Contacts of the helix formed by residues 310 - 321 (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 GLU 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A ASP* 1.3 77.1 - - - +
311A ALA* 1.3 65.4 + - - +
312A GLU 3.3 0.2 + - - -
313A ILE* 3.4 15.0 + - - +
314A ALA* 3.6 7.1 + - - +
329A ILE* 4.0 18.9 - - + +
333A ASN* 3.2 55.2 - - - +
338A SER* 4.0 16.3 + - - +
356A VAL* 4.7 1.3 - - + +
357A HIS 3.6 5.2 + - - +
358A THR* 3.9 32.5 - - + -
359A THR 5.1 1.6 + - - -
361A TYR* 4.5 4.8 + - - -
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Residues in contact with ALA 311 (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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309A ASP* 3.2 10.6 + - - +
310A GLU* 1.3 82.5 - - - +
312A GLU* 1.3 62.2 + - + +
314A ALA* 3.4 6.8 + - - +
315A GLN* 3.3 30.2 + - - +
330A PHE* 6.1 7.0 - - + -
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Residues in contact with GLU 312 (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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282A GLU* 5.6 0.3 - - - +
283A PHE* 3.8 17.7 - - + +
284A ALA* 3.1 39.2 - - - +
285A SER* 3.5 4.2 + - - +
307A GLY 4.2 0.5 - - - +
308A ILE* 3.4 16.0 - - + +
309A ASP* 2.9 48.3 + - - +
311A ALA* 1.3 76.7 - - + +
313A ILE* 1.3 65.1 + - - +
315A GLN* 3.2 22.3 + - - +
316A ILE* 2.9 29.8 + - - +
357A HIS* 5.3 1.0 + - - -
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Residues in contact with ILE 313 (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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308A ILE* 3.4 29.8 - - + +
309A ASP 3.0 15.0 + - - +
310A GLU* 3.7 9.4 - - - +
311A ALA 3.3 0.2 - - - -
312A GLU* 1.3 75.8 - - - +
314A ALA* 1.3 59.3 + - - +
316A ILE* 3.5 1.9 + - - +
317A LEU* 3.0 45.7 + - + +
329A ILE* 3.7 12.1 - - + -
338A SER* 3.7 42.0 - - - +
341A GLY 4.7 2.2 - - - -
342A GLY* 4.5 3.6 - - - +
345A ILE* 4.1 9.8 - - + +
356A VAL* 4.0 20.9 - - + -
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Residues in contact with ALA 314 (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 3.6 1.7 + - - +
311A ALA* 3.4 9.9 + - - +
312A GLU 3.2 0.6 - - - -
313A ILE* 1.3 82.0 - - - +
315A GLN* 1.3 60.2 + - - +
317A LEU* 4.4 0.7 - - - -
318A SER* 2.8 33.4 + - - -
326A ALA* 3.3 36.3 - - + +
329A ILE* 4.1 15.5 - - + -
330A PHE* 4.7 11.4 - - + +
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Residues in contact with GLN 315 (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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283A PHE* 5.0 1.6 - - + -
284A ALA 4.2 1.8 + - - -
285A SER* 3.4 38.9 + - - +
286A VAL 4.1 4.8 + - - +
287A GLN* 5.7 0.7 - - - -
292A ARG* 3.0 56.2 + - - +
311A ALA* 3.3 16.1 + - + +
312A GLU* 3.2 24.9 + - - +
314A ALA* 1.3 77.6 - - + +
316A ILE* 1.3 63.0 + - + +
318A SER* 3.5 2.9 + - - -
319A VAL* 3.3 10.6 + - - +
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Residues in contact with ILE 316 (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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283A PHE* 3.9 31.6 - - + -
296A ILE* 4.1 12.1 - - + -
300A LEU* 4.5 11.9 - - + -
308A ILE* 3.8 36.3 - - + -
312A GLU 2.9 20.7 + - - +
313A ILE 3.9 2.9 - - - +
315A GLN* 1.3 74.5 - - - +
317A LEU* 1.3 65.2 + - - +
319A VAL* 3.0 20.1 + - - +
320A LEU* 3.0 25.6 + - + +
345A ILE* 3.7 29.2 - - + -
349A LEU* 4.7 6.7 - - + -
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Residues in contact with LEU 317 (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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313A ILE* 3.0 41.1 + - + +
314A ALA* 3.7 4.3 - - - +
316A ILE* 1.3 76.8 - - - +
318A SER* 1.3 64.5 + - - +
320A LEU* 3.1 6.2 + - + +
321A GLY 3.0 6.6 + - - -
322A TYR* 2.9 42.6 + - + -
325A LEU* 4.1 11.2 - - + -
326A ALA* 4.0 9.0 - - + -
329A ILE* 3.6 18.6 - - + -
341A GLY* 3.9 21.3 - - - +
344A ILE* 3.8 28.5 - - + -
345A ILE* 4.1 9.4 - - + -
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Residues in contact with SER 318 (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* 2.2 35.3 + - - -
292A ARG* 4.5 0.7 - - - -
314A ALA 2.8 22.4 + - - -
315A GLN* 3.7 8.1 - - - -
317A LEU* 1.3 76.7 - - - +
319A VAL* 1.3 60.6 + - - +
321A GLY* 3.3 10.4 + - - -
322A TYR 4.6 2.0 - - - -
323A ARG* 3.4 25.1 + - - +
326A ALA* 3.8 14.5 - - - +
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Residues in contact with VAL 319 (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* 3.7 45.1 - - + +
292A ARG* 3.9 20.2 - - - +
293A LYS* 3.9 33.9 + - + +
296A ILE* 3.3 33.7 - - + -
315A GLN 3.3 6.2 + - - +
316A ILE 3.0 12.2 + - - +
318A SER* 1.3 74.6 - - - +
320A LEU* 1.3 63.7 + - + +
321A GLY* 3.3 0.6 + - - -
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Residues in contact with LEU 320 (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 LYS* 4.4 15.3 - - + +
296A ILE* 4.3 21.3 - - + -
316A ILE* 3.0 34.6 + - + +
317A LEU* 3.1 6.5 + - - +
319A VAL* 1.3 81.4 - - + +
321A GLY* 1.3 55.4 + - - +
322A TYR* 3.6 22.7 - - + -
344A ILE* 5.2 1.1 - - + -
345A ILE* 4.5 12.3 - - + -
348A GLU* 4.2 37.1 - - + +
349A LEU* 4.4 15.0 - - + -
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Residues in contact with GLY 321 (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 3.0 2.0 + - - -
318A SER 3.3 6.4 + - - -
319A VAL 3.3 4.0 - - - -
320A LEU* 1.3 77.7 - - - +
322A TYR* 1.3 65.1 + - - +
323A ARG* 3.1 18.7 + - - +
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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