Contacts of the helix formed by residues 285 - 308 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ARG* 3.4 21.7 - - - +
283A PRO 3.6 1.0 + - - +
284A LEU* 1.3 74.2 - - - +
286A GLU* 1.3 54.3 + - - +
287A GLU* 3.0 21.9 + - - +
288A GLU* 2.8 49.1 + - - +
289A MET* 2.7 35.1 + - - +
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Residues in contact with GLU 286 (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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285A ASN* 1.3 75.0 - - - +
287A GLU* 1.3 72.2 + - - +
289A MET* 3.7 5.9 - - - +
290A ALA* 2.9 30.3 + - - +
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASN* 3.0 21.4 + - - +
286A GLU* 1.3 90.8 + - - +
288A GLU* 1.3 62.6 + - + +
290A ALA* 3.5 7.1 + - - +
291A LEU* 3.3 28.9 + - + +
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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
----------------------------------------------------------
180A VAL* 4.8 2.4 - - - +
182A LEU* 4.1 24.6 - - + +
183A PRO* 6.0 0.3 - - - +
184A ARG* 2.8 53.6 + - - +
185A PHE* 3.9 6.7 - - - -
284A LEU* 3.3 17.4 - - + +
285A ASN* 2.8 36.0 + - - +
287A GLU* 1.3 76.4 - - + +
289A MET* 1.3 60.6 + - - +
291A LEU* 3.2 14.2 + - + +
292A LEU* 2.9 28.3 + - - +
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Residues in contact with MET 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A TYR* 3.8 31.9 - - + +
284A LEU* 3.8 36.3 - - + +
285A ASN 2.7 22.8 + - - +
286A GLU* 3.8 7.0 - - - +
288A GLU* 1.3 69.6 - - - +
290A ALA* 1.3 60.7 + - - +
292A LEU* 3.6 14.0 - - + +
293A ASN* 2.8 60.6 + - - +
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Residues in contact with ALA 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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286A GLU 2.9 18.1 + - - +
287A GLU* 3.6 8.3 - - - +
289A MET* 1.3 77.9 - - - +
291A LEU* 1.3 63.3 + - + +
293A ASN* 4.0 6.7 - - - +
294A ALA* 3.0 23.7 + - - +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLU 4.4 1.4 - - - +
180A VAL* 3.6 34.7 - - + +
181A PRO 5.5 2.5 - - - +
182A LEU* 6.0 0.4 - - + -
210A ARG* 5.1 12.1 - - - +
287A GLU* 3.3 17.2 + - + +
288A GLU* 3.2 13.8 + - + +
290A ALA* 1.3 76.0 - - + +
292A LEU* 1.3 66.6 + - - +
294A ALA* 3.2 8.2 + - + +
295A SER* 3.0 17.2 + - - -
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Residues in contact with LEU 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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172A MET* 3.9 33.0 - - + -
173A GLY* 4.1 4.7 - - - +
180A VAL* 3.9 10.0 - - + +
258A TYR* 3.8 28.5 - - + -
260A LEU* 5.0 2.9 - - + -
265A PHE* 3.4 32.7 - - + -
284A LEU* 3.6 25.1 - - + -
288A GLU 2.9 16.1 + - - +
289A MET* 3.6 15.9 - - + +
291A LEU* 1.3 75.7 - - - +
293A ASN* 1.3 58.2 + - - +
295A SER* 2.8 19.8 + - - -
296A ALA* 2.8 12.5 + - - +
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Residues in contact with ASN 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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258A TYR 4.7 1.2 - - - +
260A LEU* 4.5 16.9 - - - +
289A MET* 2.8 51.6 + - - +
290A ALA* 4.0 6.2 - - - +
292A LEU* 1.3 72.9 - - - +
294A ALA* 1.3 64.2 + - - +
296A ALA* 3.2 6.9 + - - +
297A LYS* 3.0 23.2 + - - +
300A ARG* 4.1 5.9 + - - +
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Residues in contact with ALA 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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178A GLU* 4.2 9.7 - - + +
290A ALA 3.0 18.8 + - - +
291A LEU* 3.5 9.0 - - + +
293A ASN* 1.3 76.7 - - - +
295A SER* 1.3 61.6 + - - +
297A LYS* 3.4 13.4 - - + +
298A ALA* 3.2 19.6 + - - +
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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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173A GLY* 3.6 1.3 - - - -
174A GLY* 3.0 29.5 + - - -
178A GLU* 3.3 36.3 + - - +
180A VAL* 4.2 5.8 - - - -
265A PHE* 3.7 7.9 - - - -
291A LEU 3.0 8.9 + - - -
292A LEU 2.8 11.1 + - - -
294A ALA* 1.3 74.1 - - - +
296A ALA* 1.3 60.4 + - - +
297A LYS 3.0 1.6 - - - -
298A ALA* 2.9 5.4 + - - +
299A VAL* 2.9 28.4 + - - +
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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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260A LEU* 3.9 21.8 - - + -
263A ILE* 4.5 4.2 - - + +
265A PHE* 3.3 25.5 - - + -
292A LEU 2.8 8.5 + - - +
293A ASN* 3.7 9.9 - - - +
295A SER* 1.3 77.3 - - - +
297A LYS* 1.3 56.5 + - - +
299A VAL* 3.6 2.5 - - - +
300A ARG* 2.9 51.7 + - - +
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Residues in contact with LYS 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 ASN 3.0 13.1 + - - +
294A ALA* 3.4 15.5 - - - +
