Contacts of the helix formed by residues 284 - 302 (chain A) in PDB entry 2NZ2
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 THR 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A TYR* 6.2 0.2 - - - -
88A LEU* 3.9 33.6 - - + +
90A GLY* 5.7 1.2 + - - -
186A MET* 3.3 26.0 - - + +
187A HIS* 3.6 12.6 + - + +
264A GLY* 2.8 12.0 + - - -
266A ILE* 5.3 2.3 - - - +
282A TYR* 4.3 9.0 - - - +
283A GLU* 1.3 75.6 + - - +
285A PRO* 1.3 66.0 - - - +
286A ALA 3.8 0.4 - - - -
287A GLY* 3.9 13.5 - - - -
288A THR* 2.5 35.8 + - - -
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Residues in contact with PRO 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A MET 4.1 5.4 - - - +
209A LYS* 4.2 22.9 - - + +
210A THR* 3.9 21.3 - - + -
255A ASN* 3.7 26.0 - - - +
258A ALA* 3.4 28.4 - - + +
259A GLY* 3.9 4.9 - - - +
263A VAL* 3.4 14.9 - - - +
283A GLU 3.6 7.0 - - - +
284A THR* 1.3 87.9 - - - +
286A ALA* 1.3 63.4 + - - +
288A THR* 3.1 9.7 + - - -
289A ILE* 3.4 8.7 + - - +
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A PHE* 3.6 27.1 - - + +
254A LEU* 3.7 18.2 + - + -
255A ASN* 3.0 36.4 + - - +
258A ALA* 4.6 0.7 - - - -
285A PRO* 1.3 75.0 - - - +
287A GLY* 1.3 66.8 + - - +
289A ILE* 3.0 6.1 + - - +
290A LEU* 3.0 29.0 + - + +
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 6.0 2.3 - - - +
88A LEU* 3.9 9.7 - - - +
186A MET* 4.4 14.9 + - - -
251A PHE* 4.4 8.9 - - - -
255A ASN* 4.7 0.2 + - - -
284A THR* 3.9 18.4 + - - +
285A PRO 3.3 1.0 - - - -
286A ALA* 1.3 77.9 - - - +
288A THR* 1.3 57.4 + - - +
290A LEU* 3.6 5.3 + - - +
291A TYR* 2.9 30.5 + - - +
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.6 16.9 - - + +
263A VAL* 4.0 14.4 - - + -
264A GLY* 3.4 18.8 + - - +
266A ILE* 6.0 1.0 - - - +
284A THR* 2.5 25.7 + - - -
285A PRO 3.1 5.1 + - - -
287A GLY* 1.3 75.4 - - - +
289A ILE* 1.3 63.5 + - - +
291A TYR* 3.6 3.2 + - + +
292A HIS* 3.1 48.5 + - + +
357A GLN* 6.2 0.2 - - - +
358A VAL* 4.5 3.1 - - + -
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Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LEU* 4.6 1.3 - - + -
225A ILE* 3.7 27.8 - - + -
254A LEU* 3.9 28.0 - - + +
257A VAL* 4.8 0.2 - - + -
258A ALA* 3.4 30.1 - - + +
263A VAL* 4.4 0.4 - - + -
285A PRO 3.4 9.2 + - - +
286A ALA* 3.0 8.1 + - - +
288A THR* 1.3 76.3 - - - +
290A LEU* 1.3 60.5 + - + +
292A HIS* 3.5 3.6 + - - +
293A ALA* 2.9 26.9 + - - +
351A VAL* 4.5 8.1 - - + -
353A VAL* 4.1 18.6 - - + -
358A VAL* 4.0 33.0 - - + +
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ILE* 4.1 28.2 - - + +
225A ILE* 4.1 23.1 - - + -
227A PHE* 4.4 7.2 - - + -
232A PRO* 4.2 20.4 - - + -
251A PHE* 3.8 30.5 - - + -
254A LEU* 3.5 33.7 - - + -
286A ALA 3.0 19.3 + - - +
287A GLY* 4.0 4.0 - - - +
289A ILE* 1.3 77.2 - - - +
291A TYR* 1.3 59.5 + - - +
293A ALA* 4.3 1.6 - - - -
294A HIS* 2.9 34.8 + - - +
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Residues in contact with TYR 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ILE* 5.5 4.7 - - - +
80A SER* 4.1 30.1 + - - -
81A ALA 4.6 1.3 - - - -
82A LEU* 3.4 45.2 - - + +
88A LEU* 4.0 16.4 - - + -
287A GLY 2.9 20.1 + - - +
288A THR* 3.7 6.5 - - + +
290A LEU* 1.3 77.2 - - - +
292A HIS* 1.3 89.3 + + - +
294A HIS* 4.2 3.3 + - - +
295A LEU* 3.3 52.4 + - + +
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Residues in contact with HIS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A THR* 3.1 35.6 + - + +
289A ILE 3.5 6.0 + - - +
290A LEU 3.3 0.2 - - - -
291A TYR* 1.3 101.9 - + - +
293A ALA* 1.3 64.6 + - - +
295A LEU* 3.5 9.7 + - + +
296A ASP* 3.2 22.2 + - - +
357A GLN* 5.0 9.4 + - - -
358A VAL* 4.6 20.6 - - + +
360A ILE* 3.7 18.4 - - + +
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Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ILE* 4.1 19.3 - - + -
227A PHE* 3.7 23.6 - - + -
289A ILE 2.9 21.8 + - - +
