Contacts of the helix formed by residues 282 - 305 (chain A) in PDB entry 5WWW
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 ARG 282 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LYS 5.2 1.8 + - - +
229A SER* 3.2 53.6 + - - +
230A VAL* 4.7 1.2 - - - +
231A ASN* 3.6 10.3 - - - +
263A ASN* 5.1 6.8 + - - +
281A GLY* 1.3 72.2 - - - -
283A LYS* 1.3 67.8 + - - +
284A GLU* 3.1 37.0 + - - +
285A ASP* 2.9 29.4 + - - +
286A VAL* 2.8 21.5 + - - +
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASN* 2.8 17.9 + - - +
232A THR* 3.2 29.7 - - + +
282A ARG* 1.3 73.0 - - - +
284A GLU* 1.3 65.4 + - - +
286A VAL* 3.3 2.9 + - - +
287A ALA* 3.0 28.9 + - + +
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASN* 5.5 0.9 + - - -
282A ARG* 3.1 38.7 + - - +
283A LYS* 1.3 83.2 + - - +
285A ASP* 1.3 67.0 + - - +
287A ALA* 3.5 8.6 + - - +
288A MET* 3.1 27.8 + - - +
291A ARG* 5.0 1.7 + - - -
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Residues in contact with ASP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A THR* 3.0 29.8 - - - +
263A ASN* 3.9 18.8 + - - +
264A THR* 3.7 9.5 - - + +
282A ARG* 2.9 33.2 + - + +
284A GLU* 1.3 85.7 - - - +
286A VAL* 1.3 64.8 + - - +
288A MET* 3.2 14.8 + - - +
289A ALA* 3.0 23.2 + - - +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 3.8 15.0 - - + +
234A GLU* 3.5 34.8 - - + -
264A THR* 4.2 0.7 - - + -
279A VAL* 3.7 25.8 - - + +
280A THR* 3.6 8.5 - - - -
281A GLY* 3.3 33.0 - - - +
282A ARG 2.8 19.6 + - - +
283A LYS 3.8 4.5 - - - +
285A ASP* 1.3 71.0 - - - +
287A ALA* 1.3 57.4 + - - +
289A ALA* 3.3 1.0 + - - +
290A LYS* 2.8 32.0 + - + +
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LYS* 3.0 19.3 + - + +
284A GLU* 3.6 10.1 - - - +
285A ASP 3.2 0.2 - - - -
286A VAL* 1.3 78.5 - - - +
288A MET* 1.3 56.0 + - - +
290A LYS* 3.8 9.0 - - - +
291A ARG* 3.0 48.5 + - - +
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Residues in contact with MET 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LYS* 4.5 20.0 - - - +
262A THR* 3.8 23.6 - - + -
284A GLU 3.1 14.9 + - - +
285A ASP* 3.2 15.7 + - - +
287A ALA* 1.3 75.2 - - - +
289A ALA* 1.3 65.8 + - - +
291A ARG* 3.3 26.1 + - + +
292A GLU* 3.0 38.2 + - + +
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Residues in contact with ALA 289 (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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258A LEU* 4.0 14.3 - - + +
262A THR* 3.8 25.0 - - + +
264A THR* 4.0 4.0 - - - +
266A ILE* 4.4 4.0 - - + -
279A VAL* 3.8 23.8 - - + -
285A ASP 3.0 15.2 + - - +
288A MET* 1.3 75.6 - - - +
290A LYS* 1.3 57.8 + - - +
292A GLU* 3.2 1.9 + - - +
293A ILE* 2.9 36.6 + - - +
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Residues in contact with LYS 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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234A GLU* 5.2 16.9 + - + +
235A CYS 5.1 5.3 + - - -
236A VAL* 3.9 34.8 - - + +
237A PRO* 6.2 1.6 - - - -
279A VAL* 5.0 0.8 - - - +
286A VAL* 2.8 20.8 + - + +
287A ALA* 3.8 7.6 - - - +
289A ALA* 1.3 76.4 - - - +
291A ARG* 1.3 63.2 + - - +
293A ILE* 3.3 1.7 + - - +
294A LEU* 2.9 52.8 + - + +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU 5.0 2.0 + - - -
287A ALA* 3.0 42.4 + - - +
288A MET* 3.5 34.6 - - - +
290A LYS* 1.3 78.3 - - - +
292A GLU* 1.3 58.8 + - + +
294A LEU* 3.9 5.1 - - - +
295A SER* 2.9 39.8 + - - +
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Residues in contact with GLU 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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258A LEU* 3.4 30.9 - - + +
261A LYS* 2.6 40.3 + - - +
288A MET* 3.0 31.5 + - + +
289A ALA 3.2 3.3 + - - +
291A ARG* 1.3 74.6 - - + +
293A ILE* 1.3 61.3 + - - +
295A SER* 3.9 5.0 - - - -
296A ALA* 2.9 29.8 + - - +
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Residues in contact with ILE 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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236A VAL* 3.8 16.6 - - + -
238A VAL* 3.7 24.5 - - + -
247A ILE* 3.8 10.1 - - + +
255A ILE* 4.5 10.3 - - + -
258A LEU* 3.8 19.3 - - + -
266A ILE* 4.6 2.7 - - + -
277A PHE* 3.9 30.3 - - + -
279A VAL* 3.9 26.9 - - + -
289A ALA 2.9 22.5 + - - +
290A LYS 3.8 3.4 - - - +
292A GLU* 1.3 76.4 - - - +
294A LEU* 1.3 57.9 + - - +
296A ALA* 3.2 6.5 + - - +
297A ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 294 (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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236A VAL* 3.6 15.5 - - + -
