Contacts of the helix formed by residues 280 - 298 (chain A) in PDB entry 4NZP
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 280 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 6.0 1.2 - - - -
92A LEU* 3.8 34.2 + - + +
187A LEU* 3.3 36.8 - - + +
188A HIS* 3.7 11.0 - - + +
260A GLY* 2.9 13.5 + - - -
262A LEU* 6.0 0.5 - - - +
278A TYR* 4.3 10.6 - - - +
279A GLU* 1.3 74.5 + - - +
281A PRO* 1.3 63.7 - - - +
282A GLY 3.5 0.9 - - - -
283A GLY* 3.9 5.4 - - - -
284A THR* 2.5 38.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU 4.5 0.4 - - - +
210A TRP* 3.6 23.1 - - + -
211A SER* 5.2 1.8 - - - -
250A LEU 4.2 2.5 - - - -
251A ASN* 3.6 21.1 - - - +
254A GLY* 3.7 2.0 - - - -
255A CYS* 3.7 32.1 - - - +
259A ILE* 3.2 26.7 - - - +
279A GLU* 3.3 13.2 - - + +
280A THR* 1.3 90.0 - - - +
282A GLY* 1.3 62.0 + - - +
284A THR* 3.9 2.6 - - - -
285A ILE* 3.5 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 4.4 6.7 - - - -
250A LEU* 3.6 31.4 - - - +
251A ASN* 3.0 21.9 + - - +
281A PRO* 1.3 79.1 - - - +
283A GLY* 1.3 58.2 + - - +
285A ILE* 3.3 6.0 + - - +
286A LEU* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 3.2 27.1 - - - -
92A LEU* 4.0 6.9 - - - +
187A LEU* 4.1 10.0 + - - +
247A LEU* 4.4 1.9 - - - +
251A ASN* 4.5 0.8 + - - -
280A THR* 3.6 15.8 + - - +
281A PRO 3.4 0.4 - - - -
282A GLY* 1.3 73.2 - - - +
284A THR* 1.3 65.2 + - - +
286A LEU* 3.2 6.0 + - - -
287A LEU* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.8 18.0 - - + +
259A ILE* 4.1 14.8 - - + -
260A GLY* 3.3 20.4 + - - +
280A THR* 2.5 25.0 + - - -
281A PRO 3.9 4.3 - - - -
282A GLY 3.3 0.2 - - - -
283A GLY* 1.3 77.7 - - - +
285A ILE* 1.3 60.4 + - - +
287A LEU* 3.7 4.7 + - - +
288A LYS* 3.6 19.2 + - - +
352A GLY 6.1 0.2 - - - +
354A VAL* 4.5 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ILE* 4.0 15.0 - - + -
226A LEU* 4.3 6.3 - - + -
250A LEU* 3.9 26.0 - - + +
253A LEU* 4.6 2.9 - - + -
254A GLY* 4.0 20.0 - - - +
259A ILE* 4.1 4.3 - - + -
281A PRO 3.5 14.8 + - - +
282A GLY 3.3 7.8 + - - +
283A GLY 3.3 0.2 - - - -
284A THR* 1.3 75.6 - - - +
286A LEU* 1.3 66.2 + - - +
288A LYS* 3.4 2.9 + - - +
289A ALA* 3.2 21.0 + - - +
347A LEU* 4.4 3.1 - - + +
349A LEU* 3.8 30.5 - - + -
354A VAL* 4.1 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 5.1 1.6 - - + -
78A PHE* 3.9 26.2 - - + -
81A PHE* 3.7 36.6 - - + -
226A LEU* 5.1 1.6 - - + -
228A PHE* 4.1 25.4 - - + -
233A LEU* 4.2 16.8 - - + +
247A LEU* 4.9 10.8 - - + -
250A LEU* 4.2 16.8 - - + +
282A GLY 2.9 14.0 + - - +
283A GLY* 3.2 8.9 + - - +
285A ILE* 1.3 77.0 - - - +
287A LEU* 1.3 57.0 + - - +
289A ALA* 3.3 3.2 + - - +
290A HIS* 2.8 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 3.8 17.6 - - + -
84A ASN* 3.6 47.6 - - + +
86A ILE* 4.2 26.5 - - + -
92A LEU* 4.3 10.5 - - + -
283A GLY 3.0 16.0 + - - +
284A THR* 4.0 6.5 - - - +
285A ILE 3.4 0.2 - - - -
286A LEU* 1.3 75.0 - - - +
288A LYS* 1.3 62.9 + - - +
290A HIS* 3.4 2.0 + - - +
291A ARG* 3.1 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A THR 3.6 6.8 + - - +
285A ILE 3.4 8.4 + - - +
286A LEU 3.3 0.4 - - - -
287A LEU* 1.3 81.5 - - - +
289A ALA* 1.3 61.5 + - - +
291A ARG* 3.5 7.7 + - + +
292A ALA* 3.2 21.0 + - - +
347A LEU* 4.2 1.1 - - + -
354A VAL* 3.3 45.9 + - + +
355A MET* 5.2 1.8 - - - +
356A VAL* 3.9 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 3.7 25.8 - - + -
