Contacts of the helix formed by residues 290 - 299 (chain B) in PDB entry 1UPX
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 LYS 290 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286B ASN* 4.0 23.1 - - + +
287B ALA 3.2 5.7 + - - +
288B TRP 3.2 1.2 - - - -
289B TRP* 1.3 120.0 - - + +
291B GLN* 1.3 63.3 + - - +
292B LYS 3.3 2.5 - - - -
293B GLU* 3.2 18.9 + - + +
294B GLU* 3.0 48.2 + - + +
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Residues in contact with GLN 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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262B HIS* 4.2 5.5 - - - +
287B ALA 4.4 0.2 + - - -
288B TRP* 2.9 30.0 + - - +
289B TRP 3.2 1.8 - - - -
290B LYS* 1.3 76.5 - - - +
292B LYS* 1.3 63.5 + - - +
293B GLU 3.1 0.2 - - - -
294B GLU* 3.7 5.6 - - - +
295B PHE* 2.8 77.3 + - + +
308B CYS 2.9 25.1 + - - -
309B LEU* 3.7 9.4 - - - +
310B VAL* 3.0 45.6 + - + +
316B TYR* 3.9 1.5 + - - +
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Residues in contact with LYS 292 (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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289B TRP 4.8 3.1 + - - +
290B LYS 3.3 1.6 + - - -
291B GLN* 1.3 77.8 - - - +
293B GLU* 1.3 73.7 + - - +
296B GLU* 3.6 9.4 - - - +
310B VAL* 3.7 24.9 - - + -
311B PRO* 3.5 27.5 + - - +
313B LYS* 4.0 31.8 - - + +
316B TYR* 3.4 30.3 - - - +
402B ARG* 5.5 4.5 - - - +
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Residues in contact with GLU 293 (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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289B TRP 4.6 1.7 - - - +
290B LYS* 3.4 23.2 - - + +
291B GLN 3.1 0.2 - - - -
292B LYS* 1.3 90.7 + - - +
294B GLU* 1.3 64.2 + - + +
296B GLU* 3.3 6.7 + - - +
297B SER* 3.1 27.9 + - - -
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Residues in contact with GLU 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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262B HIS* 4.2 12.8 + - + +
284B TYR* 3.3 20.3 - - + -
285B GLY* 3.2 12.8 - - - -
286B ASN* 2.8 49.9 + - - +
290B LYS* 3.0 34.0 + - + +
291B GLN* 4.4 3.1 - - - -
293B GLU* 1.3 78.9 - - + +
295B PHE* 1.3 66.4 + - + +
297B SER* 3.6 5.8 - - - -
298B PHE* 3.0 20.1 + - - +
360B ILE* 4.0 15.4 - - + +
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Residues in contact with PHE 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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236B LEU* 3.7 18.4 - - + -
238B SER* 4.2 5.6 - - - -
262B HIS* 3.5 42.2 - + + -
291B GLN* 2.8 59.7 + - + +
294B GLU* 1.3 73.6 - - - +
296B GLU* 1.3 60.0 + - - +
298B PHE* 3.5 8.6 + - - +
302B VAL* 3.5 38.3 - - + +
304B LEU* 3.9 14.1 - - + -
309B LEU* 4.9 2.0 - - + -
316B TYR* 3.9 27.1 - + + -
319B ARG* 2.9 25.3 + - - -
320B VAL* 5.1 0.9 - - + -
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Residues in contact with GLU 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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292B LYS 3.6 13.9 + - - +
293B GLU* 3.3 11.9 + - - +
294B GLU 3.2 0.2 - - - -
295B PHE* 1.3 80.2 - - - +
297B SER* 1.3 63.0 + - - +
299B ASN* 3.2 9.2 + - - +
315B SER* 2.6 44.4 + - - +
316B TYR* 3.7 7.9 - - + +
319B ARG* 2.9 32.8 + - - +
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Residues in contact with SER 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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284B TYR* 2.8 21.4 + - - -
293B GLU 3.1 13.4 + - - -
294B GLU* 3.3 13.0 + - - +
296B GLU* 1.3 76.3 - - - +
298B PHE* 1.3 63.8 + - - +
299B ASN* 3.2 7.7 + - - -
358B THR* 3.0 39.2 + - - -
360B ILE* 3.8 14.7 - - - +
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Residues in contact with PHE 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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234B GLY* 3.4 27.8 + - - -
235B ILE 3.6 6.7 - - - -
236B LEU* 3.4 47.6 - - + -
260B TYR* 3.6 29.4 - + + -
284B TYR* 3.4 29.4 + + + -
294B GLU 3.0 17.7 + - - +
295B PHE 3.7 7.2 - - - +
296B GLU 3.2 0.8 - - - -
297B SER* 1.3 76.5 - - - +
299B ASN* 1.3 60.4 - - - +
300B GLY* 2.9 27.5 + - - -
301B PRO 3.6 3.4 - - - -
302B VAL* 4.7 1.1 - - + -
355B PRO 4.4 0.2 - - - +
357B PRO* 3.2 39.3 - - + +
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Residues in contact with ASN 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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296B GLU 3.2 12.8 + - - +
297B SER* 3.2 13.2 + - - +
298B PHE* 1.3 74.5 - - - +
300B GLY* 1.3 56.9 + - - +
319B ARG* 3.3 32.3 + - - +
354B CYS* 3.5 14.0 - - - +
355B PRO* 3.6 33.6 - - + +
356B ALA 2.8 20.4 + - - +
358B THR* 3.0 25.4 + - - +
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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
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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