Contacts of the helix formed by residues 288 - 300 (chain B) in PDB entry 1U2X
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 ASP 288 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B THR* 4.7 12.5 + - - +
286B VAL* 3.4 4.8 - - + +
287B GLN* 1.3 80.6 - - + +
289B ARG* 1.3 60.2 + - - +
290B LYS* 3.3 13.6 + - - +
291B LEU* 2.9 37.6 + - + +
292B ARG* 2.9 28.6 + - - +
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Residues in contact with ARG 289 (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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287B GLN 3.3 4.6 + - - +
288B ASP* 1.3 73.7 + - - +
290B LYS* 1.3 57.2 + - - +
292B ARG* 3.4 33.8 + - - +
293B LYS* 3.0 28.9 + - - +
318B SER* 3.2 24.0 + - - -
319B VAL* 3.9 22.3 - - + +
323B ARG* 3.1 30.5 - - - +
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B THR* 5.1 16.8 - - + -
288B ASP* 3.2 12.9 + - - +
289B ARG* 1.3 75.8 - - - +
291B LEU* 1.3 65.3 + - - +
293B LYS* 3.4 6.5 + - - +
294B LYS* 3.1 59.6 + - - +
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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
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245B TYR 4.5 0.2 - - - +
246B GLN 4.4 8.3 - - - +
248B LEU* 3.4 39.0 - - + +
249B ARG* 4.9 4.7 - - - +
250B THR* 5.2 4.7 - - - +
258B ALA* 3.6 31.0 - - + -
262B LEU* 5.2 0.4 - - + -
286B VAL* 4.0 15.5 - - + -
288B ASP* 2.9 26.4 + - + +
290B LYS* 1.3 74.3 - - - +
292B ARG* 1.3 66.5 + - - +
294B LYS* 3.2 9.0 + - + -
295B ILE* 3.0 40.5 + - + +
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B PHE* 4.3 10.7 - - + -
286B VAL* 3.0 42.1 + - + +
287B GLN* 3.4 16.8 + - - +
288B ASP 2.9 16.9 + - - +
289B ARG* 3.5 32.8 - - - +
291B LEU* 1.3 78.1 - - - +
293B LYS* 1.3 61.3 + - - +
295B ILE* 3.3 4.0 + - - +
296B ILE* 3.2 35.2 + - + +
315B GLN* 3.1 62.9 + - - +
316B ILE 4.7 0.2 - - - +
318B SER* 4.6 1.2 - - - -
319B VAL* 3.9 17.4 - - - +
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Residues in contact with LYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ARG 3.0 17.4 + - - +
290B LYS* 3.7 6.5 - - - +
292B ARG* 1.3 77.2 - - - +
294B LYS* 1.3 58.3 + - + +
296B ILE* 3.3 7.1 + - + +
297B THR* 2.9 50.0 + - - +
319B VAL* 3.6 44.7 + - + +
320B LEU* 5.2 10.3 - - - +
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Residues in contact with LYS 294 (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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250B THR* 6.2 2.0 - - - -
258B ALA* 4.5 17.5 - - + -
259B ASN* 3.3 36.2 + - - +
262B LEU* 3.6 16.4 - - + -
290B LYS* 3.1 57.4 + - + +
291B LEU* 3.2 10.7 + - + +
293B LYS* 1.3 79.4 - - + +
295B ILE* 1.3 55.6 + - - +
297B THR* 4.5 2.5 - - - -
298B ASN* 2.7 41.9 + - - +
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Residues in contact with ILE 295 (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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245B TYR* 3.5 53.6 - - + +
246B GLN* 4.0 3.6 - - - +
248B LEU* 5.1 0.2 - - + -
262B LEU* 4.6 10.1 - - + -
281B VAL* 6.0 0.2 - - + -
283B PHE* 3.7 26.0 - - + -
286B VAL* 4.1 17.5 - - + -
291B LEU* 3.0 33.4 + - + +
292B ARG* 3.6 6.3 - - - +
294B LYS* 1.3 74.1 - - - +
296B ILE* 1.3 57.8 + - - +
299B ILE* 2.9 49.5 + - + +
300B LEU* 3.8 1.5 + - + -
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Residues in contact with ILE 296 (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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283B PHE* 3.9 17.3 - - + -
292B ARG* 3.2 22.2 + - + +
293B LYS* 3.6 10.5 - - - +
294B LYS 3.2 0.2 - - - -
295B ILE* 1.3 79.2 - - - +
297B THR* 1.3 63.2 + - - +
300B LEU* 3.4 16.5 + - + +
301B PRO* 3.2 21.1 - - - +
316B ILE* 3.9 23.3 - - + -
319B VAL* 3.3 34.3 - - + -
320B LEU* 4.4 12.1 - - + -
349B LEU* 4.0 30.9 - - + +
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Residues in contact with THR 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 LYS* 2.9 37.3 + - - +
294B LYS* 3.8 5.3 - - - -
296B ILE* 1.3 81.4 - - - +
298B ASN* 1.3 70.6 + - - +
301B PRO* 3.6 9.7 - - - +
302B PHE* 3.4 17.5 - - - -
349B LEU* 5.5 2.2 - - - -
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Residues in contact with ASN 298 (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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259B ASN* 4.5 8.5 + - - +
262B LEU* 3.6 39.6 - - + +
263B ARG* 4.9 1.4 + - - +
266B LYS* 2.7 52.3 + - + +
269B ILE* 5.0 0.2 - - - +
294B LYS* 2.7 35.6 + - - +
297B THR* 1.3 89.5 - - - +
299B ILE* 1.3 59.3 + - + +
302B PHE* 3.1 19.7 - - - +
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Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B TYR* 3.8 39.7 - - + +
262B LEU* 4.1 16.2 - - + -
265B ALA* 3.8 31.0 - - + -
266B LYS* 4.8 1.1 - - + +
269B ILE* 4.1 11.4 - - + -
281B VAL* 3.8 23.6 - - + -
295B ILE* 2.9 24.6 + - + +
298B ASN* 1.3 87.6 - - + +
300B LEU* 1.3 68.6 + - + +
301B PRO* 3.4 2.0 - - - -
302B PHE* 3.0 16.2 + - - +
303B VAL* 3.5 14.7 + - + +
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B VAL* 4.0 25.4 - - + -
283B PHE* 4.4 17.7 - - + -
295B ILE* 4.6 1.8 - - + +
296B ILE* 3.4 31.7 + - + +
299B ILE* 1.3 83.8 - - + +
301B PRO* 1.3 69.6 - - + +
302B PHE 3.1 0.9 + - - -
303B VAL* 3.5 8.3 + - - +
306B VAL* 3.9 29.2 - - + -
316B ILE* 4.5 13.0 - - + -
345B ILE* 5.7 0.9 - - + -
349B LEU* 4.0 26.5 - - + -
351B PHE* 3.5 27.9 - - + +
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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