Contacts of the helix formed by residues 290 - 299 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A ASN* 4.1 22.6 - - + +
287A ALA 3.2 10.2 + - - +
288A TRP 3.1 1.4 - - - -
289A TRP* 1.3 120.2 - - + +
291A GLN* 1.3 58.2 + - - +
292A LYS 3.3 2.5 - - - -
293A GLU* 3.1 18.1 + - + +
294A GLU* 3.0 48.1 + - + +
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Residues in contact with GLN 291 (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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262A HIS* 4.2 6.5 - - + -
287A ALA 4.3 0.2 + - - -
288A TRP* 2.9 29.7 + - - +
289A TRP 3.2 1.4 - - - -
290A LYS* 1.3 76.5 - - - +
292A LYS* 1.3 64.8 + - - +
293A GLU 3.1 0.2 - - - -
294A GLU* 3.7 5.4 - - - +
295A PHE* 2.8 79.2 + - + +
308A CYS 2.9 24.4 + - - -
309A LEU* 3.7 9.5 - - - +
310A VAL* 3.0 44.8 + - + +
316A TYR* 4.2 1.6 + - - +
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Residues in contact with LYS 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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289A TRP 4.5 13.3 + - - +
290A LYS 3.3 1.6 + - - -
291A GLN* 1.3 77.5 - - - +
293A GLU* 1.3 76.3 + - - +
296A GLU* 3.6 8.3 - - - +
310A VAL* 3.6 27.0 - - + +
311A PRO 4.3 9.4 - - - +
313A LYS* 3.6 31.5 + - + +
316A TYR* 3.4 29.0 - - - +
402A ARG* 5.0 12.7 - - - +
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Residues in contact with GLU 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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289A TRP* 4.5 3.5 - - - +
290A LYS* 3.3 24.0 - - + +
292A LYS* 1.3 99.1 + - - +
294A GLU* 1.3 65.3 + - + +
296A GLU* 3.3 6.9 + - - +
297A SER* 3.1 27.9 + - - -
313A LYS* 5.7 1.4 + - - +
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Residues in contact with GLU 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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262A HIS* 4.2 11.4 + - - +
284A TYR* 3.3 20.9 - - + -
285A GLY* 3.3 9.4 - - - -
286A ASN* 2.8 54.6 + - - +
287A ALA 4.4 0.2 - - - +
290A LYS* 3.0 33.1 + - + +
291A GLN* 4.4 3.6 - - - -
293A GLU* 1.3 79.3 - - + +
295A PHE* 1.3 66.5 + - + +
297A SER* 3.4 6.4 + - - +
298A PHE* 3.0 20.3 + - - +
360A ILE* 3.9 14.0 - - + +
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Residues in contact with PHE 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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236A LEU* 3.7 18.6 - - + -
238A SER* 4.3 3.4 - - - -
262A HIS* 3.5 37.5 - + - -
291A GLN* 2.8 60.0 + - + +
294A GLU* 1.3 73.5 - - - +
296A GLU* 1.3 60.7 + - - +
298A PHE* 3.5 10.1 + - - +
302A VAL* 3.5 35.4 - - + +
304A LEU* 4.0 15.5 - - + -
309A LEU* 4.9 2.0 - - + -
316A TYR* 3.8 32.8 - + + -
319A ARG* 2.9 25.8 + - - -
320A VAL* 5.1 2.0 - - + -
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Residues in contact with GLU 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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292A LYS 3.6 10.0 + - - +
293A GLU* 3.3 11.3 + - - +
294A GLU 3.2 0.6 - - - -
295A PHE* 1.3 78.0 - - - +
297A SER* 1.3 62.5 - - - +
299A ASN* 3.2 10.4 + - - +
313A LYS* 3.0 25.5 + - - +
315A SER* 2.8 31.4 + - - +
316A TYR* 3.9 9.7 - - + -
319A ARG* 3.0 27.3 + - - +
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Residues in contact with SER 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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284A TYR* 2.8 20.4 + - - -
293A GLU 3.1 12.7 + - - -
294A GLU* 3.4 12.5 + - - +
296A GLU* 1.3 74.7 - - - +
298A PHE* 1.3 63.9 + - - +
299A ASN* 3.2 9.2 + - - -
358A THR* 3.0 35.1 + - - -
360A ILE* 3.9 15.4 - - - +
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Residues in contact with PHE 298 (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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234A GLY* 3.4 26.0 - - - -
235A ILE 3.6 7.0 - - - -
236A LEU* 3.4 45.8 - - + -
260A TYR* 3.7 29.2 - + + -
284A TYR* 3.7 28.0 - + + -
294A GLU 3.0 16.8 + - - +
295A PHE* 3.7 7.2 - - - +
296A GLU 3.2 0.6 - - - -
297A SER* 1.3 78.2 - - - +
299A ASN* 1.3 56.1 + - - +
300A GLY* 2.8 31.2 + - - -
301A PRO 3.6 2.7 - - - -
302A VAL* 4.5 1.3 - - + -
357A PRO* 3.1 41.7 - - + +
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Residues in contact with ASN 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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296A GLU 3.2 15.8 + - - +
297A SER* 3.2 10.1 + - - +
298A PHE* 1.3 73.4 - - - +
300A GLY* 1.3 58.2 + - - +
319A ARG* 3.2 32.4 + - - +
354A CYS* 3.4 13.2 - - - +
355A PRO* 3.4 34.9 - - + +
356A ALA 2.8 20.2 + - - -
358A THR* 2.9 25.8 + - - +
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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