Contacts of the helix formed by residues 343 - 360 (chain B) in PDB entry 1U5U
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 343 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B VAL* 6.4 1.8 - - - -
197B THR* 4.6 4.2 - - - +
287B PHE* 3.6 33.7 - - - +
334B LEU* 3.3 42.4 - - + +
335B GLU 3.6 25.6 + - - +
336B ALA* 3.6 8.4 - - - +
341B ASP* 2.8 18.6 + - - +
342B TYR* 1.3 76.1 - - - +
344B SER* 1.3 64.2 + - - +
345B ILE 3.3 1.7 + - - -
346B GLY* 3.4 11.0 + - - +
347B GLU* 3.6 6.2 + - - +
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Residues in contact with SER 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.3 8.5 - - - +
146B ASN* 3.4 12.8 - - - -
147B SER 3.6 1.7 + - - -
336B ALA* 3.5 13.8 - - - +
338B SER 3.5 19.5 - - - -
339B PRO* 3.2 18.4 + - - -
341B ASP 2.6 21.0 + - - -
343B ASN* 1.3 76.2 - - - +
345B ILE* 1.3 67.5 + - - +
347B GLU* 3.1 3.8 + - - +
348B LEU* 2.8 32.2 + - - +
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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
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144B PHE* 3.7 23.3 - - + +
145B TRP* 3.4 29.2 - - - +
146B ASN* 3.6 26.2 - - - +
150B LEU* 4.5 4.3 - - + -
196B VAL* 4.5 8.5 - - + -
342B TYR 4.4 4.5 - - - +
343B ASN 3.3 0.8 - - - -
344B SER* 1.3 77.4 + - - +
346B GLY* 1.3 63.7 + - - +
348B LEU* 3.7 9.8 - - + +
349B ARG* 3.0 47.4 + - - +
999B HEM 4.1 33.2 - - + -
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Residues in contact with GLY 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 4.8 14.1 - - - +
324B ILE* 3.8 18.0 - - - +
333B LEU* 4.9 9.4 - - - -
334B LEU 5.6 2.2 - - - -
343B ASN 3.4 7.7 + - - -
344B SER 3.2 0.8 - - - -
345B ILE* 1.3 80.1 - - - +
347B GLU* 1.3 61.7 + - - +
349B ARG* 3.4 2.8 + - - +
350B VAL* 3.2 28.1 + - - +
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.5 9.6 - - + +
46B LYS* 2.7 40.1 + - - +
334B LEU 4.4 10.9 + - - +
335B GLU* 3.5 7.8 - - - +
336B ALA* 2.6 47.0 + - + +
343B ASN 3.6 4.8 + - - +
344B SER* 3.1 7.2 + - - +
346B GLY* 1.3 71.9 - - - +
348B LEU* 1.3 66.2 + - - +
350B VAL* 3.3 8.8 + - - +
351B ALA* 3.1 23.0 + - - +
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Residues in contact with LEU 348 (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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42B LEU* 4.4 8.3 - - + -
45B LYS* 4.0 12.6 - - + +
46B LYS* 3.7 40.8 - - + +
49B PHE* 4.2 13.7 - - + -
147B SER* 4.6 11.2 - - - -
150B LEU* 4.4 20.6 - - + -
344B SER* 2.8 38.7 + - - +
345B ILE* 3.7 10.8 - - + +
347B GLU* 1.3 72.3 - - - +
349B ARG* 1.3 58.0 + - - +
351B ALA* 3.2 4.5 + - - +
352B VAL* 2.8 36.7 + - + +
999B HEM 4.2 12.8 - - + -
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Residues in contact with ARG 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 3.5 24.2 + - - +
194B SER 4.5 2.8 + - - -
196B VAL* 3.6 13.1 - - - +
198B MET* 5.2 1.2 - - - +
323B ASN* 5.2 0.2 - - - -
324B ILE* 3.8 32.8 - - + +
345B ILE* 3.0 30.0 + - - +
346B GLY* 3.7 5.2 - - - +
348B LEU* 1.3 73.4 - - - +
350B VAL* 1.3 60.4 + - - +
352B VAL* 4.6 2.0 - - - -
353B TYR* 2.7 75.6 + - + +
999B HEM 3.2 80.7 - - + +
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ASN* 4.2 7.6 - - - -
324B ILE* 4.2 5.4 - - + -
325B ALA* 3.9 26.7 - - + -
333B LEU* 3.4 33.2 - - + -
346B GLY 3.2 8.4 + - - +
347B GLU* 3.3 10.7 + - - +
349B ARG* 1.3 75.4 - - - +
351B ALA* 1.3 65.0 + - - +
354B THR* 2.6 34.9 + - - +
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Residues in contact with ALA 351 (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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46B LYS* 4.1 32.1 - - + -
50B LYS* 3.9 14.7 - - + +
347B GLU 3.1 12.8 + - - +
348B LEU 3.5 7.0 - - - +
350B VAL* 1.3 79.1 - - - +
352B VAL* 1.3 63.1 + - + +
354B THR* 4.1 2.3 - - - -
355B TRP* 3.3 23.2 + - - +
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Residues in contact with VAL 352 (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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46B LYS* 4.9 2.5 - - - +
