Contacts of the helix formed by residues 344 - 357 (chain B) in PDB entry 5U3W
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 ASP 344 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B LYS* 4.9 3.6 - - - -
342B GLU 3.8 1.4 + - - +
343B LEU* 1.3 76.9 - - - +
345B ASP* 1.3 64.9 + - - +
346B SER* 2.5 28.4 + - - -
347B ASP* 2.9 13.9 + - - +
348B LEU* 3.0 23.3 + - - +
388B ASN* 2.8 28.6 + - - +
389B HIS* 4.5 2.2 + - + -
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Residues in contact with ASP 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 3.8 16.7 - - + +
186B TYR* 2.9 32.9 + - + -
187B LEU* 4.9 2.1 - - + +
193B THR* 3.4 12.5 - - - -
194B LYS* 2.7 30.0 + - - +
195B LYS* 2.9 31.5 + - - +
344B ASP* 1.3 74.6 - - - +
346B SER* 1.3 57.1 + - - +
348B LEU* 3.7 7.7 - - - +
349B ALA* 2.9 31.0 + - - +
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Residues in contact with SER 346 (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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179B SER 5.5 0.9 - - - +
183B TYR* 3.6 39.0 + - - +
344B ASP* 2.5 24.1 + - - -
345B ASP* 1.3 78.7 - - - +
347B ASP* 1.3 59.8 - - - +
349B ALA* 3.8 7.4 + - - +
350B LEU* 3.9 12.8 + - - +
384B HIS* 2.7 39.8 + - - -
388B ASN* 3.6 3.1 + - - -
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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 LEU* 3.6 20.0 - - + -
344B ASP* 2.9 25.1 + - - +
346B SER* 1.3 74.3 - - - +
348B LEU* 1.3 67.7 + - - +
350B LEU* 3.2 6.4 + - - +
351B PHE* 3.0 22.0 + - - +
381B LEU* 4.1 6.8 - - + +
384B HIS* 3.0 24.9 - - - -
385B LEU* 3.6 14.1 - - + +
388B ASN* 2.9 20.1 + - - -
389B HIS* 2.7 29.6 + - - -
399B LEU* 5.9 0.2 - - + -
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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
----------------------------------------------------------
186B TYR* 4.0 21.1 - - + +
194B LYS* 4.0 19.7 - - + +
292B ALA 5.0 5.8 - - - +
293B MET* 5.9 4.9 - - + -
296B SER* 3.5 25.1 - - - +
338B PHE* 3.8 23.3 - - + -
343B LEU* 3.6 27.4 - - + +
344B ASP 3.0 17.1 + - - +
345B ASP* 3.7 11.9 - - - +
347B ASP* 1.3 77.8 - - - +
349B ALA* 1.3 55.6 + - - +
351B PHE* 3.1 8.5 + - + +
352B ILE* 2.8 40.2 + - + +
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Residues in contact with ALA 349 (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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182B ILE* 3.5 19.6 - - + +
183B TYR* 4.0 10.5 - - - +
186B TYR* 3.6 37.6 - - + -
263B PHE* 3.5 12.6 - - - -
345B ASP 2.9 17.1 + - - +
346B SER 4.0 4.9 - - - +
347B ASP 3.2 0.4 - - - -
348B LEU* 1.3 75.3 - - - +
350B LEU* 1.3 57.5 + - + +
352B ILE* 4.0 0.8 - - - +
353B ALA 3.1 22.0 + - - -
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Residues in contact with LEU 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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178B PHE* 4.4 5.8 - - + -
179B SER* 3.3 43.5 - - - +
182B ILE* 4.1 21.5 - - + -
346B SER 3.9 9.1 + - - +
347B ASP 3.2 7.4 + - - +
349B ALA* 1.3 78.1 - - + +
351B PHE* 1.3 66.3 + - - +
353B ALA* 3.2 1.2 + - - -
354B ALA* 2.9 24.1 + - - +
377B ILE* 3.5 13.4 - - + +
380B ALA* 4.2 12.3 - - + -
381B LEU* 3.8 27.4 - - + -
384B HIS* 3.6 29.4 - - + -
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Residues in contact with PHE 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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292B ALA* 3.9 8.3 - - + -
338B PHE* 3.8 33.7 - + - -
343B LEU* 4.9 4.3 - - + -
