Contacts of the helix formed by residues 285 - 306 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B GLU* 3.2 22.9 - - + +
282B LYS 4.1 5.8 - - - +
283B VAL 3.6 8.1 - - - +
284B LEU* 1.4 93.0 - - - +
286B VAL* 1.3 65.2 - - - +
287B SER* 3.1 19.3 - - - +
288B GLU* 3.0 17.4 + - + +
289B LEU* 3.0 18.5 + - - +
383B ARG* 4.2 0.4 - - - -
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLU* 5.6 1.3 - - + +
285B PRO* 1.3 72.2 - - - +
287B SER* 1.3 57.4 + - - +
289B LEU* 3.2 12.9 + - + +
290B LEU* 2.9 43.4 + - + +
381B PHE* 4.0 9.2 - - + -
383B ARG* 4.1 6.4 - - - +
411B GLU* 3.7 50.5 - - + +
413B PRO* 4.2 9.4 - - + -
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PRO* 3.8 17.2 - - - +
286B VAL* 1.3 79.1 - - - +
288B GLU* 1.3 61.9 + - - +
290B LEU* 3.4 13.9 + - - +
291B ASP* 3.2 28.1 + - - +
444B PHE 4.9 1.9 - - - +
446B SER* 5.0 9.3 + - - -
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B VAL 5.5 0.9 - - - +
284B LEU* 3.7 21.3 - - + -
285B PRO* 3.0 28.7 + - + +
287B SER* 1.3 78.2 + - - +
289B LEU* 1.3 64.7 + - - +
291B ASP* 3.1 21.2 + - - +
292B ILE* 3.0 35.0 + - + +
295B GLN* 4.8 1.7 + - - -
324B THR* 3.3 39.2 + - + +
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 5.6 0.4 - - + -
276B LEU* 3.6 29.6 - - + -
284B LEU* 3.8 21.8 - - + +
285B PRO 3.0 13.0 + - - +
286B VAL* 3.2 13.9 + - + +
288B GLU* 1.3 75.3 - - - +
290B LEU* 1.3 58.4 + - - +
292B ILE* 3.4 10.3 + - + +
293B ALA* 2.9 27.9 + - - +
380B MET* 3.9 28.1 - - + +
381B PHE* 3.7 30.8 - - + -
383B ARG* 4.0 27.6 - - + +
411B GLU* 5.9 1.1 - - + -
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B VAL* 2.9 33.1 + - + +
287B SER* 3.6 10.8 - - - +
288B GLU 3.2 0.2 - - - -
289B LEU* 1.3 74.7 - - - +
291B ASP* 1.3 64.7 + - - +
293B ALA* 3.4 6.8 + - + +
294B TRP* 3.1 18.4 + - - +
381B PHE* 3.7 22.7 - - + -
413B PRO* 4.5 9.2 - - + -
416B VAL* 3.7 20.0 - - + -
441B LEU* 4.9 8.3 - - + +
444B PHE* 3.5 48.7 - - + +
445B THR* 3.6 9.1 - - - +
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Residues in contact with ASP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B SER 3.2 13.8 + - - +
288B GLU* 3.1 28.3 + - - +
290B LEU* 1.3 74.4 - - - +
292B ILE* 1.3 62.4 + - - +
294B TRP* 3.3 6.4 + - - +
295B GLN* 3.1 32.4 + - - +
445B THR* 3.3 13.6 - - - -
446B SER* 2.6 48.1 + - - -
447B HIS* 4.5 9.2 - - - +
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Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 3.8 23.8 - - + -
275B LEU* 4.8 3.6 - - + -
284B LEU* 3.9 27.1 - - + -
288B GLU* 3.0 34.6 + - + +
289B LEU* 3.6 11.9 - - + +
291B ASP* 1.3 72.2 - - - +
293B ALA* 1.3 66.1 + - - +
295B GLN* 3.2 11.6 + - - +
296B VAL* 3.0 24.8 + - + +
324B THR* 4.2 7.9 - - - +
326B CYS* 3.7 27.4 - - - -
380B MET* 3.8 22.0 - - + -
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU 2.9 14.2 + - - +
290B LEU* 3.4 13.0 - - - +
292B ILE* 1.3 77.0 - - - +
294B TRP* 1.3 61.6 + - - +
296B VAL* 3.3 5.5 + - - +
297B ALA* 3.1 17.8 + - - +
373B PHE* 3.8 8.0 - - - -
377B LEU* 3.7 28.5 - - + -
380B MET* 4.4 13.9 - - - -
381B PHE* 4.9 5.2 - - + -
441B LEU* 4.3 14.8 - - + -
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Residues in contact with TRP 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LYS* 6.2 2.0 - - - -
246B HIS* 4.4 11.2 - + - -
290B LEU 3.1 6.2 + - - +
291B ASP 3.6 2.7 - - - +
292B ILE 3.3 0.2 - - - -
293B ALA* 1.3 77.0 - - - +
295B GLN* 1.3 84.7 + - + +
297B ALA* 3.1 8.5 + - - +
298B GLU* 2.8 58.8 + - + +
438B ARG* 3.5 37.9 + - + +
441B LEU* 4.3 9.8 - - + +
442B SER* 3.9 23.0 + - - -
445B THR* 3.5 23.6 - - + -
447B HIS* 3.4 35.0 - + - -
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Residues in contact with GLN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B HIS* 3.1 37.4 - - + +
288B GLU* 4.8 2.0 + - - -
291B ASP* 3.1 24.1 + - + +
292B ILE* 3.4 17.8 - - - +
294B TRP* 1.3 90.3 - - + +
296B VAL* 1.3 58.6 + - - +
298B GLU* 3.1 8.3 + - - +
299B GLY 2.9 24.8 + - - -
324B THR* 3.3 19.6 + - - +
325B LEU* 3.7 2.8 - - - +
