Contacts of the helix formed by residues 338 - 349 (chain D) in PDB entry 2NPP
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 ASN 338 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296D ALA* 3.7 24.6 - - + +
299D ARG* 4.3 2.7 - - - +
300D ALA* 5.2 0.4 - - - +
336D ASP* 2.6 19.0 + - - +
337D ALA* 1.3 72.6 - - - +
339D GLN* 1.3 70.9 + - - +
340D HIS* 3.6 20.9 + - - +
341D VAL* 3.0 44.0 + - + +
342D LYS* 3.1 13.9 + - - +
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Residues in contact with GLN 339 (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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337D ALA 3.7 5.0 + - - +
338D ASN* 1.3 71.1 + - - +
340D HIS* 1.3 70.4 + - + +
342D LYS* 2.7 20.3 + - - +
343D SER* 2.6 37.0 + - - -
376D GLU* 6.3 0.2 - - - +
377D CYS* 4.0 37.0 - - + +
378D PRO* 5.7 1.2 - - - +
379D GLU* 5.5 1.7 - - - +
380D VAL* 4.5 0.3 - - - +
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Residues in contact with HIS 340 (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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300D ALA* 4.3 9.4 - - + +
338D ASN* 3.4 16.6 + - - +
339D GLN* 1.3 89.5 - - + +
341D VAL* 1.3 53.6 + - - +
343D SER* 3.6 9.3 - - - -
344D ALA* 2.6 36.6 + - - +
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Residues in contact with VAL 341 (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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296D ALA* 3.9 10.1 - - + +
299D ARG* 4.2 11.4 - - + -
300D ALA* 3.8 26.5 - - + +
303D SER* 3.9 17.0 + - - +
333D LEU* 4.3 12.3 - - + +
336D ASP* 3.7 29.2 - - + +
338D ASN* 3.0 32.8 + - + +
340D HIS* 1.3 75.5 - - - +
342D LYS* 1.3 68.3 + - - +
344D ALA* 3.1 2.9 + - - +
345D LEU* 3.1 21.5 + - - +
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Residues in contact with LYS 342 (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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333D LEU 4.2 14.6 - - - +
334D VAL* 4.1 14.1 - - - +
335D SER 4.7 1.6 - - - -
336D ASP* 3.2 30.2 + - + +
337D ALA* 4.7 5.0 + - - +
338D ASN 3.1 5.8 + - - +
339D GLN* 2.7 32.3 + - - +
341D VAL* 1.3 78.1 - - - +
343D SER* 1.3 64.3 + - - +
345D LEU* 3.2 4.3 + - - +
346D ALA* 3.0 22.0 + - - +
372D GLN* 4.5 4.6 + - - +
375D ASP* 3.4 36.1 + - - +
376D GLU* 4.4 7.1 + - - +
377D CYS* 5.2 1.9 - - - +
380D VAL* 3.7 15.3 - - + -
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Residues in contact with SER 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D GLN 2.6 19.9 + - - -
340D HIS* 3.6 11.2 - - - -
342D LYS* 1.3 74.2 - - - +
344D ALA* 1.3 63.9 + - - +
346D ALA* 3.5 8.0 + - - +
377D CYS* 4.7 2.0 - - - -
379D GLU* 3.6 26.6 - - - +
380D VAL* 3.3 21.0 - - - +
383D ASN* 3.4 22.5 + - - -
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Residues in contact with ALA 344 (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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300D ALA* 4.1 15.5 - - + +
303D SER* 4.1 3.8 - - - -
304D HIS* 3.3 38.9 - - + +
340D HIS 2.6 23.1 + - - +
341D VAL* 3.4 6.1 - - - +
343D SER* 1.3 72.7 + - - +
345D LEU* 1.3 57.9 + - - +
347D SER* 2.7 34.1 + - - -
348D VAL* 3.9 1.8 + - - +
383D ASN* 5.4 0.2 - - - +
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Residues in contact with LEU 345 (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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303D SER* 4.0 11.8 - - - -
306D VAL* 5.1 6.3 - - + -
330D ILE* 4.0 23.1 - - + +
333D LEU* 3.4 41.5 - - + +
334D VAL* 4.1 10.8 - - + -
341D VAL 3.1 12.2 + - - +
342D LYS* 3.9 3.4 - - - +
344D ALA* 1.3 79.1 - - - +
346D ALA* 1.3 56.0 + - - +
347D SER 3.0 0.7 - - - -
348D VAL* 4.0 11.7 - - + -
349D ILE* 3.0 47.2 + - + +
372D GLN* 3.2 24.5 - - - +
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Residues in contact with ALA 346 (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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342D LYS 3.0 16.0 + - - +
343D SER 3.7 8.3 - - - +
344D ALA 3.0 0.8 + - - -
345D LEU* 1.3 76.6 - - - +
347D SER* 1.3 59.7 + - - +
349D ILE* 4.0 8.3 - - - +
350D MET* 5.3 0.7 + - - +
372D GLN* 3.5 26.5 - - - +
380D VAL* 3.9 29.2 - - + +
383D ASN* 3.4 18.4 - - + +
384D ILE* 3.9 7.2 - - + +
387D ASN* 4.2 1.7 + - - -
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Residues in contact with SER 347 (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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304D HIS* 4.3 8.7 - - - -
307D LYS* 5.6 0.5 - - - +
343D SER 3.8 0.6 + - - -
344D ALA* 2.7 20.2 + - - -
346D ALA* 1.3 81.1 - - - +
348D VAL* 1.3 72.5 + - - +
350D MET* 4.7 1.8 + - - +
383D ASN* 3.6 27.8 - - - +
387D ASN* 3.7 23.9 + - - +
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Residues in contact with VAL 348 (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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303D SER 3.5 23.6 - - - +
304D HIS* 3.5 21.3 - - + +
306D VAL* 4.2 11.0 - - + -
307D LYS* 3.5 33.1 - - + +
344D ALA 4.2 2.5 - - - +
345D LEU* 3.8 15.9 - - + +
347D SER* 1.3 87.2 + - - +
349D ILE* 1.3 54.0 + - - +
350D MET 3.1 2.9 - - - -
351D GLY* 2.6 33.3 + - - -
352D LEU* 4.2 0.5 + - - +
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Residues in contact with ILE 349 (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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306D VAL* 5.5 3.1 - - - -
330D ILE* 4.0 11.0 - - + -
334D VAL* 4.4 0.4 - - + -
345D LEU* 3.0 39.9 + - + +
346D ALA 4.0 9.9 - - - +
348D VAL* 1.3 77.2 - - - +
350D MET* 1.3 77.6 + - + +
351D GLY 2.9 1.2 + - - -
352D LEU* 3.0 32.0 + - + +
353D SER 4.1 1.0 + - - -
365D LEU* 4.6 4.8 - - + +
368D LEU* 3.9 39.5 - - + -
369D PHE* 4.0 20.1 - - + -
372D GLN* 3.3 23.8 - - - +
384D ILE* 4.9 1.8 - - + -
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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