Contacts of the helix formed by residues 285 - 308 (chain B) in PDB entry 1UXI
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 ASN 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B ARG* 3.3 34.2 - - - +
283B PRO 3.6 0.6 + - - -
284B LEU* 1.3 75.2 - - - +
286B GLU* 1.3 58.3 + - - +
287B GLU* 3.1 24.0 + - - +
288B GLU* 2.7 41.6 + - - +
289B MET* 2.9 28.3 + - - +
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Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASN* 1.3 75.7 - - - +
287B GLU* 1.3 67.9 + - + +
289B MET* 3.4 6.1 + - - +
290B ALA* 3.0 23.6 + - + +
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASN* 3.1 18.8 + - - +
286B GLU* 1.3 76.5 - - + +
288B GLU* 1.3 67.3 + - + +
290B ALA* 2.9 18.4 + - - +
291B LEU* 3.0 21.0 + - + +
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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
----------------------------------------------------------
180B VAL* 4.7 2.4 - - - +
182B LEU* 4.1 21.1 - - + +
183B PRO* 6.1 0.8 - - + +
184B ARG* 2.7 60.6 + - - +
185B PHE* 3.8 10.2 - - - -
284B LEU* 3.2 18.0 - - + +
285B ASN* 2.7 35.1 + - - +
287B GLU* 1.3 76.1 - - + +
289B MET* 1.3 57.1 + - - +
291B LEU* 3.1 15.3 + - + +
292B LEU* 2.8 29.2 + - - +
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Residues in contact with MET 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B TYR* 3.6 29.4 - - - +
284B LEU* 3.7 25.1 - - + +
285B ASN 2.9 21.4 + - - +
286B GLU* 3.7 6.7 - - - +
288B GLU* 1.3 73.2 - - - +
290B ALA* 1.3 59.4 + - - +
292B LEU* 3.6 26.1 - - + +
293B ASN* 2.7 63.5 + - - +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLU* 3.0 13.7 + - + +
287B GLU* 2.9 12.2 + - - +
289B MET* 1.3 75.9 - - - +
291B LEU* 1.3 65.6 + - + +
293B ASN* 3.4 6.6 + - - +
294B ALA* 3.0 22.7 + - - +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU 4.6 0.7 - - - +
180B VAL* 3.8 31.9 - - + +
181B PRO 5.5 2.9 - - - +
182B LEU* 6.2 0.2 - - + -
210B ARG* 3.7 27.6 - - - +
287B GLU* 3.0 18.9 + - + +
288B GLU* 3.3 14.6 - - + +
290B ALA* 1.3 77.2 - - + +
292B LEU* 1.3 64.2 + - - +
294B ALA* 2.9 19.9 + - + +
295B SER 3.0 10.4 + - - -
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B MET* 4.4 13.7 - - + -
180B VAL* 4.0 12.3 - - + +
258B TYR* 3.7 22.7 - - + -
260B LEU* 3.5 21.8 - - + -
265B PHE* 3.4 27.1 - - + -
284B LEU* 3.2 31.4 - - + -
288B GLU 2.8 19.7 + - - +
289B MET* 3.6 17.9 - - + +
291B LEU* 1.3 72.8 - - - +
293B ASN* 1.3 60.6 + - - +
295B SER* 3.1 5.2 + - - -
296B ALA 2.8 23.6 + - - -
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Residues in contact with ASN 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B TYR 4.9 1.4 + - - -
260B LEU* 4.1 21.6 - - - +
289B MET* 2.7 50.8 + - - +
290B ALA* 3.8 5.8 - - - +
292B LEU* 1.3 70.8 - - - +
294B ALA* 1.3 66.6 + - - +
296B ALA* 3.3 5.8 + - - +
297B LYS* 3.0 23.9 + - - +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 4.2 11.5 - - + +
290B ALA 3.0 13.0 + - - +
291B LEU* 2.9 17.4 + - + +
293B ASN* 1.3 74.8 - - - +
295B SER* 1.3 64.4 + - - +
297B LYS* 3.1 10.4 + - - +
298B ALA* 3.1 19.9 + - - +
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Residues in contact with SER 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLY* 3.3 2.3 - - - -
174B GLY* 2.8 32.4 + - - -
178B GLU* 3.3 36.4 + - - +
180B VAL* 4.1 8.1 - - - -
265B PHE* 3.6 6.7 - - - -
291B LEU 3.0 8.7 + - - -
292B LEU 3.4 8.1 - - - -
294B ALA* 1.3 77.3 - - - +
296B ALA* 1.3 63.3 + - - +
298B ALA* 3.0 4.3 + - - +
299B VAL* 2.9 23.9 + - - +
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 3.8 29.6 - - + -
263B ILE* 4.0 7.2 - - + +
265B PHE* 3.3 20.6 - - + -
292B LEU 2.8 13.6 + - - +
293B ASN* 3.5 12.1 - - - +
295B SER* 1.3 77.6 - - - +
297B LYS* 1.3 57.4 + - - +
299B VAL* 3.3 1.9 + - - +
300B ARG* 2.9 30.4 + - - +
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Residues in contact with LYS 297 (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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293B ASN 3.0 12.1 + - - +
