Contacts of the helix formed by residues 322 - 333 (chain A) 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 TYR 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A LEU* 2.9 27.5 + - + +
318A SER 4.4 0.2 + - - -
320A LEU* 3.9 27.8 - - + -
321A GLY* 1.3 80.0 - - - +
323A ARG* 1.3 62.2 + - - +
324A GLU* 3.4 2.5 - - - -
325A LEU* 3.4 11.6 + - + -
326A ALA* 3.0 22.7 + - - +
344A ILE* 3.5 43.8 - - + +
348A GLU* 2.7 31.1 + - - +
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Residues in contact with ARG 323 (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 ARG* 3.5 18.6 - - - +
318A SER* 3.4 37.2 + - - +
321A GLY* 3.1 15.4 + - - +
322A TYR* 1.3 75.2 - - - +
324A GLU* 1.3 58.1 + - - +
326A ALA* 3.2 6.5 + - - +
327A ASP* 2.9 43.3 + - - +
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Residues in contact with GLU 324 (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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322A TYR 3.4 0.4 - - - -
323A ARG* 1.3 76.7 - - - +
325A LEU* 1.3 63.7 + - - +
327A ASP* 3.2 10.4 + - - +
328A ARG* 3.0 23.0 + - - +
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Residues in contact with LEU 325 (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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317A LEU* 4.1 7.6 - - + -
322A TYR* 3.4 13.4 + - + +
323A ARG 3.4 0.4 - - - -
324A GLU* 1.3 78.8 - - - +
326A ALA* 1.3 63.6 + - - +
328A ARG* 3.3 13.2 + - - +
329A ILE* 3.0 29.4 + - + +
337A ASP* 3.9 35.2 - - + +
340A LEU* 4.0 18.4 - - + -
341A GLY* 3.7 31.4 - - - +
344A ILE* 3.9 21.3 - - + -
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Residues in contact with ALA 326 (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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314A ALA* 3.3 39.2 - - + +
317A LEU* 4.0 5.5 - - + +
318A SER* 3.8 17.0 - - - +
322A TYR 3.0 17.2 + - - +
323A ARG 3.6 4.7 - - - +
325A LEU* 1.3 78.1 - - - +
327A ASP* 1.3 65.4 + - - +
329A ILE* 3.2 5.8 + - - +
330A PHE* 3.0 23.1 + - - +
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Residues in contact with ASP 327 (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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323A ARG* 2.9 24.3 + - - +
324A GLU* 3.4 11.0 - - - +
326A ALA* 1.3 78.4 - - - +
328A ARG* 1.3 56.4 + - - +
330A PHE* 3.2 8.3 + - - +
331A THR* 2.9 36.9 + - - +
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Residues in contact with ARG 328 (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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324A GLU 3.0 12.5 + - - +
325A LEU* 3.5 17.9 - - + +
326A ALA 3.3 0.2 - - - -
327A ASP* 1.3 73.1 - - - +
329A ILE* 1.3 67.2 + - - +
331A THR* 4.5 0.2 - - - -
332A TYR* 2.8 53.3 + - + +
333A ASN 3.8 0.2 + - - -
334A ARG* 2.7 34.7 - - - +
337A ASP* 3.3 28.2 + - - +
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Residues in contact with ILE 329 (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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310A GLU* 4.0 37.0 - - + +
313A ILE* 3.7 13.5 - - + -
314A ALA* 4.1 8.5 - - + +
317A LEU* 3.6 30.1 - - + -
325A LEU* 3.0 18.0 + - + +
326A ALA* 3.6 7.2 - - - +
328A ARG* 1.3 75.3 - - - +
330A PHE* 1.3 67.3 + - - +
333A ASN* 3.0 32.6 + - - +
334A ARG 5.4 0.9 - - - +
337A ASP* 3.6 40.6 - - + +
338A SER* 4.3 7.4 - - - +
341A GLY* 4.7 0.2 - - - -
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Residues in contact with PHE 330 (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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311A ALA* 6.1 6.7 - - + -
314A ALA* 4.7 10.1 - - + -
326A ALA 3.0 15.9 + - - +
327A ASP* 3.2 8.5 + - - +
329A ILE* 1.3 83.0 - - - +
331A THR* 1.3 68.4 + - - +
333A ASN* 3.9 13.4 + - - +
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Residues in contact with THR 331 (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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327A ASP* 2.9 19.0 + - - +
330A PHE* 1.3 87.1 - - - +
332A TYR* 1.3 98.8 + - + +
333A ASN* 4.9 3.0 + - - -
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Residues in contact with TYR 332 (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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328A ARG* 2.8 43.0 + - + +
331A THR* 1.3 102.6 - - + +
333A ASN* 1.3 73.0 + - - +
334A ARG* 3.1 29.2 + - + +
337A ASP* 5.2 0.9 - - - +
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Residues in contact with ASN 333 (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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310A GLU* 3.2 39.2 - - - +
328A ARG 3.8 1.6 + - - -
329A ILE* 3.0 26.6 + - - +
330A PHE* 3.9 13.1 + - - +
331A THR 4.9 2.2 + - - -
332A TYR* 1.3 80.0 - - - +
334A ARG* 1.3 61.7 + - - +
335A LEU 3.9 1.2 + - - -
338A SER* 5.5 0.2 - - - -
361A TYR* 5.5 3.6 + - - -
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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