Contacts of the helix formed by residues 282 - 296 (chain D) in PDB entry 1NZX
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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281D ALA* 1.3 70.5 - - - +
283D MET* 1.3 63.6 + - - +
284D ASP* 3.4 9.2 + - - +
285D TRP* 2.9 38.7 + - + +
286D ALA* 2.8 23.2 + - - +
432D PHE* 6.1 1.0 - - - -
434D LYS* 4.0 23.5 + - + +
454D ASN* 5.7 2.0 + - - -
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Residues in contact with MET 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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281D ALA* 3.1 9.6 + - - +
282D ASP* 1.3 70.7 + - - +
284D ASP* 1.3 68.2 + - - +
286D ALA* 3.7 4.2 - - - +
287D VAL* 3.0 46.1 + - - +
314D ILE* 4.0 43.5 - - + +
317D GLU* 3.7 35.7 - - + +
318D PHE* 4.1 18.8 - - + -
321D ARG* 3.9 16.2 - - - +
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Residues in contact with ASP 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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282D ASP* 3.4 6.9 + - - +
283D MET* 1.3 79.9 - - - +
285D TRP* 1.3 63.3 + - - +
287D VAL* 3.4 6.8 + - - +
288D GLU* 3.1 23.8 + - - +
321D ARG* 3.9 29.0 + - - +
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Residues in contact with TRP 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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494C LYS* 3.8 32.9 - - + +
282D ASP* 2.9 33.7 + - + +
284D ASP* 1.3 73.3 - - - +
286D ALA* 1.3 57.9 + - - +
288D GLU* 3.2 7.9 + - + +
289D GLN* 2.9 73.7 + - + +
432D PHE* 3.8 16.2 - + - -
454D ASN* 2.8 28.5 + - + -
455D CYS* 5.0 4.3 - - + -
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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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277D ILE* 3.6 34.4 - - + +
281D ALA* 4.5 2.7 - - + -
282D ASP 2.8 22.9 + - - +
283D MET* 3.7 4.7 - - - +
285D TRP* 1.3 73.1 - - - +
287D VAL* 1.3 58.0 + - - +
289D GLN* 4.0 0.5 - - - +
290D ALA* 2.8 34.0 + - - +
318D PHE* 4.0 5.2 - - + -
432D PHE* 3.9 22.4 - - + -
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Residues in contact with VAL 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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283D MET* 3.0 48.6 + - - +
284D ASP* 3.6 5.6 - - - +
286D ALA* 1.3 76.8 - - - +
288D GLU* 1.3 59.1 + - - +
290D ALA* 3.8 1.9 - - - +
291D HIS* 3.0 28.1 + - - +
318D PHE* 3.8 20.0 - - + +
321D ARG* 3.8 45.8 - - + +
322D SER* 3.9 11.3 + - - +
325D ARG* 5.0 7.4 - - + -
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Residues in contact with GLU 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 ASP 3.1 13.7 + - - +
285D TRP* 3.2 8.3 + - + +
287D VAL* 1.3 80.1 - - - +
289D GLN* 1.3 70.2 + - - +
291D HIS* 3.3 9.3 + - - +
292D PHE* 3.0 28.2 + - + +
325D ARG* 2.9 49.0 + - - -
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Residues in contact with GLN 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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275D ASN* 4.8 0.9 - - - -
285D TRP* 2.9 78.6 + - + +
286D ALA 4.0 0.2 - - - +
288D GLU* 1.3 83.1 - - - +
290D ALA* 1.3 56.5 + - - +
292D PHE* 3.5 16.6 - - - +
293D ALA* 2.7 37.1 + - - +
432D PHE* 3.5 26.2 - - + -
455D CYS* 4.7 1.6 - - - +
456D TYR* 4.3 17.5 + - + +
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Residues in contact with ALA 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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275D ASN* 3.6 23.1 + - - +