237A PRO* 3.4 30.1 - - + +
238A VAL* 5.1 1.3 - - + -
290A LYS* 2.9 47.0 + - + +
291A ARG* 4.0 4.5 - - - +
293A ILE* 1.3 77.3 - - + +
295A SER* 1.3 58.2 + - - +
297A ALA* 3.3 5.7 + - + +
298A GLU* 3.0 30.2 + - - +
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Residues in contact with SER 295 (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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291A ARG* 2.9 26.7 + - - +
292A GLU* 3.9 5.4 - - - -
294A LEU* 1.3 76.8 - - - +
296A ALA* 1.3 56.0 + - - +
298A GLU* 3.4 6.8 + - - +
299A HIS* 2.9 29.0 + - - +
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Residues in contact with ALA 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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247A ILE* 3.8 21.1 - - + -
292A GLU 2.9 18.5 + - - +
293A ILE* 3.6 5.4 - - - +
295A SER* 1.3 75.8 - - - +
297A ALA* 1.3 65.6 + - - +
299A HIS* 3.2 7.7 + - - +
300A PHE* 3.0 38.6 + - + -
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Residues in contact with ALA 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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237A PRO 5.5 0.7 - - - +
238A VAL* 3.7 24.9 - - + -
239A PRO* 4.0 17.7 - - + -
243A HIS* 3.4 10.8 - - + -
247A ILE* 3.8 9.3 - - + +
293A ILE 2.9 17.3 + - - +
294A LEU* 3.7 7.2 - - + +
296A ALA* 1.3 75.4 - - - +
298A GLU* 1.3 62.9 + - - +
300A PHE* 3.3 1.4 + - - -
301A SER* 3.0 25.3 + - - -
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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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294A LEU 3.0 17.4 + - - +
295A SER* 3.8 5.8 - - - +
297A ALA* 1.3 76.7 - - - +
299A HIS* 1.3 57.3 + - - +
301A SER* 3.3 8.2 + - - -
302A MET* 2.9 49.1 + - + +
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Residues in contact with HIS 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 SER 2.9 14.9 + - - +
296A ALA* 3.3 11.9 - - - +
298A GLU* 1.3 75.9 - - - +
300A PHE* 1.3 85.7 + + - +
302A MET* 3.2 6.0 + - - +
303A ILE* 3.0 49.2 + - + +
4B G 4.8 6.2 + - - -
5B U 2.6 31.2 + + - -
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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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243A HIS* 4.4 14.6 - + + -
246A GLU* 3.2 71.1 - - + +
247A ILE* 4.3 13.0 - - + -
254A LYS* 5.2 0.4 - - - -
296A ALA* 3.0 35.2 + - + +
297A ALA* 3.3 3.6 + - - +
299A HIS* 1.3 86.3 - + - +
301A SER* 1.3 61.7 + - - +
303A ILE* 3.9 13.7 - - + -
304A ARG* 3.0 32.3 + - + +
5B U 3.6 42.2 - + - -
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Residues in contact with SER 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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239A PRO* 4.3 7.6 - - - +
243A HIS* 2.7 29.5 + - - -
297A ALA 3.0 10.7 + - - -
298A GLU* 3.5 12.3 - - - -
300A PHE* 1.3 76.8 - - - +
302A MET* 1.3 60.3 + - - +
304A ARG* 5.1 0.4 - - - -
305A ALA* 2.9 38.4 + - - +
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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* 2.9 37.8 + - + +
299A HIS* 3.2 6.9 + - - +
301A SER* 1.3 79.8 - - - +
303A ILE* 1.3 63.8 + - + +
305A ALA* 4.3 8.4 + - - +
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Residues in contact with ILE 303 (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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299A HIS* 3.0 41.2 + - + +
300A PHE* 3.7 15.9 - - + +
302A MET* 1.3 81.2 - - + +
304A ARG* 1.3 77.7 + - + +
305A ALA 3.7 1.2 - - - +
5B U 3.6 37.5 - - + +
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Residues in contact with ARG 304 (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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242A GLU* 5.1 4.9 - - - -
246A GLU* 2.8 40.0 + - - +
300A PHE* 3.0 22.7 + - + +
301A SER* 5.1 0.2 - - - -
303A ILE* 1.3 94.7 + - + +
305A ALA* 1.3 67.0 + - - +
306A SER* 3.4 2.6 + - - -
4B G 5.8 0.2 - - - -
5B U 2.9 46.4 + - - -
6B U 3.1 26.0 + - - +
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Residues in contact with ALA 305 (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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301A SER* 2.9 24.4 + - - +
302A MET* 4.3 7.3 + - - +
303A ILE 3.7 1.6 - - - +
304A ARG* 1.3 79.3 - - - +
306A SER* 1.3 65.3 + - - +
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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