290A LEU* 4.1 2.2 - - - +
292A HIS* 1.3 71.6 - - - +
294A HIS* 1.3 57.4 + - - +
296A ASP* 3.2 5.5 + - - +
297A ILE* 3.1 22.3 + - - +
349A VAL* 3.6 14.1 - - + +
351A VAL* 4.3 10.8 - - + -
360A ILE* 4.1 11.5 - - - +
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Residues in contact with HIS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 2.9 33.1 + - + -
78A GLN* 3.3 6.9 + - - -
80A SER* 2.7 31.5 + - - -
227A PHE* 3.6 14.5 - + + -
230A GLY* 3.1 29.0 + - - -
290A LEU 2.9 20.2 + - - +
291A TYR* 4.2 3.8 + - - +
293A ALA* 1.3 74.3 - - - +
295A LEU* 1.3 60.5 + - - +
297A ILE* 3.2 2.7 + - - +
298A GLU* 2.8 44.1 + - - +
342A GLN* 2.8 22.3 + - - -
345A VAL* 4.3 5.8 - - + +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER* 3.7 33.7 - - - +
291A TYR* 3.3 51.3 + - + +
292A HIS* 3.6 13.0 - - - +
294A HIS* 1.3 77.2 + - - +
296A ASP* 1.3 64.1 + - - +
298A GLU* 3.7 6.6 - - - +
299A ALA* 3.0 27.2 + - - +
307A ARG* 3.9 23.7 + - - +
311A GLN* 4.5 1.8 - - - +
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A HIS 3.2 10.0 + - - +
293A ALA 3.4 9.2 - - - +
294A HIS 3.2 0.4 - - - -
295A LEU* 1.3 82.0 - - - +
297A ILE* 1.3 55.4 + - - +
299A ALA* 3.7 5.5 + - - +
300A PHE* 3.3 24.1 + - - +
349A VAL* 3.9 9.0 - - + +
360A ILE* 3.3 20.3 - - + +
363A ARG* 2.5 59.1 + - - +
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Residues in contact with ILE 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A PHE* 3.9 23.1 - - + -
293A ALA 3.1 6.1 + - - -
294A HIS* 3.2 16.1 + - - +
296A ASP* 1.3 75.3 + - - +
298A GLU* 1.4 59.2 + - - +
300A PHE* 3.5 11.9 + - + -
301A THR* 2.5 33.6 + - - +
345A VAL* 3.7 17.0 - - + -
346A GLU 4.0 22.9 - - - +
347A GLY* 4.0 11.2 - - - +
348A LYS 4.0 2.5 - - - +
349A VAL* 3.7 26.7 - - + +
363A ARG* 4.5 5.6 - - + -
364A GLU 3.9 20.9 - - - +
365A SER* 4.5 3.4 - - - -
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER* 2.7 29.2 + - - -
294A HIS* 2.8 30.0 + - + +
295A LEU* 3.7 7.6 - - - +
297A ILE* 1.4 71.2 - - - +
299A ALA* 1.3 61.6 + - - +
301A THR* 3.2 5.5 + - - -
302A MET* 2.8 46.0 + - + +
307A ARG* 4.0 20.1 + - - +
310A LYS* 3.0 25.3 + - - +
311A GLN* 3.9 6.1 + - - -
342A GLN* 3.4 13.3 + - - -
345A VAL* 3.8 23.8 - - + -
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A LEU 3.0 20.6 + - - +
296A ASP* 3.9 6.1 - - - +
298A GLU* 1.3 77.2 - - - +
300A PHE* 1.3 59.3 + - - +
301A THR 3.7 0.3 + - - -
302A MET* 4.1 10.2 - - - +
307A ARG* 4.5 22.9 - - - +
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Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ASP 3.3 16.1 + - - +
297A ILE* 3.7 9.6 - - + +
298A GLU 3.2 0.8 - - - -
299A ALA* 1.3 76.6 - - - +
301A THR* 1.3 59.0 + - + +
302A MET 3.7 0.7 - - - -
363A ARG* 3.6 40.8 - - + -
364A GLU* 3.9 21.8 - - - -
365A SER* 4.0 16.6 - - - -
368A SER* 3.2 27.3 + - - -
369A LEU* 3.1 25.3 + - - +
370A TYR* 3.5 36.5 + + + +
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Residues in contact with THR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ILE* 2.5 24.3 + - + +
298A GLU* 3.4 8.5 + - - -
300A PHE* 1.3 82.3 - - + +
302A MET* 1.3 60.7 + - - +
344A ARG* 2.7 44.0 + - - +
345A VAL* 3.7 13.6 - - - +
346A GLU 3.5 11.7 - - - +
365A SER* 3.4 32.8 - - - +
367A LEU 4.0 13.7 - - - +
369A LEU* 3.7 6.5 - - - +
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Residues in contact with MET 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A GLU* 2.8 29.5 + - + +
299A ALA* 4.1 10.1 + - - +
300A PHE 3.7 0.2 - - - -
301A THR* 1.3 80.2 - - - +
303A ASP* 1.3 73.8 + - - +
304A ARG* 3.6 1.9 + - - -
306A VAL* 4.2 16.2 - - + -
307A ARG* 3.8 34.3 - - + -
310A LYS* 4.5 7.0 - - + -
341A SER* 3.2 33.9 - - - +
342A GLN* 3.3 23.6 - - - +
345A VAL* 3.6 11.0 - - + -
369A LEU* 3.2 11.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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