Contacts of the helix formed by residues 292 - 303 (chain A) in PDB entry 1UA4
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 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ALA* 4.6 10.7 + - - +
291A LEU* 1.3 74.6 - - - +
293A GLU* 1.3 71.7 + - - +
294A VAL* 3.0 11.3 + - - +
295A GLU* 2.7 59.3 + - - +
296A LEU* 3.0 29.6 + - - +
341A PHE* 3.7 5.3 - - - -
342A HIS* 3.2 20.4 - - + +
1456A AMP 2.5 33.6 + - - +
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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
----------------------------------------------------------
85A LYS* 3.5 23.7 - - - +
86A ALA* 5.0 2.3 + - - +
194A ARG* 3.6 20.1 + - - +
292A ASN* 1.3 83.9 + - - +
294A VAL* 1.3 85.8 + - - +
296A LEU* 3.9 1.7 - - - -
297A ALA* 3.0 25.3 + - - +
312A LEU* 3.3 27.5 - - + +
318A VAL* 4.3 9.9 - - + -
341A PHE* 3.6 21.2 - - + -
342A HIS 3.9 1.0 - - - +
343A THR* 2.6 36.7 + - - +
1456A AMP 4.7 0.9 + - - -
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP* 4.7 6.3 - - + -
85A LYS* 3.8 24.7 - - + -
86A ALA 3.7 22.0 - - - +
269A PHE* 3.7 35.7 - - + -
292A ASN* 3.0 10.4 + - - +
293A GLU* 1.3 92.9 - - - +
295A GLU* 1.3 60.0 + - + +
297A ALA* 3.4 2.8 + - - +
298A SER* 3.0 25.6 + - - -
313A LEU* 4.1 19.2 - - + +
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Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 5.5 0.2 - - - +
267A PHE* 3.4 25.3 - - + +
268A ALA* 3.2 32.4 - - - +
269A PHE* 3.6 11.6 + - + +
291A LEU* 3.1 18.7 - - + +
292A ASN* 2.7 51.5 + - - +
294A VAL* 1.3 73.6 - - + +
296A LEU* 1.3 64.7 + - - +
298A SER* 2.7 24.8 + - - -
299A ILE* 3.2 14.0 + - - +
342A HIS* 5.1 1.6 - - - -
1456A AMP 4.6 1.3 + - - -
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 4.0 25.5 - - + +
292A ASN 3.0 18.3 + - - +
293A GLU* 4.0 2.2 - - - +
295A GLU* 1.3 76.9 - - - +
297A ALA* 1.3 62.2 + - - +
299A ILE* 3.2 6.5 + - + +
300A MET* 3.0 28.9 + - + +
312A LEU* 3.6 15.7 - - + -
323A VAL* 3.9 16.2 - - + +
326A ALA* 3.8 32.1 - - + +
327A MET* 4.1 9.2 - - + +
330A LEU* 4.3 14.8 - - + -
341A PHE* 3.9 22.7 - - + -
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Residues in contact with ALA 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 GLU 3.0 19.6 + - - +
294A VAL 3.5 4.7 - - - +
295A GLU 3.2 0.2 - - - -
296A LEU* 1.3 77.5 - - - +
298A SER* 1.3 56.4 + - - +
300A MET* 3.2 3.7 + - - +
301A GLU* 2.9 27.9 + - - +
309A ALA* 3.6 31.1 - - + +
312A LEU* 3.6 16.7 - - + +
313A LEU* 3.8 18.6 - - + -
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Residues in contact with SER 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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267A PHE* 4.7 4.0 - - - -
268A ALA 5.7 0.2 + - - -
269A PHE* 5.7 10.8 - - - -
270A THR 5.3 5.0 + - - -
276A ARG* 2.8 53.1 + - - +
294A VAL 3.0 13.3 + - - -
295A GLU* 2.7 23.5 + - - +
297A ALA* 1.3 76.7 - - - +
299A ILE* 1.3 61.6 + - - +
301A GLU* 3.3 13.7 - - - +
302A ILE 3.5 3.3 + - - -
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Residues in contact with ILE 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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267A PHE* 3.9 34.3 - - + -
276A ARG* 4.4 3.1 - - + +
280A LEU* 4.0 29.4 - - + -
283A LEU* 5.9 0.2 - - + -
291A LEU* 3.6 30.7 - - + -
295A GLU 3.2 11.6 + - - +
296A LEU* 3.5 8.1 - - + +
297A ALA 3.1 0.4 - - - -
298A SER* 1.3 77.7 + - - +
300A MET* 1.3 74.4 - - + +
301A GLU 3.1 1.3 - - - -
302A ILE* 3.1 23.2 - - - +
303A LEU* 3.2 21.3 + - + +
330A LEU* 4.2 16.2 - - + -
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Residues in contact with MET 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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296A LEU* 3.0 21.2 + - + +
297A ALA 3.5 7.4 - - - +
299A ILE* 1.3 85.5 - - + +
301A GLU* 1.3 64.4 + - - +
303A LEU* 3.0 30.1 + - + -
305A GLU* 2.9 59.1 + - - +
308A LEU* 3.8 14.1 - - + -
309A ALA 4.0 5.4 - - - +
312A LEU* 4.1 5.4 - - + -
326A ALA* 3.4 50.5 - - + +
329A LYS* 4.2 5.2 - - + -
330A LEU* 4.6 2.5 - - + +
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Residues in contact with GLU 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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273A GLU* 4.0 17.2 - - - +
276A ARG* 2.9 29.5 + - - -
297A ALA 2.9 12.8 + - - +
298A SER* 3.3 11.3 - - - +
300A MET* 1.3 78.9 - - - +
302A ILE* 1.3 59.9 + - + +
304A GLY* 3.4 10.4 + - - -
305A GLU 4.8 2.2 - - - +
306A LYS* 5.6 1.8 - - - +
309A ALA* 4.2 11.6 - - + +
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Residues in contact with ILE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLU* 4.1 29.4 - - + +
276A ARG* 3.6 45.5 - - + +
277A GLU* 3.8 29.5 - - + +
280A LEU* 3.5 28.9 - - + -
298A SER 3.8 2.5 - - - +
299A ILE* 3.1 15.3 - - - +
301A GLU* 1.3 75.9 - - + +
303A LEU* 1.3 61.1 + - + +
304A GLY 3.2 3.7 + - - -
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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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280A LEU* 4.1 15.0 - - + -
299A ILE* 3.2 22.6 + - + +
300A MET* 3.0 33.6 + - + +
302A ILE* 1.3 80.5 - - + +
304A GLY* 1.3 60.8 + - - +
305A GLU* 3.3 14.9 + - + +
329A LYS* 4.7 19.3 - - + +
330A LEU* 4.9 2.7 - - + +
333A LYS* 4.1 36.1 - - + +
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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