49B PHE* 3.9 24.9 - - + +
50B LYS* 4.2 11.2 - - + +
53B PHE* 4.0 20.6 - - + -
348B LEU* 2.8 24.6 + - + +
349B ARG 4.0 1.3 - - - +
351B ALA* 1.3 72.0 - - + +
353B TYR* 1.3 67.6 + - + +
355B TRP* 3.2 3.5 + - - +
356B VAL* 2.9 26.0 + - + +
999B HEM 3.6 53.6 - - + -
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Residues in contact with TYR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 4.8 4.3 - - + -
322B PHE 3.3 26.5 - - - -
323B ASN* 3.5 22.4 - - - +
324B ILE* 5.0 3.6 - - + -
349B ARG* 2.7 72.3 + - + +
352B VAL* 1.3 71.5 - - + +
354B THR* 1.3 57.1 + - - +
356B VAL* 3.8 7.4 - - - -
357B GLN* 2.8 46.1 + - - +
999B HEM 2.2 85.8 + + + -
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Residues in contact with THR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ASN* 3.2 17.2 + - - +
325B ALA* 4.9 1.7 - - - +
350B VAL* 2.6 31.5 + - - +
351B ALA* 4.1 3.1 - - - -
353B TYR* 1.3 79.1 - - - +
355B TRP* 1.3 64.3 + - - +
357B GLN* 4.2 3.0 - - - +
358B HIS* 3.4 18.4 + - - +
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Residues in contact with TRP 355 (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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51A THR* 3.4 21.5 - - + +
52A LEU* 4.8 14.6 - - + -
55A LEU* 4.1 27.6 - - + -
50B LYS* 3.9 31.6 - - + -
54B THR* 2.7 30.7 + - + -
351B ALA 3.3 15.9 + - - +
352B VAL 3.2 3.8 + - - +
354B THR* 1.3 80.0 - - - +
356B VAL* 1.3 65.2 + - + +
358B HIS* 3.1 28.8 + + + +
359B LEU* 2.6 46.0 - - + +
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Residues in contact with VAL 356 (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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50B LYS* 5.2 1.1 - - - +
53B PHE* 3.8 28.9 - - + +
54B THR* 4.4 2.7 - - - +
57B THR* 3.7 23.3 - - - +
352B VAL* 2.9 27.2 + - + +
353B TYR* 3.5 11.9 - - - +
355B TRP* 1.3 82.7 - - + +
357B GLN* 1.3 59.6 + - - +
359B LEU* 3.1 11.1 + - - +
360B ARG* 3.0 30.5 + - - +
999B HEM 3.6 33.7 - - + +
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Residues in contact with GLN 357 (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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321B ALA* 3.6 23.6 - - + +
322B PHE 2.8 33.7 + - - +
323B ASN* 3.3 26.2 + - - +
353B TYR* 2.8 36.3 + - - +
354B THR* 4.3 3.5 - - - +
356B VAL* 1.3 70.0 - - - +
358B HIS* 1.3 62.7 + - - +
359B LEU 3.3 0.2 - - - -
360B ARG* 3.5 16.6 + - - +
361B LYS* 3.5 22.1 + - - +
999B HEM 3.2 33.0 + - - +
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Residues in contact with HIS 358 (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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55A LEU* 5.5 2.0 - - + +
354B THR 3.4 12.9 + - - +
355B TRP* 3.1 29.9 + + + +
357B GLN* 1.3 76.2 - - - +
359B LEU* 1.3 79.5 + - + +
361B LYS* 3.1 25.7 + - - +
362B LEU* 3.5 33.6 - - + +
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Residues in contact with LEU 359 (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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55A LEU* 3.2 45.1 - - + -
54B THR* 4.9 11.9 - - + +
57B THR* 4.6 12.8 - - + -
58B THR* 6.0 0.2 - - - +
62B PHE* 3.3 22.9 - - + -
355B TRP* 2.6 62.6 - - + +
356B VAL* 3.1 13.4 + - + +
358B HIS* 1.3 87.0 - - + +
360B ARG* 1.3 56.3 + - - +
361B LYS 3.0 0.2 - - - -
362B LEU* 2.9 29.2 + - + +
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Residues in contact with ARG 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B THR* 4.0 11.4 - - + -
62B PHE* 3.6 22.7 + - - +
63B ARG 3.5 27.4 - - - -
64B ARG* 3.7 12.6 - - - +
318B GLU* 2.9 27.9 + - - +
319B LYS* 4.3 7.3 + - - +
320B THR 3.3 21.8 + - - -
321B ALA* 3.9 14.1 - - - +
356B VAL 3.0 18.1 + - - +
357B GLN* 3.9 10.2 - - - +
358B HIS 3.2 1.0 - - - -
359B LEU* 1.3 75.0 - - - +
361B LYS* 1.3 61.2 + - + +
362B LEU 3.3 5.6 - - - +
999B HEM 2.7 41.4 + - - +
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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