228A PHE* 3.9 12.8 - - + -
285A ILE 3.2 15.0 + - - +
286A LEU 3.7 2.9 - - - +
288A LYS* 1.3 76.8 - - - +
290A HIS* 1.3 62.0 + - - +
292A ALA 3.1 1.4 + - - -
293A LEU* 2.9 25.3 + - - +
345A VAL* 3.5 16.5 - - + +
347A LEU* 4.1 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 3.2 17.4 + - + +
82A ARG* 3.1 21.1 - - - -
84A ASN* 2.6 21.4 + - - +
228A PHE* 4.0 12.7 - + + -
231A GLY 3.3 24.4 + - - -
286A LEU* 2.8 20.6 + - + +
287A LEU* 3.9 4.9 - - - +
288A LYS 3.3 0.2 - - - -
289A ALA* 1.3 74.9 - - - +
291A ARG* 1.3 63.9 + - - +
293A LEU* 3.4 13.2 + - + +
294A GLU* 2.9 52.8 + - - +
338A GLN* 2.8 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN* 3.3 43.6 + - - +
287A LEU* 3.1 28.2 + - + +
288A LYS* 3.7 8.3 - - + +
290A HIS* 1.3 76.0 - - - +
292A ALA* 1.3 61.9 + - - +
294A GLU* 3.2 10.9 + - - +
295A SER* 3.0 24.4 + - - -
303A ALA* 6.3 0.4 - - - +
307A ASP* 2.7 38.4 + - - +
310A MET* 4.8 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS 3.2 10.2 + - - +
289A ALA 3.1 9.9 + - - +
291A ARG* 1.3 79.0 - - - +
293A LEU* 1.3 63.7 + - - +
295A SER* 2.5 26.9 + - - -
296A ILE* 3.8 2.1 + - - +
345A VAL* 3.6 24.9 - - + -
356A VAL* 4.0 20.4 - - + -
359A ARG* 3.9 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PHE* 3.5 31.4 - - + -
231A GLY* 4.1 6.3 - - - -
289A ALA 2.9 13.3 + - - +
290A HIS* 3.5 17.0 - - + +
292A ALA* 1.3 78.5 - - - +
294A GLU* 1.3 62.6 + - + +
295A SER 3.2 1.0 + - - -
296A ILE* 3.3 10.3 + - + +
297A THR* 2.9 29.4 + - + +
341A ALA* 3.5 31.4 - - + +
342A ASN 3.7 7.2 - - - +
343A GLY* 3.5 37.9 - - - +
344A ARG 4.6 0.7 - - - +
345A VAL* 3.6 12.2 - - + +
359A ARG* 5.4 0.2 - - - -
360A GLU 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN* 2.9 22.5 + - - +
290A HIS* 2.9 38.7 + - + +
291A ARG* 3.2 14.8 + - - +
293A LEU* 1.3 82.4 - - + +
295A SER* 1.3 60.4 + - - +
297A THR* 3.7 7.4 - - - -
298A LEU* 2.9 54.3 + - + +
303A ALA* 5.6 5.8 - - + +
306A LYS* 2.6 33.2 + - - -
338A GLN* 3.2 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG 3.0 13.0 + - - -
292A ALA* 2.5 25.1 + - - -
294A GLU* 1.3 78.8 - - - +
296A ILE* 1.3 61.0 + - - +
298A LEU 4.9 3.8 - - - +
359A ARG* 3.9 14.7 + - - -
367A PHE* 6.1 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA 4.1 3.1 - - - +
293A LEU* 3.5 12.8 - - + +
295A SER* 1.3 82.0 + - - +
297A THR* 1.3 64.6 + - + +
298A LEU 3.8 1.3 - - - -
344A ARG 5.1 0.2 - - - +
359A ARG* 3.6 26.0 - - + +
360A GLU* 3.5 47.1 - - - +
361A SER* 3.9 7.4 - - - +
365A SER* 3.5 12.5 - - - +
366A LEU* 2.7 37.3 + - - +
367A PHE* 3.9 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 2.9 29.8 + - + +
294A GLU* 3.7 3.5 - - - -
296A ILE* 1.3 89.7 - - + +
298A LEU* 1.3 67.0 + - - +
299A ASP 4.0 0.2 + - - -
340A HIS* 3.4 28.2 - - - +
341A ALA* 3.6 13.9 - - - -
342A ASN 3.5 24.7 - - - +
361A SER* 4.0 6.7 - - - -
364A ASP 3.6 19.3 - - - +
366A LEU* 3.9 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLU* 2.9 46.0 + - + +
295A SER 4.9 3.8 - - - +
296A ILE 5.1 0.7 - - - -
297A THR* 1.3 94.2 + - - +
299A ASP* 1.3 70.9 + - - +
300A ARG* 3.5 2.3 + - - -
302A ALA* 4.6 3.4 - - + -
303A ALA* 4.0 32.0 - - + +
306A LYS* 4.3 5.6 - - - -
337A SER* 3.4 31.6 - - - +
338A GLN* 4.1 4.9 - - - +
340A HIS* 5.2 0.9 - - + -
341A ALA* 4.1 18.6 - - + +
366A LEU* 3.8 7.2 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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