Contacts of the helix formed by residues 285 - 306 (chain A) in PDB entry 5H2U
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 PRO 285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A GLU* 3.2 31.6 - - - +
282A LYS 4.4 4.3 - - - +
283A VAL 3.7 6.7 - - - +
284A LEU* 1.3 92.9 - - - +
286A VAL* 1.3 60.3 + - - +
287A SER* 3.1 20.6 - - - +
288A GLU* 2.9 31.6 + - + +
289A LEU* 3.0 11.1 + - - +
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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
----------------------------------------------------------
281A GLU* 3.4 10.7 + - + +
284A LEU 3.8 0.6 + - - -
285A PRO* 1.3 71.4 - - - +
287A SER* 1.3 57.0 + - - +
289A LEU* 3.1 14.4 + - + +
290A LEU* 2.8 44.2 + - + +
381A PHE* 4.1 4.7 - - + -
383A ARG* 4.3 3.1 - - - +
411A GLU* 3.6 42.2 - - + +
413A PRO* 3.9 24.9 - - + -
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Residues in contact with SER 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLU* 5.1 0.2 + - - -
285A PRO* 3.6 17.0 - - - +
286A VAL* 1.3 79.1 - - - +
288A GLU* 1.3 63.6 + - - +
290A LEU* 3.3 14.5 + - - +
291A ASP* 3.2 27.5 + - - +
444A PHE 5.1 1.4 - - - +
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A VAL 5.6 0.9 - - - +
284A LEU* 4.0 19.7 - - + -
285A PRO* 2.9 29.3 + - + +
287A SER* 1.3 78.9 + - - +
289A LEU* 1.3 59.5 + - - +
291A ASP* 3.2 20.4 + - - +
292A ILE* 3.0 36.7 + - + +
324A THR* 2.6 39.2 - - + +
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 5.6 0.2 - - + -
276A LEU* 3.6 30.7 - - + -
284A LEU* 3.8 20.6 - - + +
285A PRO 3.0 13.2 + - - +
286A VAL* 3.3 19.1 - - + +
288A GLU* 1.3 76.0 - - - +
290A LEU* 1.3 56.3 + - - +
292A ILE* 3.5 11.4 + - + +
293A ALA* 3.0 28.9 + - - +
380A MET* 3.8 25.2 - - + +
381A PHE* 3.6 33.0 - - + -
383A ARG* 4.1 22.2 - - + +
411A GLU* 5.9 1.3 - - + -
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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
----------------------------------------------------------
286A VAL* 2.8 31.1 + - + +
287A SER* 3.5 14.6 - - - +
288A GLU 3.1 0.2 - - - -
289A LEU* 1.3 74.8 - - - +
291A ASP* 1.3 64.3 + - - +
293A ALA* 3.4 5.2 + - + +
294A TRP* 3.3 20.6 + - - +
381A PHE* 3.7 17.9 - - + -
413A PRO* 4.4 9.0 - - + -
416A VAL* 3.7 30.1 - - + -
441A LEU* 5.1 8.5 - - + +
444A PHE* 3.8 43.1 - - + +
445A THR* 4.2 4.9 - - - +
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Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A SER 3.2 13.3 + - - +
288A GLU* 3.2 26.5 + - - +
290A LEU* 1.3 76.8 - - - +
292A ILE* 1.3 60.6 + - - +
294A TRP* 3.5 6.6 + - - +
295A GLN* 3.2 31.1 + - - +
445A THR* 3.3 13.9 - - - -
446A SER* 2.9 48.5 + - - -
447A HIS* 5.2 5.1 + - - +
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Residues in contact with ILE 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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272A LEU* 3.9 40.4 - - + -
275A LEU* 5.1 3.6 - - + -
284A LEU* 4.2 16.2 - - + -
288A GLU* 3.0 33.2 + - + +
289A LEU* 3.7 11.4 - - + +
290A LEU 3.3 0.2 - - - -
291A ASP* 1.3 71.5 - - - +
293A ALA* 1.3 65.2 + - - +
295A GLN* 3.1 12.0 + - - +
296A VAL* 3.0 24.2 + - + +
324A THR* 4.1 18.6 - - + +
