Contacts of the helix formed by residues 334 - 350 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ARG* 3.5 25.3 - - - +
329B ILE* 5.3 0.4 - - - +
332B TYR* 3.2 45.7 - - + +
333B ASN* 1.3 77.1 - - - +
335B LEU* 1.3 66.5 + - - +
336B GLU* 4.4 5.4 - - + +
337B ASP* 3.0 50.0 + - - +
338B SER* 3.1 14.1 + - - -
421B ARG* 6.0 3.4 - - - +
1002B SO4 3.5 19.7 - - - +
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ASN 3.6 1.0 + - - -
334B ARG* 1.3 71.7 - - - +
336B GLU* 1.3 63.9 + - - +
338B SER* 3.1 3.3 + - - -
339B ILE* 3.0 42.5 + - + +
361B TYR* 3.4 50.3 - - + +
363B MSE 5.3 0.4 - - - -
418B VAL* 4.5 4.7 - - + +
421B ARG* 3.7 17.3 - - + +
422B PHE* 3.6 37.9 - - + +
425B ALA* 4.5 2.0 - - + -
438B VAL* 4.8 8.7 - - + -
1002B SO4 3.0 26.0 + - - +
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Residues in contact with GLU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ARG* 4.4 5.8 - - + +
335B LEU* 1.3 79.6 - - - +
337B ASP* 1.3 66.6 + - - +
339B ILE* 3.3 0.9 + - - -
340B LEU* 3.0 27.2 + - + +
421B ARG* 5.7 0.3 + - - -
425B ALA* 4.4 15.6 - - + +
428B ARG* 3.4 46.8 + - - +
429B LEU* 3.4 37.1 - - + +
1002B SO4 5.0 0.8 + - - +
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Residues in contact with ASP 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 4.1 8.4 - - + +
328B ARG* 3.8 32.0 + - - +
329B ILE* 3.7 26.4 - - + +
334B ARG* 3.0 52.1 + - + +
336B GLU* 1.3 84.7 - - - +
338B SER* 1.3 57.5 + - - +
340B LEU* 3.4 8.7 + - - +
341B GLY* 2.9 26.2 + - - -
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Residues in contact with SER 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B GLU* 4.5 11.4 + - - +
313B ILE* 3.8 26.3 - - - +
329B ILE* 4.3 16.6 - - - +
333B ASN* 5.2 2.1 - - - -
334B ARG 3.1 11.1 + - - -
335B LEU 3.1 9.1 + - - -
337B ASP* 1.3 74.3 - - - +
339B ILE* 1.3 59.3 + - - +
341B GLY* 3.8 0.4 - - - +
342B GLY* 2.8 26.0 + - - -
356B VAL* 5.6 0.2 - - - -
361B TYR* 3.6 20.0 + - - -
363B MSE 3.8 11.9 - - - +
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 3.0 33.7 + - + +
336B GLU 3.7 5.2 - - - +
337B ASP 3.3 0.2 - - - -
338B SER* 1.3 74.5 - - - +
340B LEU* 1.3 65.2 + - - +
342B GLY* 3.2 1.9 + - - -
343B MSE 3.0 30.4 + - + +
363B MSE 3.6 24.9 - - - -
365B ILE* 3.8 1.3 - - + +
422B PHE* 4.0 20.0 - - + -
425B ALA* 3.7 29.6 - - + -
429B LEU* 3.9 12.6 - - + -
431B MSE 5.0 4.9 - - + -
436B VAL* 4.1 27.4 - - + -
438B VAL* 5.0 0.2 - - + -
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 4.0 18.8 - - + -
328B ARG* 4.7 10.1 - - - +
336B GLU* 3.0 18.1 + - + +
337B ASP* 3.7 7.9 - - - +
339B ILE* 1.3 76.4 - - - +
341B GLY* 1.3 57.2 + - - +
343B MSE 3.3 22.7 + - + -
344B ILE* 2.9 50.1 + - + +
429B LEU* 4.1 19.5 - - + +
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Residues in contact with GLY 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ILE* 4.4 3.6 - - - -
317B LEU* 3.7 26.2 - - - +
325B LEU* 3.7 6.3 - - - +
337B ASP 2.9 17.3 + - - -
338B SER 3.8 1.3 - - - -
340B LEU* 1.3 75.5 - - - +
342B GLY* 1.3 63.0 + - - +
344B ILE* 3.2 3.5 + - - +
345B ILE* 2.9 32.6 + - - +
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Residues in contact with GLY 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ILE* 4.7 4.3 - - - +
338B SER 2.8 15.0 + - - -
