Contacts of the helix formed by residues 286 - 307 (chain B) in PDB entry 4UFT
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 LEU 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B PRO 4.7 1.6 - - - +
283B ALA* 3.5 17.3 - - + +
284B LEU 3.0 37.8 + - - +
285B GLY* 1.3 79.3 - - - +
287B HIS* 1.3 64.2 + - - +
288B GLU* 3.1 11.2 - - + +
289B PHE* 3.3 18.5 + - + -
290B ASP* 2.9 29.8 + - - +
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Residues in contact with HIS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 1.3 75.6 - - - +
288B GLU* 1.3 67.5 + - + +
290B ASP* 3.6 19.6 + - - +
291B GLY 4.5 1.9 + - - -
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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
----------------------------------------------------------
286B LEU* 3.1 5.3 - - + -
287B HIS* 1.3 83.8 - - + +
289B PHE* 1.3 71.7 + - + +
290B ASP 3.6 0.2 + - - -
291B GLY 4.3 0.9 + - - -
292B GLU* 2.9 18.7 - - - +
331B LEU* 3.8 24.3 - - + +
361B TYR* 2.9 38.6 + - + +
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Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ALA 4.9 4.3 - - - -
284B LEU* 3.5 29.2 - - + +
285B GLY* 6.1 0.7 - - - -
286B LEU* 3.3 24.5 + - + +
288B GLU* 1.3 82.9 - - + +
290B ASP* 1.3 58.5 + - - +
291B GLY 3.3 1.8 - - - -
292B GLU* 4.0 6.2 - - - +
293B LEU* 3.0 32.5 + - + +
331B LEU* 3.4 26.9 - - + -
332B LEU* 3.8 33.3 - - + +
335B TYR* 3.6 31.9 - + + -
361B TYR* 3.6 31.4 - + - -
364B LEU* 5.3 5.2 - - + -
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Residues in contact with ASP 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLY* 6.2 0.7 - - - -
286B LEU 2.9 17.1 + - - +
287B HIS* 3.7 16.2 + - - +
288B GLU 3.3 1.4 - - - -
289B PHE* 1.3 78.8 - - - +
291B GLY* 1.3 63.0 + - - +
293B LEU* 3.9 10.5 - - - +
294B SER* 3.5 20.1 + - - -
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Residues in contact with GLY 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B HIS 4.5 2.4 + - - -
288B GLU 4.3 2.0 + - - -
289B PHE 3.3 0.2 - - - -
290B ASP* 1.3 81.0 - - - +
292B GLU* 1.3 66.2 + - - +
294B SER* 2.9 21.9 + - - -
295B THR* 3.6 10.2 + - - +
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Residues in contact with GLU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLU 2.9 25.6 - - - +
289B PHE* 3.6 4.3 + - - +
290B ASP 3.4 0.2 - - - -
291B GLY* 1.3 75.8 + - - +
293B LEU* 1.3 65.0 + - - +
295B THR* 3.4 8.5 - - + +
296B LEU* 3.2 25.1 + - - +
328B SER 4.6 5.3 - - - +
329B TYR* 3.7 29.4 - - + +
330B PRO* 5.0 1.9 - - - +
331B LEU* 4.0 24.9 - - + +
332B LEU* 3.7 30.2 - - + +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE* 3.7 31.6 - - + -
284B LEU* 4.9 19.5 - - + +
285B GLY* 5.7 6.1 - - - -
289B PHE* 3.0 20.9 + - + +
290B ASP* 3.9 11.4 - - - +
292B GLU* 1.3 77.9 - - - +
294B SER* 1.3 62.9 + - - +
296B LEU* 3.4 15.3 + - + +
297B GLU* 3.5 25.3 - - + +
332B LEU* 5.1 7.8 - - + +
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 6.5 0.9 - - - -
290B ASP* 3.5 11.9 + - - -
291B GLY* 2.9 15.1 + - - -
293B LEU* 1.3 80.4 - - - +
295B THR* 1.3 69.5 + - - +
297B GLU* 3.2 21.4 + - - +
298B SER* 3.7 5.2 + - - -
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 3.9 23.4 + - - +
291B GLY 3.7 11.2 - - - +
292B GLU* 3.4 18.2 - - + +
294B SER* 1.3 81.7 + - - +
296B LEU* 1.3 63.7 + - - +
298B SER* 2.8 25.2 + - - -
299B LEU* 3.4 10.2 + - - +
328B SER* 5.1 9.6 - - - +
329B TYR* 5.1 12.3 - - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 5.3 5.2 - - + -
272B THR* 4.7 8.7 - - + -
273B ILE* 3.8 27.1 - - + -
277B ILE* 4.3 14.4 - - + -
292B GLU 3.2 20.3 + - - +
293B LEU* 3.6 7.6 - - + +
294B SER 3.1 0.6 - - - -
295B THR* 1.3 77.1 - - - +
297B GLU* 1.3 64.6 + - - +
299B LEU* 3.3 12.6 + - + +
300B MET* 3.0 26.7 + - + +
329B TYR* 3.9 39.5 - - + +
332B LEU* 3.9 25.8 - - + -
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 5.3 2.4 - - - +
277B ILE* 5.2 8.9 - - - +
293B LEU* 3.5 31.1 - - + +
294B SER* 3.2 10.0 + - - +
296B LEU* 1.3 86.9 - - - +
298B SER* 1.3 64.1 + - - +
300B MET* 3.3 33.9 + - + +
301B ASN* 3.2 21.0 + - - +
