Contacts of the helix formed by residues 329 - 338 (chain B) 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 HIS 329 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B SER* 3.5 29.6 + - - -
292B VAL* 5.4 0.6 - - - +
327B SER* 2.9 14.3 + - - +
328B PRO* 1.3 78.6 - - - +
330B PHE* 1.3 66.6 + - - +
331B GLN* 3.3 31.3 + - + +
332B VAL* 3.0 41.8 + - + +
333B ALA* 3.1 20.6 + - - +
125C GLN* 2.8 46.9 + - + +
130C TYR* 3.6 22.7 - + + +
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Residues in contact with PHE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B PRO 3.3 4.2 + - - -
329B HIS* 1.3 71.3 - - - +
331B GLN* 1.3 93.4 + - + +
332B VAL 3.1 0.2 + - - -
333B ALA* 4.6 4.9 - - - -
334B GLU* 2.7 55.2 + - - +
371B HIS* 4.6 4.5 - - + -
372B TRP* 3.8 21.5 - + + -
373B ASN* 3.9 27.4 - - + +
376B ILE* 5.4 0.8 - - - +
122C GLN* 3.1 52.5 - - + -
125C GLN* 2.8 30.7 + - + -
126C VAL* 3.9 10.5 - - + -
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B PRO* 6.1 0.9 - - - +
292B VAL* 3.5 15.7 - - + +
329B HIS* 3.3 22.8 + - + +
330B PHE* 1.3 104.5 - - + +
332B VAL* 1.3 57.0 + - - +
334B GLU* 3.9 6.1 - - - +
335B ARG* 3.2 26.2 + - - +
125C GLN 4.2 2.3 - - - +
126C VAL* 3.7 32.7 - - - +
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B SER* 4.5 5.6 - - - -
291B GLU* 3.4 49.8 - - + +
292B VAL* 4.1 11.9 - - + -
295B LEU* 3.7 12.9 - - + +
324B CYS* 4.3 11.0 - - + -
327B SER* 3.9 12.6 - - - +
329B HIS* 3.0 33.6 + - + +
330B PHE 3.1 0.6 - - - -
331B GLN* 1.3 75.2 - - - +
333B ALA* 1.3 68.4 + - - +
334B GLU 3.1 0.8 + - - -
335B ARG 3.2 1.6 + - - -
336B ALA* 2.9 22.3 + - - +
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B CYS 3.4 16.1 + - - +
325B VAL* 3.6 17.6 - - - +
327B SER 3.5 23.6 - - - +
329B HIS 3.1 7.5 + - - +
330B PHE* 3.8 5.2 - - - +
332B VAL* 1.3 78.4 - - - +
334B GLU* 1.3 67.7 + - - +
336B ALA* 3.2 2.3 + - - +
337B LEU* 2.9 31.0 + - + +
371B HIS* 5.1 6.3 - - + -
376B ILE* 5.1 5.2 - - + -
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Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B PHE* 2.7 42.5 + - + +
331B GLN* 3.9 5.6 - - - +
333B ALA* 1.3 71.4 - - - +
335B ARG* 1.3 67.1 + - - +
336B ALA 2.7 1.9 + - - -
337B LEU* 2.8 21.6 + - - +
338B TYR* 3.0 19.5 + - + +
373B ASN* 5.5 0.2 + - - -
375B THR* 4.9 7.4 - - - +
376B ILE* 5.8 3.3 - - + +
379B LEU* 4.7 24.9 - - + +
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Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B VAL* 3.9 25.1 - - + +
295B LEU* 4.0 17.7 - - + -
296B ASN* 3.1 41.8 + - - +
299B GLU* 3.1 39.9 + - - +
331B GLN 3.2 16.6 + - - +
332B VAL 3.2 4.5 + - - +
334B GLU* 1.3 80.7 - - - +
336B ALA* 1.3 63.4 + - - +
338B TYR* 3.4 26.4 - - - +
339B TYR* 3.6 8.4 - - - -
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B LEU* 4.1 10.2 - - + +
321B LEU* 4.5 6.5 - - + +
324B CYS* 3.5 32.5 - - + -
325B VAL* 4.1 10.1 - - + +
332B VAL 2.9 8.0 + - - +
333B ALA 3.5 7.2 - - - +
334B GLU 2.7 4.2 + - - -
335B ARG* 1.3 69.6 - - - +
337B LEU* 1.3 65.5 + - - +
338B TYR 2.9 1.6 - - - -
339B TYR* 2.7 38.2 + - - +
340B TRP* 3.7 5.3 - - - -
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B VAL* 3.3 42.4 - - + +
333B ALA* 2.9 20.0 + - + +
334B GLU* 2.8 17.2 + - - +
336B ALA* 1.3 72.6 - - - +
338B TYR* 1.3 54.3 + - - -
339B TYR 3.0 5.8 + - - -
340B TRP* 3.0 31.5 + - + +
341B ASN* 5.8 0.2 - - - -
364B LEU* 4.4 10.8 - - + -
376B ILE* 4.8 7.2 - - + -
379B LEU* 3.9 41.0 - - + +
380B ILE* 3.9 24.2 - - + -
383B ALA* 4.8 3.7 - - + +
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Residues in contact with TYR 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B GLU* 4.4 8.0 - - - +
334B GLU* 3.0 16.6 + - + +
335B ARG* 3.4 32.8 - - - +
336B ALA 2.8 4.4 + - - -
337B LEU* 1.3 70.8 - - - +
339B TYR* 1.3 60.4 + - - +
340B TRP 3.0 7.1 + - - -
341B ASN* 3.4 40.7 + - + +
342B ASN* 4.4 1.9 + - - +
379B LEU* 5.3 13.7 - - + -
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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