341B GLY* 1.3 77.7 - - - +
343B MSE 1.3 56.2 + - - +
345B ILE* 3.2 6.6 + - - +
346B LEU* 2.9 31.0 + - - +
354B LEU* 3.6 24.2 - - - +
363B MSE 5.1 1.6 - - - -
365B ILE* 3.6 17.2 - - - +
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Residues in contact with MSE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ILE* 3.0 21.4 + - + +
340B LEU* 3.7 35.0 - - + +
342B GLY* 1.3 76.2 - - - +
344B ILE* 1.3 60.3 + - + +
346B LEU* 3.4 2.4 + - - +
347B ASP* 2.8 31.1 + - - +
365B ILE* 4.0 25.4 - - + -
429B LEU* 4.4 11.0 - - + -
430B ARG* 3.3 32.1 - - + +
431B MSE 4.7 0.9 - - - +
434B TYR* 4.2 34.3 - - + -
436B VAL* 4.5 11.7 - - + -
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 3.9 11.2 - - + -
320B LEU* 5.3 0.4 - - + -
322B TYR* 3.6 49.1 - - + +
325B LEU* 3.5 26.9 - - + -
340B LEU* 2.9 37.1 + - + +
341B GLY 3.7 3.4 - - - +
343B MSE 1.3 76.6 - - + +
345B ILE* 1.3 59.1 + - - +
347B ASP* 3.7 5.2 - - - +
348B GLU* 2.9 31.8 + - + +
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Residues in contact with ILE 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 5.7 0.7 - - + -
306B VAL* 6.2 0.7 - - + -
308B ILE* 4.3 13.9 - - + -
313B ILE* 4.0 32.3 - - + +
316B ILE* 4.0 27.8 - - + -
317B LEU* 4.0 13.0 - - + -
320B LEU* 4.5 6.3 - - + -
341B GLY 2.9 18.8 + - - +
342B GLY* 3.5 8.5 - - - +
344B ILE* 1.3 75.6 - - - +
346B LEU* 1.3 57.1 + - - +
348B GLU 3.4 0.2 + - - -
349B LEU* 2.9 45.9 + - + +
351B PHE* 4.0 20.4 - - + -
354B LEU* 4.3 9.2 - - + -
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B GLY 2.9 17.0 + - - +
343B MSE 3.9 4.9 - - - +
345B ILE* 1.3 75.0 - - - +
347B ASP* 1.3 58.3 + - - +
350B ASN* 2.9 30.9 + - - +
351B PHE* 3.4 57.7 - - + +
352B GLU 4.2 4.3 - - - -
353B ILE 4.3 0.4 - - - +
354B LEU* 4.6 5.2 - - + +
365B ILE* 3.8 25.4 - - + +
366B THR* 4.0 10.8 - - - -
367B HIS* 3.9 16.1 - - + +
434B TYR* 3.7 28.1 + - + -
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Residues in contact with ASP 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B MSE 2.8 17.3 + - - +
344B ILE* 3.7 7.0 - - + +
346B LEU* 1.3 79.8 - - - +
348B GLU* 1.3 66.0 + - + +
350B ASN* 4.4 6.8 + - - +
433B GLU* 6.1 0.3 - - - +
434B TYR* 2.9 31.2 + - + +
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Residues in contact with GLU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU* 4.1 29.0 - - + +
322B TYR* 2.6 43.1 + - + +
344B ILE* 2.9 20.1 + - + +
345B ILE 3.9 2.2 - - - +
347B ASP* 1.3 82.9 - - - +
349B LEU* 1.3 66.8 + - + +
350B ASN* 4.7 1.9 - - - +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ILE* 4.0 26.0 - - + +
297B THR* 5.5 1.1 - - - -
300B LEU* 4.0 28.7 - - + -
301B PRO* 3.1 47.9 - - + +
316B ILE* 4.5 2.2 - - + -
320B LEU* 4.0 21.3 - - + -
345B ILE* 2.9 32.2 + - + +
348B GLU* 1.3 84.2 - - + +
350B ASN* 1.3 72.6 + - - +
351B PHE* 3.4 12.3 - - + -
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Residues in contact with ASN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B PRO 4.1 7.2 - - - +
346B LEU 2.9 18.3 + - - +
347B ASP 4.5 8.1 - - - +
348B GLU 4.7 2.2 - - - +
349B LEU* 1.3 82.7 - - - +
351B PHE* 1.3 63.6 + - - +
367B HIS* 3.7 19.8 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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