326A CYS* 3.9 27.1 - - + -
380A MET* 4.2 6.5 - - - -
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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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289A LEU 3.0 17.7 + - - +
290A LEU* 3.5 8.3 - - - +
291A ASP 3.4 0.4 - - - -
292A ILE* 1.3 76.2 - - - +
294A TRP* 1.3 56.4 + - - +
296A VAL* 3.3 5.7 + - - +
297A ALA* 3.0 27.2 + - - +
373A PHE* 3.8 4.5 - - - -
377A LEU* 3.8 27.1 - - + -
380A MET* 4.2 15.0 - - + -
381A PHE* 4.8 5.4 - - + -
441A LEU* 4.2 14.6 - - + -
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Residues in contact with TRP 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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245A LYS* 6.2 1.3 - - - -
246A HIS* 4.0 22.2 - + - -
290A LEU 3.3 3.4 + - - +
291A ASP 3.5 5.4 - - - +
293A ALA* 1.3 77.7 - - - +
295A GLN* 1.3 77.3 + - + +
297A ALA* 3.1 7.4 + - - +
298A GLU* 2.7 65.6 + - + +
438A ARG* 3.6 39.3 + - + +
441A LEU* 4.4 7.5 - - + +
442A SER* 3.8 20.6 + - - -
445A THR* 3.5 22.0 - - + -
447A HIS* 3.4 32.4 - + - -
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Residues in contact with GLN 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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246A HIS* 3.2 41.2 - - + +
291A ASP* 3.2 20.4 + - - +
292A ILE* 3.1 16.5 + - - +
294A TRP* 1.3 89.8 - - + +
296A VAL* 1.3 59.9 + - - +
298A GLU* 3.7 2.9 - - - +
299A GLY* 2.9 23.2 + - - -
324A THR* 3.2 25.3 + - - +
325A LEU* 3.7 2.6 - - - +
326A CYS* 2.8 37.3 + - + +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 5.0 0.2 - - + -
292A ILE* 3.0 21.5 + - + +
293A ALA* 3.7 8.3 - - - +
295A GLN* 1.3 75.2 - - + +
297A ALA* 1.3 52.7 + - - +
299A GLY* 3.2 1.4 + - - -
300A MET* 2.7 45.8 + - + +
313A LEU* 4.4 1.1 - - + -
318A ILE* 3.8 47.8 - - + -
326A CYS* 5.3 1.6 - - + -
328A VAL* 3.9 11.3 - - + +
373A PHE* 3.6 26.0 - - + -
376A LEU* 4.2 15.9 - - + -
380A MET* 5.0 0.2 - - + -
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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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293A ALA 3.0 14.3 + - - +
294A TRP* 3.1 8.9 + - - +
296A VAL* 1.3 76.3 - - - +
298A GLU* 1.3 51.7 + - - +
300A MET* 3.4 6.0 + - - +
301A CYS* 2.7 40.4 + - - +
373A PHE* 4.1 10.5 - - + -
434A PHE* 4.3 5.7 - - + +
437A LEU* 4.6 1.8 - - + -
438A ARG* 3.9 27.4 - - - +
441A LEU* 4.0 14.6 - - + -
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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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244A HIS* 3.7 22.0 + - + -
246A HIS* 3.6 24.6 - - + -
294A TRP* 2.7 46.1 + - + +
295A GLN* 3.7 7.4 - - - +
297A ALA* 1.3 72.7 - - - +
299A GLY* 1.3 60.5 + - - +
301A CYS* 3.2 17.5 - - - +
302A TYR 3.3 5.9 + - - -
438A ARG* 2.5 49.1 + - - +
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Residues in contact with GLY 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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244A HIS* 4.4 1.8 - - - -
246A HIS* 3.5 30.8 - - - +
247A ILE* 2.9 29.9 - - - +
295A GLN 2.9 12.4 + - - -
296A VAL 3.6 3.4 - - - -
298A GLU* 1.3 76.2 - - - +
300A MET* 1.3 60.3 + - - +
