Contacts of the helix formed by residues 329 - 338 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288E SER* 3.5 21.5 + - - +
292E VAL* 5.6 0.6 - - - +
327E SER* 2.9 14.6 + - - +
328E PRO* 1.3 79.2 - - - +
330E PHE* 1.3 66.3 + - - +
331E GLN* 3.4 29.4 + - + +
332E VAL* 2.9 45.6 + - + +
333E ALA* 3.0 10.2 + - - +
125F GLN* 2.9 46.6 + - + +
130F TYR* 3.5 31.2 - + + -
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Residues in contact with PHE 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E PRO 3.3 4.6 + - - -
329E HIS* 1.3 70.5 - - - +
331E GLN* 1.3 100.9 + - + +
332E VAL 2.8 1.0 + - - -
333E ALA* 4.4 5.8 - - - -
334E GLU* 2.6 51.9 + - + +
371E HIS* 4.5 5.6 - - + -
372E TRP* 3.9 19.5 - + + -
373E ASN* 3.9 26.0 - - - +
376E ILE* 5.2 1.5 - - + +
122F GLN* 3.3 43.5 - - + -
125F GLN* 2.9 30.7 + - + -
126F VAL* 3.6 15.7 - - + -
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Residues in contact with GLN 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289E PRO* 5.9 3.8 - - - +
292E VAL* 3.8 15.8 - - + +
329E HIS* 3.3 23.7 + - + +
330E PHE* 1.3 118.3 - - + +
332E VAL* 1.3 56.4 + - - +
334E GLU* 3.9 6.2 - - - +
335E ARG* 3.1 28.2 + - - +
125F GLN 4.8 0.2 - - - +
126F VAL* 3.9 25.0 - - - +
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Residues in contact with VAL 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288E SER* 4.4 9.0 - - - -
291E GLU* 3.6 45.1 - - + +
292E VAL* 4.3 9.9 - - + -
295E LEU* 3.9 12.4 - - + +
324E CYS* 4.2 9.2 - - + -
327E SER* 3.9 16.4 - - - +
329E HIS* 2.9 33.8 + - + +
330E PHE 2.8 3.6 + - - -
331E GLN* 1.3 71.9 - - - +
333E ALA* 1.3 69.3 + - - +
334E GLU 3.0 1.0 + - - -
335E ARG* 3.1 3.3 + - - +
336E ALA* 2.9 22.3 + - - +
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Residues in contact with ALA 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324E CYS 3.2 15.4 + - - +
325E VAL* 3.5 19.1 - - - +
327E SER 3.5 23.3 - - - +
329E HIS 3.0 2.9 + - - +
330E PHE* 3.6 8.7 - - - +
332E VAL* 1.3 78.5 - - - +
334E GLU* 1.3 69.1 + - - +
336E ALA* 3.3 2.3 + - - +
337E LEU* 2.9 26.6 + - + +
371E HIS* 5.0 1.6 - - + -
376E ILE* 5.0 13.2 - - + -
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Residues in contact with GLU 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E PHE* 2.6 41.2 + - + +
331E GLN* 3.9 5.5 - - - +
333E ALA* 1.3 71.5 - - - +
335E ARG* 1.3 57.3 + - - +
336E ALA 2.6 13.9 + - - -
337E LEU* 2.7 22.2 + - - +
338E TYR* 3.0 17.9 + - + +
373E ASN* 5.5 0.2 + - - -
375E THR* 4.9 7.6 - - - +
376E ILE* 5.6 3.9 - - + +
379E LEU* 4.8 25.9 - - + +
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Residues in contact with ARG 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292E VAL* 3.9 25.4 - - + +
295E LEU* 4.0 18.2 - - + -
296E ASN* 3.1 42.0 + - - +
299E GLU* 3.1 38.8 + - - +
331E GLN 3.1 16.6 + - - +
332E VAL 3.1 3.6 + - - +
334E GLU* 1.3 80.2 - - - +
336E ALA* 1.3 61.6 + - - +
338E TYR* 3.6 28.9 - - - +
339E TYR* 3.6 8.9 - - - -
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Residues in contact with ALA 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295E LEU* 3.9 12.5 - - + +
321E LEU* 4.6 5.8 - - + +
324E CYS* 3.5 31.9 - - + -
325E VAL* 4.2 9.9 - - + +
332E VAL 2.9 12.5 + - - +
333E ALA 3.6 3.8 - - - +
334E GLU 2.6 4.8 + - - -
335E ARG* 1.3 70.3 - - - +
337E LEU* 1.3 59.4 + - - +
338E TYR 3.0 1.8 - - - -
339E TYR* 2.8 40.3 + - - +
340E TRP* 3.4 6.1 - - - -
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Residues in contact with LEU 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325E VAL* 3.4 37.9 - - + +
333E ALA* 2.9 17.8 + - + +
334E GLU* 2.7 16.4 + - - +
336E ALA* 1.3 72.5 - - - +
338E TYR* 1.3 57.3 + - - +
339E TYR 3.0 1.3 + - - -
340E TRP* 2.8 34.4 + - + +
341E ASN* 5.8 0.2 - - - -
364E LEU* 4.3 10.5 - - + -
376E ILE* 4.5 7.4 - - + +
379E LEU* 3.7 45.5 - - + +
380E ILE* 3.8 19.7 - - + -
383E ALA* 4.4 10.6 - - + +
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Residues in contact with TYR 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299E GLU* 4.4 4.6 - - - +
334E GLU* 3.0 15.8 + - + +
335E ARG* 3.6 33.2 - - - +
336E ALA 3.0 0.8 + - - -
337E LEU* 1.3 72.2 - - - +
339E TYR* 1.3 61.5 + - - +
340E TRP 2.9 7.1 + - - -
341E ASN* 3.4 39.0 + - + +
342E ASN* 4.4 2.3 + - - +
379E LEU* 4.8 17.3 - - + -
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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