277D ILE* 4.7 1.8 - - + -
286D ALA 2.8 19.9 + - - +
287D VAL 3.8 2.5 - - - +
289D GLN* 1.3 78.0 - - - +
291D HIS* 1.3 61.5 + - - +
293D ALA* 3.4 2.8 + - - +
294D LEU* 3.2 19.1 + - - +
305D GLY 5.2 0.7 - - - +
308D THR* 4.2 11.0 + - + +
318D PHE* 3.6 25.6 - - + -
322D SER* 5.6 0.2 - - - +
405D MET* 3.7 13.1 - - + +
432D PHE* 5.2 0.2 - - - -
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Residues in contact with HIS 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 VAL* 3.0 15.0 + - + +
288D GLU* 3.4 11.9 - - - +
290D ALA* 1.3 76.9 - - - +
292D PHE* 1.3 60.4 + - - +
294D LEU 3.3 1.4 + - - -
295D PHE* 2.8 69.9 + + - +
322D SER* 5.0 3.0 + - - -
325D ARG* 3.4 56.9 + - + +
326D ALA* 4.0 14.8 + - - +
329D ARG* 3.1 35.0 + - - -
405D MET* 3.7 11.0 - - + +
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Residues in contact with PHE 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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116D ILE* 6.6 0.2 - - + -
288D GLU* 3.0 20.0 + - + +
289D GLN* 3.5 17.9 - - - +
291D HIS* 1.3 82.1 - - + +
293D ALA* 1.3 63.6 + - - +
295D PHE* 5.2 0.4 - - - -
296D PHE* 3.0 73.0 + + + +
329D ARG* 5.9 0.9 - - - +
456D TYR* 3.8 14.6 - - + -
457D ASP* 3.7 28.5 - - + -
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Residues in contact with ALA 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D ASN* 4.2 3.6 - - - +
289D GLN 2.7 21.4 + - - +
290D ALA* 3.5 11.7 - - - +
292D PHE* 1.3 74.5 - - - +
294D LEU* 1.3 56.5 + - - +
296D PHE* 5.0 0.7 + - - +
301D CYS* 5.7 0.7 - - - +
304D ALA* 3.4 9.7 - - - +
305D GLY* 2.9 24.6 + - - +
456D TYR* 3.3 47.3 - - + -
457D ASP* 4.0 6.1 - - - +
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Residues in contact with LEU 294 (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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290D ALA 3.2 12.5 + - - +
291D HIS 4.1 1.6 - - - +
292D PHE 3.1 0.4 - - - -
293D ALA* 1.3 81.5 - - - +
295D PHE* 1.3 79.8 + - + +
296D PHE 3.5 1.8 + - - +
299D GLY* 3.2 23.0 - - - +
301D CYS* 6.0 0.2 - - - +
304D ALA* 4.3 9.4 - - + +
305D GLY 3.6 24.0 - - - +
306D SER* 3.6 21.1 - - - +
402D GLY 4.2 5.8 - - - +
404D VAL 3.6 36.1 - - - +
405D MET* 3.6 28.3 - - + +
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Residues in contact with PHE 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D HIS* 2.8 59.1 + + - +
294D LEU* 1.3 77.7 - - + +
296D PHE* 1.3 64.6 + - - +
298D GLN* 3.2 4.0 + - - -
299D GLY 3.1 11.7 + - - +
326D ALA* 4.3 6.3 - - + -
329D ARG* 3.0 37.2 + - - +
341D GLN* 4.0 7.6 - - - -
383D PRO* 3.8 21.3 - - + -
384D THR 3.9 16.2 - - - -
385D VAL* 4.2 6.5 - - + -
403D PRO* 3.5 43.1 - - + -
405D MET* 3.6 22.9 - - + -
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Residues in contact with PHE 296 (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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116D ILE* 4.1 27.1 - - + -
120D VAL* 4.2 24.7 - - + -
121D ASP* 5.2 0.2 - - - -
170D PHE* 3.4 37.7 - + - -
292D PHE* 3.0 58.6 + + + +
293D ALA 5.3 0.9 - - - +
294D LEU 3.5 2.3 - - - +
295D PHE* 1.3 73.3 - - - +
297D ASN* 1.3 72.3 + - + +
299D GLY* 2.9 21.5 + - - -
300D GLN 3.7 1.4 + - - -
301D CYS* 4.3 16.0 - - + +
329D ARG* 4.6 3.4 - - - +
457D ASP* 4.1 18.4 - - + +
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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