Contacts of the helix formed by residues 352 - 365 (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 ASN 352 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307E PRO 5.5 1.0 + - - -
310E PHE* 4.0 9.7 - - - -
311E VAL* 4.1 16.2 - - - +
314E MET* 3.7 33.3 - - + +
348E LEU* 3.6 19.1 + - - +
349E ILE 3.2 3.9 + - - +
350E SER 2.4 13.1 + - - -
351E ASP* 1.3 83.5 + - - +
353E ALA* 1.3 51.5 + - - -
354E ALA* 2.7 20.0 + - - +
355E LYS* 3.0 14.3 + - + +
356E ILE* 3.4 11.4 + - + +
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Residues in contact with ALA 353 (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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349E ILE 2.6 13.7 + - - -
350E SER* 2.7 13.8 + - - +
352E ASN* 1.3 72.6 - - - +
354E ALA* 1.3 61.6 + - - +
356E ILE* 3.9 1.8 - - - +
357E LEU* 3.0 34.4 + - + +
390E MET* 3.5 31.9 - - + +
391E ASN* 4.8 8.7 - - + +
394E LEU* 4.0 14.7 - - + +
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Residues in contact with ALA 354 (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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352E ASN* 2.7 8.6 + - - +
353E ALA* 1.3 74.6 - - - +
355E LYS* 1.3 60.9 + - + +
358E PRO* 3.1 20.8 - - - +
394E LEU* 3.8 24.1 - - + +
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Residues in contact with LYS 355 (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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314E MET* 4.0 24.9 - - + -
315E GLU* 3.8 30.1 + - + +
352E ASN* 3.0 6.1 + - + +
354E ALA* 1.3 81.9 - - + +
356E ILE* 1.3 61.4 + - - +
358E PRO* 3.2 16.4 - - + +
359E ILE* 3.4 17.4 - - - +
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Residues in contact with ILE 356 (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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310E PHE* 3.7 24.7 - - + -
314E MET* 3.6 35.0 - - + +
318E PHE* 3.7 34.3 - - + -
349E ILE* 3.7 35.0 - - + +
352E ASN* 3.4 12.6 + - + +
353E ALA 4.3 0.2 - - - +
355E LYS* 1.3 75.2 - - - +
357E LEU* 1.3 59.0 + - - +
358E PRO 3.2 1.6 - - - -
359E ILE* 2.7 39.1 + - + +
360E MET* 3.2 11.9 + - + -
387E PHE* 4.6 1.3 - - + -
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Residues in contact with LEU 357 (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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353E ALA* 3.0 20.6 + - + +
356E ILE* 1.3 72.8 - - - +
358E PRO* 1.3 65.0 - - + +
359E ILE 2.9 0.3 + - - -
360E MET* 4.6 1.1 - - + +
361E PHE* 2.8 64.6 + - + +
364E LEU* 6.1 0.9 - - + -
384E LEU* 6.1 0.2 - - + -
387E PHE* 3.5 54.7 - - + +
390E MET* 5.1 2.7 - - + -
391E ASN* 5.0 2.5 - - + +
394E LEU* 4.3 12.1 - - + -
395E PHE* 4.2 25.4 - - + +
398E CYS* 4.1 12.8 - - - -
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Residues in contact with PRO 358 (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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354E ALA 3.1 24.2 - - - +
355E LYS* 3.2 17.9 - - + +
356E ILE 3.3 2.0 - - - -
357E LEU* 1.3 96.0 - - + +
359E ILE* 1.3 55.7 + - + +
361E PHE* 4.4 2.5 - - + -
362E PRO* 3.3 19.7 - - - +
394E LEU* 6.2 1.1 - - + -
398E CYS* 4.2 20.6 - - - -
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Residues in contact with ILE 359 (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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315E GLU* 4.2 36.8 - - + +
318E PHE* 4.0 4.3 - - + -
319E ARG* 3.7 40.2 - - + +
322E ALA* 3.8 11.1 - - + +
355E LYS 3.4 21.5 - - - +
356E ILE* 2.7 23.7 + - + +
358E PRO* 1.3 75.2 - - + +
360E MET* 1.3 68.5 + - + +
362E PRO* 3.5 13.2 - - - +
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Residues in contact with MET 360 (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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318E PHE* 2.7 60.6 - - + +
321E LEU 3.8 2.7 - - - +
322E ALA* 3.0 33.0 - - + +
325E VAL* 5.2 2.2 - - - -
340E TRP* 3.9 31.0 - - + -
356E ILE* 3.2 13.5 + - + +
357E LEU 4.1 2.9 - - - +
359E ILE* 1.3 83.1 - - + +
361E PHE* 1.3 68.5 + - - +
362E PRO* 3.3 0.4 - - - -
363E SER* 2.6 28.9 + - - -
364E LEU* 3.1 20.7 + - + +
387E PHE* 4.4 7.9 - - + -
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Residues in contact with PHE 361 (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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357E LEU* 2.8 45.1 + - + +
358E PRO* 4.4 3.6 - - + -
360E MET* 1.3 70.6 - - - +
362E PRO* 1.3 63.5 - - + +
364E LEU* 2.7 13.3 + - - +
365E TYR* 2.7 72.3 + + + +
384E LEU* 4.0 8.1 - - + -
395E PHE* 3.6 34.5 - + - -
398E CYS* 4.0 13.7 - - + -
399E THR* 3.3 24.7 - - - -
402E PHE* 3.8 25.8 - + + -
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Residues in contact with PRO 362 (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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358E PRO* 3.3 18.2 - - + +
359E ILE 3.5 13.5 - - - +
360E MET 3.3 1.3 - - - -
361E PHE* 1.3 101.3 - - + +
363E SER* 1.3 59.0 + - - +
366E ARG* 3.0 25.8 + - - +
402E PHE* 4.6 22.4 - - + -
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Residues in contact with SER 363 (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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322E ALA* 3.7 27.4 + - - +
325E VAL* 4.7 6.4 - - - +
326E SER* 3.4 26.8 + - - -
360E MET* 2.6 28.4 + - - -
362E PRO* 1.3 77.2 - - - +
364E LEU* 1.3 70.8 + - - +
366E ARG* 3.5 19.2 - - - +
380E ILE* 5.0 5.2 - - - +
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Residues in contact with LEU 364 (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* 3.6 31.0 - - + -
337E LEU* 4.3 10.1 - - + -
340E TRP* 4.8 4.0 - - + -
357E LEU* 6.1 0.9 - - + -
360E MET* 3.7 25.4 - - + +
361E PHE* 2.7 12.2 + - - +
363E SER* 1.3 75.1 - - - +
365E TYR* 1.3 61.7 + - - +
366E ARG 3.1 1.3 + - - -
368E SER* 3.3 9.7 + - - -
380E ILE* 3.2 30.8 - - + +
383E ALA* 4.2 15.3 - - + -
384E LEU* 3.8 28.1 - - + +
387E PHE* 4.1 30.1 - - + -
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Residues in contact with TYR 365 (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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361E PHE* 2.7 52.3 + + + +
362E PRO* 4.9 1.6 - - + -
364E LEU* 1.3 71.5 - - - +
366E ARG* 1.3 66.1 + - - +
367E ASN* 3.0 9.4 + - - +
368E SER* 4.6 1.5 + - - -
384E LEU* 4.1 17.2 - - + +
395E PHE* 5.0 4.9 - + - -
399E THR* 3.5 23.0 - - + +
402E PHE* 3.3 35.9 - + + -
403E LYS* 3.5 26.0 - - + +
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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