Contacts of the helix formed by residues 334 - 350 (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 ARG 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A ARG* 2.7 39.1 + - - +
329A ILE* 5.4 1.6 - - - +
332A TYR* 3.7 29.3 - - + +
333A ASN* 1.3 78.3 - - - +
335A LEU* 1.3 65.5 + - - +
336A GLU* 4.0 29.8 + - + +
337A ASP* 2.9 57.9 + - - +
338A SER* 3.1 14.1 + - - -
361A TYR* 4.9 1.1 - - - -
421A ARG* 5.3 15.6 - - - +
428A ARG* 5.5 3.2 - - - +
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Residues in contact with LEU 335 (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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333A ASN 3.9 2.2 + - - -
334A ARG* 1.3 70.6 - - - +
336A GLU* 1.3 62.9 + - - +
338A SER* 3.3 3.5 + - - -
339A ILE* 3.0 41.6 + - + +
361A TYR* 3.5 49.2 + - + -
363A MSE 5.0 0.2 - - - -
418A VAL* 3.8 18.2 - - + +
421A ARG* 3.8 20.8 - - + +
422A PHE* 3.4 41.1 - - + +
425A ALA* 4.9 0.4 - - + -
438A VAL* 4.5 9.0 - - + -
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Residues in contact with GLU 336 (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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334A ARG* 3.2 25.5 + - + +
335A LEU* 1.3 81.2 - - - +
337A ASP* 1.3 59.8 + - - +
339A ILE* 3.4 2.1 + - - -
340A LEU* 3.1 23.6 + - - +
421A ARG* 4.9 7.6 + - - +
425A ALA* 4.2 22.4 + - + +
428A ARG* 3.2 55.0 + - - +
429A LEU* 3.5 27.3 - - + +
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Residues in contact with ASP 337 (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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325A LEU* 3.9 15.3 - - + +
328A ARG* 3.3 29.2 + - + +
329A ILE* 3.6 28.6 - - + +
334A ARG* 2.9 59.9 + - + +
336A GLU* 1.3 77.6 - - - +
338A SER* 1.3 60.9 + - - +
340A LEU* 4.5 4.3 - - - +
341A GLY 3.0 22.3 + - - -
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Residues in contact with SER 338 (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 18.7 + - - +
313A ILE* 3.7 23.8 - - - +
329A ILE* 4.3 9.5 - - - +
334A ARG 3.1 9.8 + - - -
335A LEU 3.7 3.4 - - - -
337A ASP* 1.3 78.3 - - - +
339A ILE* 1.4 59.8 + - - +
342A GLY* 2.9 23.2 + - - -
356A VAL* 5.3 1.6 - - - -
361A TYR* 3.5 25.1 + - - -
363A MSE 3.5 16.2 - - - +
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 3.0 36.1 + - + +
336A GLU* 3.8 4.3 - - - +
338A SER* 1.4 73.5 - - - +
340A LEU* 1.3 63.9 + - - +
342A GLY* 3.4 1.2 + - - -
343A MSE 3.0 36.6 + - - +
363A MSE 3.6 25.4 - - - -
365A ILE* 3.9 1.5 - - + +
422A PHE* 4.0 19.5 - - + -
425A ALA* 3.7 29.2 - - + -
426A LYS* 6.3 0.2 - - + -
429A LEU* 3.7 14.6 - - + -
431A MSE 4.6 7.2 - - - -
436A VAL* 4.2 19.7 - - + -
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Residues in contact with LEU 340 (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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325A LEU* 4.0 24.2 - - + -
336A GLU 3.1 16.8 + - - +
337A ASP* 3.9 6.7 - - - +
339A ILE* 1.3 78.9 - - - +
341A GLY* 1.3 57.4 + - - +
343A MSE 3.4 23.0 + - + +
344A ILE* 2.9 43.6 + - + +
429A LEU* 3.9 21.7 - - + +
430A ARG* 6.5 0.7 - - + -
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Residues in contact with GLY 341 (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* 4.7 2.2 - - - -
317A LEU* 3.9 14.3 - - - +
325A LEU* 3.7 17.3 - - - -
329A ILE* 4.7 1.3 - - - -
337A ASP 3.0 18.0 + - - -
338A SER 3.8 0.9 - - - -
339A ILE 3.3 0.2 - - - -
340A LEU* 1.3 75.5 - - - +
342A GLY* 1.3 61.9 + - - +
344A ILE* 3.3 3.6 + - - +
345A ILE* 3.0 33.2 + - - +
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Residues in contact with GLY 342 (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* 4.5 5.4 - - - +
338A SER 2.9 15.0 + - - -
341A GLY* 1.3 72.7 - - - +
343A MSE 1.4 63.3 + - - +
345A ILE* 3.2 5.2 + - - -
346A LEU* 3.0 21.5 + - - +