294B ALA* 3.4 11.4 - - - +
296B ALA* 1.3 77.1 - - - +
298B ALA* 1.3 63.6 - - - +
300B ARG* 3.4 9.5 + - + +
301B ALA* 3.0 21.9 + - + +
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 3.4 41.1 - - + +
294B ALA 3.1 5.3 + - - +
295B SER 3.0 9.2 + - - +
297B LYS* 1.3 75.1 - - - +
299B VAL* 1.3 66.1 - - + +
301B ALA* 3.1 21.8 + - - +
302B THR* 3.2 12.8 + - - +
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASP* 3.8 14.1 - - + +
174B GLY* 3.5 31.6 - - - -
263B ILE* 3.7 11.7 - - + -
264B TYR 3.6 20.4 - - - +
265B PHE* 3.7 9.4 - - + -
295B SER 2.9 17.2 + - - +
296B ALA 3.7 6.1 - - - +
298B ALA* 1.3 76.0 - - + +
300B ARG* 1.3 64.5 + - - +
302B THR* 2.7 28.3 + - - +
303B LEU* 2.9 26.3 - - + +
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ASN 3.2 14.8 + - - -
262B ASP* 2.9 32.2 + - - +
263B ILE* 3.8 13.5 - - + +
296B ALA 2.9 17.9 + - - +
297B LYS* 3.6 10.3 - - + +
298B ALA 3.3 0.2 - - - -
299B VAL* 1.3 76.5 - - - +
301B ALA* 1.3 58.0 + - - +
303B LEU* 3.1 25.9 + - - +
304B ASP* 2.9 52.9 + - - +
307B LYS* 3.9 17.4 - - - +
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Residues in contact with ALA 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 LYS* 3.0 13.4 + - + +
298B ALA* 3.1 14.1 - - - +
300B ARG* 1.3 77.6 - - - +
302B THR* 1.3 63.8 + - + +
304B ASP* 3.1 12.9 + - - +
305B THR* 3.0 24.1 + - - -
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Residues in contact with THR 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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89B GLU* 3.6 31.9 - - + -
92B ILE* 3.5 9.5 - - - +
121B PRO* 5.1 5.8 - - + -
123B ASP* 5.5 0.5 - - - +
124B ALA* 3.5 18.0 + - - +
298B ALA 3.6 13.0 - - - +
299B VAL* 2.7 23.1 + - - +
301B ALA* 1.3 76.7 - - + +
303B LEU* 1.3 59.9 + - - +
305B THR* 3.0 10.5 + - - -
306B LEU* 2.6 36.2 + - - +
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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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123B ASP 5.0 1.8 - - - +
124B ALA* 4.3 14.1 - - - +
127B TYR* 3.8 41.7 - - + -
262B ASP 4.2 0.9 - - - +
263B ILE* 3.8 20.4 - - + -
264B TYR 4.8 0.9 - - - +
299B VAL* 2.9 39.9 + - + +
300B ARG* 3.4 31.6 - - - +
302B THR* 1.3 90.0 + - - +
304B ASP* 1.3 57.6 + - - +
306B LEU* 3.3 7.1 - - + +
307B LYS* 2.8 42.3 + - - +
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Residues in contact with ASP 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ARG* 2.9 45.3 + - - +
301B ALA* 3.1 10.3 + - - +
303B LEU* 1.3 73.1 - - - +
305B THR* 1.3 65.0 + - - +
307B LYS* 3.7 10.2 + - - +
308B SER* 3.3 22.2 + - - -
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Residues in contact with THR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 4.0 28.0 - - + -
301B ALA 3.0 14.9 + - - -
302B THR* 3.2 11.8 - - - -
304B ASP* 1.3 74.9 - - - +
306B LEU* 1.3 67.1 + - - +
308B SER* 2.7 24.3 + - - +
309B LEU* 3.3 16.2 - - + +
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 3.8 6.5 - - + +
96B ALA* 4.3 3.4 - - + -
100B ARG* 5.6 2.9 - - - +
124B ALA* 3.2 32.1 - - + +
125B MET* 4.0 21.3 - - + -
127B TYR* 4.4 14.8 - - + -
128B LEU* 4.1 28.5 - - + +
131B GLU* 4.9 5.8 - - - +
302B THR 2.6 19.1 + - - +
303B LEU* 3.3 9.4 - - - +
305B THR* 1.3 73.0 - - - +
307B LYS* 1.3 63.0 + - + +
309B LEU* 2.9 46.1 + - + +
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TYR* 3.3 38.9 + - + -
131B GLU* 5.1 7.2 - - - +
262B ASP* 3.9 11.3 + - - -
300B ARG* 3.9 15.7 - - - +
303B LEU* 2.8 33.4 + - - +
304B ASP* 4.2 11.0 - - - +
306B LEU* 1.3 77.8 - - + +
308B SER* 1.3 57.5 + - - +
309B LEU 3.3 1.7 + - - -
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ASP 3.3 13.6 + - - -
305B THR* 2.7 23.2 + - - +
306B LEU 3.0 0.2 + - - -
307B LYS* 1.3 78.0 - - - +
309B LEU* 1.3 68.4 + - - +
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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