.4 14.0 + - - +
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Residues in contact with CYS 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D GLN* 3.9 38.8 - - - -
291D MSE 4.1 25.6 - - + -
292D LYS* 3.6 33.0 - - + +
325D GLN 3.9 5.6 - - - -
326D ILE 3.2 5.7 + - - +
328D PRO* 1.3 78.7 - - - +
330D ILE* 1.3 57.8 + - - +
332D GLU* 3.1 10.7 + - - +
333D LEU* 3.0 29.6 + - - +
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Residues in contact with ILE 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D MSE 5.0 4.0 - - - -
306D VAL* 3.7 17.0 - - + -
322D ILE* 6.2 0.2 - - + -
326D ILE* 3.2 29.1 + - + +
327D LEU* 3.7 16.4 - - + +
328D PRO 3.2 0.6 - - - -
329D CYS* 1.3 73.7 - - - +
331D LYS* 1.3 63.3 + - - +
332D GLU 2.9 5.2 - - - -
333D LEU* 2.8 19.0 + - - +
334D VAL* 3.0 16.0 + - + +
345D LEU* 3.7 21.8 - - + -
349D ILE* 4.2 9.6 - - + -
352D LEU* 3.4 33.0 - - + -
365D LEU* 5.3 0.4 - - + -
368D LEU* 3.9 19.7 - - + -
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Residues in contact with LYS 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D LEU* 3.2 36.8 + - + +
328D PRO* 3.4 11.8 + - + +
330D ILE* 1.3 79.1 - - - +
332D GLU* 1.3 59.8 + - + +
334D VAL* 3.7 20.4 + - - +
335D SER* 4.0 7.8 + - - -
364D HIS* 4.0 28.6 + - - +
368D LEU* 4.3 22.8 - - + +
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Residues in contact with GLU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D LYS* 4.2 19.9 + - + +
328D PRO 3.4 8.6 + - - +
329D CYS* 3.1 17.2 + - - +
330D ILE 2.9 0.4 - - - -
331D LYS* 1.3 79.1 - - - +
333D LEU* 1.3 64.0 + - + +
335D SER* 3.4 22.6 + - - +
336D ASP* 3.8 1.9 + - - +
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Residues in contact with LEU 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D MSE 3.8 50.9 - - + +
299D ARG* 4.5 3.6 - - + -
303D SER* 3.6 19.3 - - - +
329D CYS 3.0 15.6 + - - +
330D ILE* 2.8 9.4 + - + +
332D GLU* 1.3 72.5 - - + +
334D VAL* 1.3 66.3 + - - +
335D SER 2.9 4.1 + - - -
336D ASP* 3.0 29.5 + - - +
341D VAL* 3.6 28.9 - - + +
342D LYS* 4.1 8.4 - - - +
345D LEU* 3.9 23.1 - - + -
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Residues in contact with VAL 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D ILE* 3.0 21.0 + - + +
331D LYS 3.8 7.9 - - - +
332D GLU 3.3 0.2 - - - -
333D LEU* 1.3 76.9 - - - +
335D SER* 1.3 60.1 + - - +
336D ASP 3.8 1.6 + - - -
342D LYS* 3.9 18.5 - - - +
345D LEU* 4.4 15.5 - - + +
368D LEU* 3.6 39.9 - - + -
371D ALA* 3.8 28.2 - - + +
372D GLN* 4.2 18.6 - - + +
375D ASP* 4.6 4.2 - - - +
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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