354A LEU* 3.6 22.3 - - - +
363A MSE 5.0 0.4 - - - -
365A ILE* 3.5 22.0 - - - -
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Residues in contact with MSE 343 (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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339A ILE* 3.0 28.1 + - + +
340A LEU* 3.6 33.2 - - + +
342A GLY* 1.4 71.3 - - - +
344A ILE* 1.3 60.0 + - - +
346A LEU* 3.4 2.5 + - - +
347A ASP* 2.8 32.7 + - - +
365A ILE* 3.4 21.6 - - + +
429A LEU* 4.7 9.9 - - + -
430A ARG* 3.3 35.2 - - + +
431A MSE 4.4 6.1 - - - +
434A TYR* 4.1 35.6 - - + -
436A VAL* 4.6 3.4 - - + -
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Residues in contact with ILE 344 (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* 3.8 11.4 - - + -
320A LEU* 5.2 0.9 - - + -
322A TYR* 3.5 52.3 - - + +
325A LEU* 3.9 23.6 - - + -
340A LEU* 2.9 36.2 + - + +
341A GLY 3.3 7.4 + - - +
343A MSE 1.3 72.9 - - + +
345A ILE* 1.3 59.1 + - - +
347A ASP* 3.4 5.7 + - - +
348A GLU* 2.9 33.7 + - + +
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Residues in contact with ILE 345 (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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300A LEU* 5.5 1.1 - - + -
306A VAL* 6.3 0.2 - - + -
308A ILE* 4.2 19.7 - - + -
313A ILE* 4.1 20.9 - - + +
316A ILE* 3.7 33.7 - - + -
317A LEU* 4.1 11.4 - - + -
320A LEU* 4.5 7.9 - - + -
341A GLY 3.0 20.7 + - - +
342A GLY* 3.2 8.9 + - - +
344A ILE* 1.3 75.7 - - - +
346A LEU* 1.3 60.2 + - - +
348A GLU 3.3 0.2 + - - -
349A LEU* 2.9 49.9 + - + +
351A PHE* 4.1 16.4 - - + -
354A LEU* 4.5 7.9 - - + -
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Residues in contact with LEU 346 (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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342A GLY 3.0 15.5 + - - +
343A MSE 3.8 4.9 - - - +
345A ILE* 1.3 79.6 - - - +
347A ASP* 1.3 57.5 + - - +
350A ASN* 2.8 30.1 + - - -
351A PHE* 3.6 56.5 - - + +
352A GLU 4.3 5.4 - - - +
353A ILE* 4.3 1.8 - - - +
354A LEU* 4.7 3.6 - - + +
365A ILE* 3.7 27.8 - - + +
366A THR* 3.9 11.2 - - - -
367A HIS* 3.9 13.4 - - + +
434A TYR* 3.7 28.9 - - + -
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Residues in contact with ASP 347 (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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343A MSE 2.8 21.7 + - - +
344A ILE* 3.8 5.7 - - - +
346A LEU* 1.3 75.0 - - - +
348A GLU* 1.3 68.5 + - - +
350A ASN* 4.3 7.8 + - - +
367A HIS* 5.7 0.9 - - - -
433A GLU* 5.0 4.6 - - - +
434A TYR* 3.1 27.9 + - + +
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Residues in contact with GLU 348 (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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320A LEU* 4.2 28.4 - - + +
322A TYR* 2.7 30.7 + - - +
344A ILE* 2.9 34.3 + - + +
345A ILE 3.9 2.7 - - - +
347A ASP* 1.3 83.8 - - - +
349A LEU* 1.3 67.2 + - + +
350A ASN* 4.7 1.7 - - - +
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Residues in contact with LEU 349 (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 ILE* 3.9 25.4 - - + +
297A THR* 5.7 1.3 - - - -
300A LEU* 3.9 30.7 - - + -
301A PRO* 3.2 42.1 - - + +
316A ILE* 4.7 2.0 - - + -
320A LEU* 4.4 19.5 - - + -
345A ILE* 2.9 33.5 + - + +
348A GLU* 1.3 86.4 - - + +
350A ASN* 1.3 70.5 + - - +
351A PHE* 3.4 13.5 - - + -
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Residues in contact with ASN 350 (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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301A PRO 4.0 8.7 - - - +
346A LEU 2.8 19.1 + - - +
347A ASP 4.5 8.5 - - - +
348A GLU 4.7 2.0 - - - +
349A LEU* 1.3 79.7 - - - +
351A PHE* 1.3 65.1 + - - +
367A HIS* 3.5 21.1 + - - -
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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