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Residues in contact with SER 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 4.1 39.4 - - - +
15B LYS* 4.4 12.2 - - - +
16B ASP* 3.5 21.6 - - - +
294B SER 3.7 4.7 + - - -
295B THR* 2.8 31.3 + - - -
297B GLU* 1.3 79.5 - - - +
299B LEU* 1.3 59.6 + - - +
301B ASN* 3.5 14.9 + - - +
302B LEU 3.6 4.9 + - - -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 6.0 9.0 - - + -
16B ASP* 5.3 0.7 - - - -
269B PHE* 4.1 20.2 - - + -
295B THR 3.4 9.2 + - - +
296B LEU* 3.3 13.8 + - + +
297B GLU 3.2 0.2 - - - -
298B SER* 1.3 79.8 + - - +
300B MET* 1.3 63.7 + - - +
302B LEU* 3.1 26.8 + - + +
303B TYR 3.6 3.8 + - - -
323B LYS* 3.3 51.8 - - + +
324B PHE* 4.1 11.9 - - + +
329B TYR* 3.6 32.5 - - + +
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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
----------------------------------------------------------
269B PHE* 4.2 20.0 - - + -
273B ILE* 4.2 31.6 - - + -
296B LEU* 3.0 13.3 + - + +
297B GLU* 3.3 33.4 + - - +
299B LEU* 1.3 76.2 - - - +
301B ASN* 1.3 62.2 + - - +
303B TYR* 3.3 19.4 + - + +
304B GLN* 3.6 8.1 + - - +
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Residues in contact with ASN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 6.0 2.2 - - - +
16B ASP* 5.6 1.3 - - - +
297B GLU 3.2 12.5 + - - +
298B SER* 3.6 12.8 - - - +
299B LEU 3.2 0.2 - - - -
300B MET* 1.3 76.0 - - - +
302B LEU* 1.3 58.3 + - - +
304B GLN* 3.3 5.9 + - - +
305B GLN* 2.9 45.3 + - - +
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Residues in contact with LEU 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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15B LYS* 4.9 2.0 - - + +
16B ASP* 3.3 29.1 + - - +
17B LYS* 5.9 5.4 - - + -
298B SER 3.6 3.5 + - - +
299B LEU* 3.1 19.4 + - + +
301B ASN* 1.3 79.6 - - - +
303B TYR* 1.3 61.8 + - - +
305B GLN* 3.4 25.5 + - - +
306B MET* 3.9 13.4 + - + +
313B MET* 5.1 4.7 - - + -
319B SER* 4.9 10.5 - - - +
323B LYS* 3.9 35.7 - - + +
324B PHE* 3.7 27.4 - - + -
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Residues in contact with TYR 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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263B GLU* 3.1 37.5 + - - +
266B LEU* 5.8 0.4 - - + -
269B PHE* 3.8 27.1 - + + -
299B LEU 3.6 1.4 + - - -
300B MET* 3.3 13.4 + - + +
301B ASN 3.2 0.4 - - - -
302B LEU* 1.3 82.1 - - - +
304B GLN* 1.3 69.2 + - + +
306B MET* 4.6 0.7 - - - +
307B GLY* 3.6 5.2 + - - -
310B ALA* 3.3 52.2 - - + +
311B PRO* 4.3 13.2 - - - +
313B MET* 4.8 6.3 - - + -
324B PHE* 4.3 11.4 - + + -
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Residues in contact with GLN 304 (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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300B MET* 3.6 8.0 + - - +
301B ASN* 3.3 9.2 + - - +
303B TYR* 1.3 86.2 - - + +
305B GLN* 1.3 66.3 + - - +
306B MET 3.1 4.8 + - - -
307B GLY* 3.5 11.3 + - - +
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Residues in contact with GLN 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP* 2.6 34.9 + - - +
17B LYS* 3.8 27.6 - - - +
301B ASN* 2.9 34.6 + - - +
302B LEU* 3.4 15.4 + - - +
304B GLN* 1.3 78.0 - - - +
306B MET* 1.3 64.3 + - + +
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Residues in contact with MET 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LYS* 5.6 15.3 - - - -
302B LEU* 3.9 16.7 + - + +
303B TYR 4.6 0.4 - - - +
304B GLN 3.1 0.6 - - - -
305B GLN* 1.3 85.9 - - + +
307B GLY* 1.3 67.1 + - - +
308B GLU* 3.9 3.8 + - - +
309B THR* 3.8 26.5 - - + -
310B ALA* 4.2 9.0 - - + -
313B MET* 3.8 37.7 - - + -
317B GLU* 5.3 10.1 - - + +
319B SER* 5.9 0.4 - - - +
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Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TYR 3.6 6.8 + - - -
304B GLN* 3.5 11.2 + - - -
306B MET* 1.3 91.8 - - - +
308B GLU* 1.3 55.7 + - - +
309B THR* 2.5 20.5 + - - +
310B ALA* 3.2 19.5 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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