347B ASP 3.0 14.1 + - - +
348B LEU* 3.1 12.1 + - + +
350B LEU* 1.3 78.2 - - - +
352B ILE* 1.3 70.6 + - + +
354B ALA* 3.3 7.3 + - - +
355B ILE* 3.1 41.7 + - + +
381B LEU* 4.4 9.1 - - + +
399B LEU* 3.6 43.5 - - + -
402B LYS* 4.4 1.1 - - + -
403B MET* 3.6 39.5 - - + -
406B LEU* 4.0 9.9 - - + -
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Residues in contact with ILE 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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186B TYR* 5.0 4.9 - - + -
190B PHE* 5.3 1.3 - - + -
260B LEU* 3.7 29.8 - - + -
263B PHE* 3.9 13.2 - - + -
289B ALA* 3.8 19.3 - - + +
292B ALA* 3.7 30.3 - - + -
293B MET* 3.8 20.0 - - + -
348B LEU* 2.8 25.9 + - + +
349B ALA* 4.0 4.3 - - - +
351B PHE* 1.3 78.7 - - + +
353B ALA* 1.3 66.0 + - - +
355B ILE* 3.1 14.1 + - + +
356B ILE* 3.1 23.5 + - + +
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Residues in contact with ALA 353 (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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182B ILE* 4.3 9.4 - - + -
263B PHE* 4.0 10.5 - - + -
267B ILE* 3.9 25.1 - - + -
349B ALA 3.1 18.7 + - - +
350B LEU 3.2 4.7 + - - +
352B ILE* 1.3 75.9 - - - +
354B ALA* 1.3 57.6 + - - +
356B ILE* 3.2 3.3 + - - -
357B LEU* 2.9 35.2 + - - +
377B ILE* 4.0 17.9 - - + -
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Residues in contact with ALA 354 (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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350B LEU 2.9 13.4 + - - +
351B PHE* 3.5 4.9 - - - +
353B ALA* 1.3 74.9 - - - +
355B ILE* 1.3 63.7 + - - +
357B LEU 3.4 9.5 - - - +
358B CYS* 4.1 0.7 - - - +
374B GLN* 3.4 23.6 + - - +
377B ILE* 3.7 18.8 - - + +
378B LEU* 3.9 15.9 - - + -
381B LEU* 5.3 1.3 - - + -
403B MET* 3.4 30.3 - - + +
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Residues in contact with ILE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLY* 3.6 24.0 - - - +
288B GLU* 3.6 32.8 - - + +
289B ALA* 3.8 5.4 - - - +
292B ALA* 4.2 0.2 - - + -
351B PHE* 3.1 38.5 + - + +
352B ILE* 3.1 20.1 + - + +
354B ALA* 1.3 79.4 - - - +
356B ILE* 1.3 63.6 + - + +
358B CYS* 3.6 5.0 - - - +
361B ARG* 3.0 26.9 + - - +
403B MET* 4.3 18.4 - - + -
406B LEU* 3.9 17.3 - - + -
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Residues in contact with ILE 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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260B LEU* 4.7 8.3 - - + -
263B PHE* 5.5 3.4 - - + -
264B ALA* 4.4 8.5 - - + -
267B ILE* 6.1 0.9 - - + -
270B PHE* 4.0 26.0 - - + -
281B LEU* 3.5 29.3 - - + +
282B LEU* 4.2 23.3 - - + -
285B GLY* 3.7 31.4 - - - +
286B VAL* 4.2 4.3 - - - +
289B ALA* 4.0 14.4 - - + -
352B ILE* 3.1 21.7 + - + +
353B ALA* 3.8 7.4 - - - +
355B ILE* 1.3 76.7 - - + +
357B LEU* 1.3 63.4 + - + +
358B CYS* 2.9 8.1 + - - +
361B ARG* 5.0 0.9 + - - -
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Residues in contact with LEU 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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267B ILE* 4.2 18.4 - - + -
270B PHE* 4.0 28.5 - - + -
273B LEU* 4.3 3.6 - - + -
281B LEU* 4.0 18.8 - - + -
353B ALA 2.9 19.3 + - - +
354B ALA 3.4 2.3 - - - +
355B ILE 3.4 0.2 - - - -
356B ILE* 1.3 78.4 - - + +
358B CYS* 1.3 59.5 + - - +
370B VAL* 4.1 10.5 - - + -
373B ILE* 3.7 44.0 - - + -
374B GLN* 3.0 30.5 + - - +
377B ILE* 3.7 16.4 - - + -
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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