Contacts of the helix formed by residues 282 - 292 (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 ASP 282 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241D GLU* 3.8 12.7 - - - +
245D MET* 3.4 28.5 - - + -
249D ARG* 3.1 30.7 + - + -
278D ILE* 2.4 40.7 + - - +
281D THR* 1.3 83.7 - - - +
283D LEU* 1.3 64.6 + - - +
285D PRO* 3.1 12.9 - - - +
286D ALA* 3.2 15.6 + - - +
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Residues in contact with LEU 283 (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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245D MET* 4.7 5.2 - - + -
248D LEU* 3.9 28.9 - - + -
267D PHE* 3.6 30.7 - - + +
270D LEU* 4.3 7.4 - - + +
271D GLN* 3.6 35.0 - - + +
274D VAL* 4.5 9.0 - - + -
278D ILE 3.4 2.6 + - - +
279D THR* 3.1 31.8 + - + +
282D ASP* 1.3 76.3 - - + +
284D VAL* 1.3 58.6 + - - +
286D ALA* 2.8 9.1 + - + +
287D PHE* 2.5 35.5 + - - +
309D PHE* 4.4 0.9 - - + -
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Residues in contact with VAL 284 (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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279D THR 2.8 25.1 + - - +
280D LYS* 3.5 20.4 - - + +
283D LEU* 1.3 71.9 - - - +
285D PRO* 1.3 74.6 - - + +
287D PHE* 3.2 4.0 + - - +
288D GLN* 3.1 19.8 + - - +
309D PHE* 4.0 23.1 - - + -
313D LEU* 4.3 12.3 - - + -
321D VAL* 4.9 8.3 - - + -
325D GLN* 3.9 33.4 - - + -
326D ILE* 3.9 13.5 - - + -
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Residues in contact with PRO 285 (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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280D LYS 3.8 3.8 - - - +
281D THR 3.4 19.1 - - - +
282D ASP 3.1 17.0 - - - +
284D VAL* 1.3 96.9 - - + +
286D ALA* 1.3 52.8 + - - +
288D GLN* 2.8 41.7 + - - +
289D ASN* 2.9 17.9 - - - +
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Residues in contact with ALA 286 (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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252D ALA* 4.8 17.7 - - + +
267D PHE* 4.5 9.4 - - + -
282D ASP 3.2 12.6 + - - +
283D LEU* 2.8 19.6 + - + +
285D PRO* 1.3 75.6 - - - +
287D PHE* 1.3 62.4 + - - +
288D GLN 3.0 1.4 + - - -
289D ASN* 3.0 20.6 + - - +
290D LEU* 3.1 17.2 + - + +
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Residues in contact with PHE 287 (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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264D ALA* 6.4 0.2 - - - -
267D PHE* 3.0 45.7 - + + -
283D LEU 2.5 14.5 + - - +
284D VAL* 3.5 8.3 - - - +
286D ALA* 1.3 73.7 - - - +
288D GLN* 1.3 60.9 + - - +
290D LEU* 3.5 6.5 + - + +
291D MET* 3.2 49.5 + - + +
302D ALA* 3.4 44.4 - - + -
305D LYS* 4.3 7.4 - - + -
306D VAL* 4.0 24.2 - - + -
309D PHE* 3.6 27.8 - + + -
326D ILE* 4.4 9.9 - - + -
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Residues in contact with GLN 288 (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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284D VAL* 3.1 14.5 + - + +
285D PRO* 2.8 28.3 + - - +
287D PHE* 1.3 75.8 - - - +
289D ASN* 1.3 66.6 - - - +
291D MET* 2.8 26.5 + - + +
292D LYS* 3.2 20.7 + - - +
325D GLN* 3.2 58.0 + - + +
326D ILE* 5.4 1.1 - - + -
329D CYS* 4.1 17.4 - - - -
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Residues in contact with ASN 289 (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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285D PRO* 2.9 27.4 - - - +
286D ALA* 3.0 9.9 + - - +
288D GLN* 1.3 76.8 - - - +
290D LEU* 1.3 59.7 + - + +
292D LYS* 3.0 11.8 + - - +
293D ASP* 3.0 27.4 + - - +
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Residues in contact with LEU 290 (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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252D ALA* 4.3 24.2 - - + +
260D ARG* 4.3 12.3 - - + +
263D VAL* 4.3 7.2 - - + -
264D ALA* 3.9 27.6 - - + +
267D PHE* 4.2 22.0 - - + -
286D ALA 3.1 13.5 + - - +
287D PHE* 3.8 12.6 - - + +
288D GLN 3.0 1.0 + - - -
289D ASN* 1.3 79.5 - - + +
291D MET* 1.3 60.7 + - - +
292D LYS 3.0 0.8 + - - -
293D ASP* 3.3 24.4 + - - +
298D VAL* 3.9 20.8 - - + +
299D ARG* 3.6 12.8 - - - -
302D ALA* 4.0 13.0 - - + -
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Residues in contact with MET 291 (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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287D PHE* 3.2 52.0 + - + +
288D GLN* 2.8 23.2 + - + +
290D LEU* 1.3 77.4 - - - +
292D LYS* 1.3 60.7 + - - +
293D ASP 3.4 0.2 - - - -
299D ARG* 3.1 23.5 - - - +
302D ALA* 4.1 18.4 - - + -
306D VAL* 4.4 9.0 - - - -
326D ILE* 4.6 13.7 - - + +
329D CYS* 3.9 29.6 - - + -
330D ILE* 5.1 3.4 - - - -
333D LEU* 3.3 40.7 - - + +
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Residues in contact with LYS 292 (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* 3.5 15.5 - - - +
289D ASN* 3.0 12.8 + - - +
291D MET* 1.3 83.7 - - + +
293D ASP* 1.3 67.9 + - - +
294D CYS* 3.6 1.0 + - - -
299D ARG* 4.2 2.0 - - - +
328D PRO 5.5 0.6 - - - -
329D CYS* 3.8 34.6 - - + +
332D GLU* 4.6 15.0 - - - +
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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