295A SER 3.0 0.2 - - - -
296A ALA* 1.3 75.3 - - - +
298A ALA* 1.3 66.4 + - - +
300A ARG* 3.5 21.2 + - - +
301A ALA* 3.1 23.3 + - + +
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLU* 3.1 43.5 - - + +
294A ALA 3.2 4.2 + - - +
295A SER* 2.9 9.7 + - - +
297A LYS* 1.3 79.9 - - - +
299A VAL* 1.3 63.8 + - + +
301A ALA* 3.4 8.8 - - - +
302A THR* 3.3 24.0 + - - +
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Residues in contact with VAL 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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123A ASP* 4.1 15.3 - - + +
174A GLY* 3.6 21.8 - - - -
263A ILE* 4.7 5.8 - - + -
264A TYR 3.7 20.6 - - - +
265A PHE* 3.6 21.1 - - + -
295A SER* 2.9 17.3 + - - +
296A ALA* 3.6 9.2 - - - +
298A ALA* 1.3 74.8 - - + +
300A ARG* 1.3 67.4 + - - +
301A ALA 3.0 1.1 - - - -
302A THR* 2.8 30.7 + - - +
303A LEU* 3.0 19.5 + - + +
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Residues in contact with ARG 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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260A LEU* 3.8 17.2 - - - +
263A ILE* 4.3 24.0 - - + +
293A ASN* 4.1 7.1 + - - +
296A ALA* 2.9 38.4 + - - +
297A LYS* 3.5 32.4 - - - +
299A VAL* 1.3 72.5 - - - +
301A ALA* 1.3 57.4 + - - +
303A LEU* 3.1 12.6 + - + +
304A ASP* 2.9 37.3 + - - +
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Residues in contact with ALA 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 LYS 3.1 13.9 + - - +
298A ALA* 3.4 14.4 - - - +
299A VAL 3.0 0.6 - - - -
300A ARG* 1.3 77.0 - - - +
302A THR* 1.3 61.8 + - + +
304A ASP* 3.4 9.7 + - - +
305A THR* 3.1 24.1 + - - -
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Residues in contact with THR 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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89A GLU* 3.8 31.6 - - + +
92A ILE* 3.4 13.9 - - - +
121A PRO* 5.0 6.7 - - + +
123A ASP* 5.4 0.9 - - - +
124A ALA* 3.5 25.0 + - - +
298A ALA 3.3 16.4 - - - +
299A VAL* 2.8 26.4 + - - +
301A ALA* 1.3 73.4 - - + +
303A LEU* 1.3 61.9 + - - +
305A THR* 3.1 9.6 + - - -
306A LEU* 2.8 24.5 + - - +
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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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123A ASP 4.7 1.1 - - - +
124A ALA* 3.8 27.6 - - + +
127A TYR* 3.9 34.1 - - + -
262A ASP 4.4 2.2 - - - +
263A ILE* 3.9 35.2 - - + -
264A TYR 4.8 1.3 - - - +
299A VAL* 3.0 18.5 + - + +
300A ARG* 3.3 12.3 - - + +
302A THR* 1.3 80.8 + - - +
304A ASP* 1.3 60.8 + - - +
306A LEU* 3.1 12.4 + - + +
307A LYS* 2.9 38.7 + - - +
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Residues in contact with ASP 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 ARG* 2.9 24.2 + - - +
301A ALA* 3.8 8.2 - - - +
302A THR 3.3 0.2 - - - -
303A LEU* 1.3 77.2 - - - +
305A THR* 1.3 61.6 + - - +
307A LYS* 2.9 47.2 + - + +
308A SER* 3.3 11.8 - - - -
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Residues in contact with THR 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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92A ILE* 3.8 31.4 - - + -
301A ALA 3.1 13.7 + - - -
302A THR* 3.1 11.7 + - - -
304A ASP* 1.3 77.3 - - - +
306A LEU* 1.3 66.2 + - - +
308A SER* 3.0 22.3 + - - +
309A LEU* 3.4 14.5 - - + +
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Residues in contact with LEU 306 (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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92A ILE* 4.1 5.4 - - + +
96A ALA* 4.3 13.2 - - + -
100A ARG* 5.8 2.2 - - - +
124A ALA* 4.0 28.3 - - + +
125A MET* 6.1 1.1 - - - -
127A TYR* 4.8 7.0 - - + -
128A LEU* 4.1 32.3 - - + +
131A GLU* 5.2 4.7 - - - +
302A THR 2.8 13.4 + - - +
303A LEU* 3.1 24.0 + - + +
305A THR* 1.3 71.5 - - - +
307A LYS* 1.3 54.4 + - - +
308A SER 2.8 4.6 + - - -
309A LEU* 2.7 54.6 + - + +
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Residues in contact with LYS 307 (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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303A LEU* 2.9 24.7 + - - +
304A ASP* 2.9 47.6 + - + +
306A LEU* 1.3 74.6 - - - +
308A SER* 1.3 57.6 + - - +
309A LEU* 3.3 3.5 + - - +
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Residues in contact with SER 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASP 3.3 13.4 + - - -
305A THR* 3.0 17.5 + - - +
306A LEU 2.8 1.0 + - - -
307A LYS* 1.3 78.8 - - - +
309A LEU* 1.3 65.1 + - - +
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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
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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