326B CYS* 2.8 37.4 + - + +
447B HIS* 5.9 0.2 - - - +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ILE* 3.0 17.2 + - + +
293B ALA* 3.6 7.2 - - - +
295B GLN* 1.3 74.1 - - - +
297B ALA* 1.3 57.8 + - - +
299B GLY 3.5 0.2 + - - -
300B MET* 2.9 33.5 + - + +
313B LEU* 4.5 1.1 - - + -
318B ILE* 3.6 41.3 - - + -
326B CYS* 5.0 4.0 - - + -
328B VAL* 3.8 15.8 - - + +
373B PHE* 3.6 25.4 - - + -
376B LEU* 4.2 10.3 - - + -
380B MET* 4.0 14.8 - - + -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA 3.1 13.5 + - - +
294B TRP 3.1 8.7 + - - +
296B VAL* 1.3 76.4 - - - +
298B GLU* 1.3 51.3 + - - +
300B MET* 3.5 5.8 - - - +
301B CYS* 2.6 41.2 + - - -
373B PHE* 4.1 10.7 - - + -
434B PHE* 4.4 5.9 - - + +
437B LEU* 4.8 2.0 - - + -
438B ARG* 3.9 27.8 - - + +
441B LEU* 4.0 13.7 - - + -
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B HIS* 4.0 15.1 + - + -
246B HIS* 4.0 16.8 - - + -
294B TRP* 2.8 58.8 + - + +
295B GLN 3.2 9.2 - - - +
297B ALA* 1.3 75.7 - - - +
299B GLY* 1.3 62.3 + - - +
301B CYS* 3.3 7.1 - - - +
302B TYR* 3.1 21.3 + - - +
438B ARG* 3.5 32.8 + - - +
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Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B HIS* 4.4 3.6 - - - -
246B HIS* 3.4 30.6 - - - +
247B ILE* 3.7 11.6 - - - +
295B GLN 2.9 11.7 + - - -
296B VAL 3.9 2.2 - - - -
298B GLU* 1.3 73.5 - - - +
300B MET* 1.3 61.3 + - - +
302B TYR* 3.3 6.8 + - - +
303B LEU* 3.2 23.9 + - - +
328B VAL* 4.1 4.3 - - - -
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Residues in contact with MET 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B VAL* 2.9 27.8 + - + +
297B ALA 3.7 0.9 - - - +
299B GLY* 1.3 73.5 - - - +
301B CYS* 1.3 58.6 + - - +
303B LEU* 3.2 32.5 + - + +
304B GLU* 2.9 29.2 + - - +
310B HIS* 4.0 7.9 - - + -
313B LEU* 3.8 27.4 - - + -
328B VAL* 3.9 17.0 - - + +
369B ASP* 3.8 20.9 - - + +
434B PHE* 3.5 50.3 - - + -
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Residues in contact with CYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B ALA 2.6 23.7 + - - +
298B GLU 3.3 8.1 - - - +
300B MET* 1.3 73.2 - - - +
302B TYR* 1.3 62.0 + - - +
304B GLU* 3.3 6.6 + - - +
305B SER* 3.0 23.7 + - - -
434B PHE* 2.9 42.1 - - - +
435B LYS* 3.5 9.0 - - - -
438B ARG* 3.6 35.9 - - - +
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Residues in contact with TYR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LYS 4.3 2.8 + - - -
242B LEU* 3.5 15.1 - - + -
243B ARG* 2.9 44.6 + - - +
244B HIS* 3.6 40.6 - + + +
247B ILE* 4.0 11.0 - - + -
298B GLU 3.1 4.6 + - - +
299B GLY 3.4 8.3 - - - +
300B MET 3.3 0.2 - - - -
301B CYS* 1.3 80.1 - - - +
303B LEU* 1.3 72.2 + - + +
305B SER* 2.6 26.6 + - - -
306B GLN* 3.1 44.5 + - + +
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B LEU* 4.0 28.0 - - + -
247B ILE* 4.4 8.5 - - + -
299B GLY 3.2 9.6 + - - +
300B MET* 3.2 39.1 + - + +
302B TYR* 1.3 87.6 - - + +
304B GLU* 1.3 66.3 + - - +
306B GLN* 3.0 10.3 + - - +
308B TYR* 3.0 44.1 + - + +
310B HIS* 4.2 7.9 - - + -
328B VAL* 4.3 7.2 - - + -
331B PHE* 3.9 30.1 - - + -
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B MET* 2.9 13.2 + - - +
301B CYS* 3.3 10.5 - - - +
303B LEU* 1.3 75.4 - - - +
305B SER* 1.3 57.8 + - - +
307B ASN* 2.9 22.2 + - - +
308B TYR 5.0 0.4 - - - -
366B THR* 3.2 42.3 + - + +
367B LYS* 5.4 0.5 - - - -
433B THR* 3.4 18.3 - - - +
434B PHE* 2.7 25.2 + - + +
435B LYS* 3.0 29.6 + - - +
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B CYS 3.0 12.9 + - - -
302B TYR* 2.6 29.0 + - - -
304B GLU* 1.3 75.1 - - - +
306B GLN* 1.3 69.8 + - - +
307B ASN 3.3 1.1 + - - -
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Residues in contact with GLN 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LYS* 6.1 0.5 - - - +
242B LEU* 3.8 24.9 - - + +
302B TYR* 3.4 46.7 + - + +
303B LEU 3.0 9.6 + - - +
305B SER* 1.3 90.0 + - - +
307B ASN* 1.3 69.9 + - - +
308B TYR* 3.2 4.7 + - + +
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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