302A TYR 3.3 7.8 + - - -
303A LEU* 3.4 2.1 + - - +
328A VAL* 4.2 4.5 - - - -
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Residues in contact with MET 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 VAL* 2.7 29.8 + - + +
297A ALA 3.8 0.4 - - - +
299A GLY* 1.3 70.1 - - - +
301A CYS* 1.3 59.2 + - - +
303A LEU* 3.4 27.6 + - + +
304A GLU* 2.9 29.3 + - - +
308A TYR 5.5 0.2 - - - +
310A HIS* 3.9 12.8 - - + -
313A LEU* 3.8 26.5 - - + -
328A VAL* 3.9 16.6 - - + -
366A THR* 5.8 0.7 - - + -
369A ASP* 3.8 22.2 - - + +
434A PHE* 3.5 49.8 - - + -
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Residues in contact with CYS 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 ALA 2.7 21.9 + - - +
298A GLU 3.2 12.6 - - - +
300A MET* 1.3 73.4 - - - +
302A TYR* 1.3 61.3 + - - +
304A GLU* 3.4 5.3 - - - +
305A SER* 3.0 23.7 + - - -
434A PHE* 3.2 37.6 - - - +
435A LYS* 3.5 6.7 - - - -
438A ARG* 3.5 43.3 - - - +
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Residues in contact with TYR 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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241A LYS 4.1 3.5 + - - -
242A LEU* 3.5 20.7 - - + -
243A ARG* 3.0 42.5 + - - +
244A HIS* 3.6 36.6 - + + +
247A ILE* 3.5 21.1 - - + -
298A GLU 3.3 3.6 + - - +
299A GLY 3.7 7.0 - - - +
300A MET 3.3 0.4 - - - -
301A CYS* 1.3 78.1 - - - +
303A LEU* 1.3 62.4 + - + +
305A SER* 2.6 27.2 + - - -
306A GLN* 3.1 46.2 + - + +
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Residues in contact with LEU 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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242A LEU* 3.8 30.5 - - + -
247A ILE* 3.6 26.0 - - + -
299A GLY 3.4 1.5 + - - +
300A MET* 3.4 40.1 + - + +
301A CYS 3.4 0.4 - - - -
302A TYR* 1.3 80.5 - - + +
304A GLU* 1.3 64.7 + - - +
306A GLN* 3.1 5.5 + - - +
307A ASN 3.1 4.3 + - - -
308A TYR* 3.0 49.6 + - + +
310A HIS* 4.3 3.4 - - + -
328A VAL* 4.3 5.6 - - + -
331A PHE* 3.8 26.7 - - + -
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Residues in contact with GLU 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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300A MET* 2.9 14.5 + - - +
301A CYS* 3.4 10.9 - - - +
303A LEU* 1.3 75.6 - - - +
305A SER* 1.3 57.3 + - - +
307A ASN* 3.0 26.3 + - - +
366A THR* 3.4 39.0 + - + +
367A LYS* 5.3 1.4 + - - +
370A VAL* 4.8 1.2 - - - +
433A THR* 3.5 19.3 - - - +
434A PHE* 2.9 24.3 + - + +
435A LYS* 3.1 30.1 + - - +
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A CYS 3.0 11.5 + - - -
302A TYR* 2.6 29.3 + - - -
304A GLU* 1.3 76.2 - - - +
306A GLN* 1.3 69.5 + - - +
307A ASN* 3.3 8.8 + - - -
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Residues in contact with GLN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LYS* 5.7 2.8 + - - +
242A LEU* 3.8 21.2 - - + +
302A TYR* 3.1 54.2 + - + +
303A LEU 3.1 8.2 + - - +
305A SER* 1.3 85.3 + - - +
307A ASN* 1.3 72.8 + - - +
308A TYR* 3.3 5.1 + - + +
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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
------------------------------------------------------------
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