Contacts of the helix formed by residues 338 - 352 (chain A) in PDB entry 3GUU
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 PRO 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A THR 4.7 1.0 - - - +
215A PRO* 5.8 0.2 - - + -
220A ASP* 4.0 17.9 - - + +
221A THR* 4.1 21.5 - - + +
224A PHE* 3.6 41.9 - - + -
330A HIS* 3.7 7.4 + - - -
336A ILE 4.2 0.7 - - - +
337A VAL* 1.3 90.4 - - + +
339A TYR* 1.3 65.2 + - - +
340A GLN 4.9 0.2 - - - +
341A PRO* 3.5 30.4 - - + +
342A ALA* 4.2 4.7 + - - +
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Residues in contact with TYR 339 (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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330A HIS* 3.7 29.8 - - + -
331A ALA 3.6 11.0 - - - +
332A ILE* 3.4 48.3 - - + +
334A ASP* 4.6 3.8 + - + +
337A VAL 3.3 3.4 + - - -
338A PRO* 1.3 70.1 - - - +
340A GLN* 1.3 92.8 + - + +
342A ALA* 3.0 8.9 + - + +
343A ALA* 3.0 34.2 + - + +
358A PHE* 3.4 27.2 - + - -
360A PRO* 3.2 33.4 - - + +
397A PRO* 5.3 1.2 - - - +
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Residues in contact with GLN 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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332A ILE* 5.4 3.4 - - - +
338A PRO* 4.9 0.4 - - - +
339A TYR* 1.3 95.2 - - + +
341A PRO* 1.4 65.7 - - + +
343A ALA* 3.2 16.1 + - - +
344A THR* 2.8 36.7 + - - +
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Residues in contact with PRO 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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216A VAL* 3.4 25.0 - - + +
217A SER* 4.8 1.3 - - - +
220A ASP* 3.6 38.4 - - + +
311A VAL* 3.9 5.8 - - + +
338A PRO* 3.5 31.2 - - + +
340A GLN* 1.4 91.1 - - + +
342A ALA* 1.3 56.5 + - - +
344A THR* 3.3 9.0 + - - +
345A TYR 2.9 23.4 + - - -
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Residues in contact with ALA 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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214A THR* 4.0 17.3 - - - +
216A VAL* 3.7 13.1 - - + +
328A ILE* 5.6 4.9 - - + -
330A HIS* 3.8 29.4 - - + +
338A PRO 4.2 1.0 + - - +
339A TYR* 3.0 11.0 + - + +
341A PRO* 1.3 75.7 - - - +
343A ALA* 1.3 59.8 + - - +
345A TYR* 3.3 5.0 + - - +
346A VAL* 2.9 33.5 + - - +
358A PHE* 4.6 4.9 - - + -
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Residues in contact with ALA 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 TYR* 3.0 41.4 + - + +
340A GLN* 3.6 16.2 - - - +
342A ALA* 1.3 76.8 - - - +
344A THR* 1.3 55.8 + - - +
346A VAL* 3.4 2.4 + - - +
347A LYS* 3.0 29.3 + - - +
358A PHE* 3.8 17.7 - - + -
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Residues in contact with THR 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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311A VAL* 3.8 24.2 - - + -
313A ALA* 5.3 3.4 - - + -
340A GLN* 2.8 28.5 + - - +
341A PRO* 3.4 8.6 - - - +
343A ALA* 1.3 69.8 - - - +
345A TYR* 1.3 66.1 + - - +
347A LYS* 3.3 7.1 + - - +
348A GLU* 3.0 40.5 + - + +
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Residues in contact with TYR 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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191A VAL* 3.6 23.1 - - + +
194A THR* 4.8 0.2 + - - -
195A SER* 4.4 6.2 + - - -
211A HIS* 5.1 1.1 - + - -
216A VAL* 4.1 23.6 - - + -
310A VAL* 3.3 41.5 - - + -
311A VAL* 4.6 4.4 - - + +
319A VAL* 4.8 0.9 - - + -
320A SER 5.0 0.2 + - - -
322A PRO* 4.4 3.1 - - - +
326A ARG* 2.5 33.9 + - - -
328A ILE* 4.2 14.4 - - + -
341A PRO 2.9 16.5 + - - +
342A ALA* 3.3 7.1 + - + +
344A THR* 1.3 74.2 - - - +
346A VAL* 1.3 72.2 + - + +
348A GLU* 3.4 9.5 + - - +
349A GLN* 3.0 61.4 + - + +
356A ILE* 4.9 0.4 - - + -
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ILE* 4.1 28.7 - - + -
342A ALA 2.9 20.0 + - - +
343A ALA 3.8 4.5 - - - +
344A THR 3.3 0.4 - - - -
345A TYR* 1.3 76.7 - - + +
347A LYS* 1.3 59.1 + - - +
349A GLN* 3.3 0.9 + - - +
350A CYS* 2.9 38.6 + - - +
356A ILE* 4.0 12.1 - - + -
358A PHE* 3.7 47.3 - - + -
395A GLY* 3.7 23.3 - - - +
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Residues in contact with LYS 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 ALA 3.0 17.8 + - - +
344A THR* 3.8 7.2 - - - +
346A VAL* 1.3 77.9 - - - +
348A GLU* 1.3 62.2 + - + +
350A CYS* 3.6 5.7 + - - +
351A ALA* 3.1 23.3 + - + +
395A GLY* 6.3 0.2 - - - -
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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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310A VAL 4.1 3.8 - - - +
311A VAL* 3.6 14.5 - - - +
312A GLN* 2.8 34.3 + - + +
313A ALA* 3.0 32.7 + - - +
321A VAL* 6.1 0.2 - - - -
344A THR* 3.0 25.1 + - + +
345A TYR* 3.6 7.5 - - - +
347A LYS* 1.3 76.5 - - + +
349A GLN* 1.3 66.6 + - + +
351A ALA* 3.1 15.1 + - - +
352A LYS* 3.3 19.2 + - - +
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Residues in contact with GLN 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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310A VAL 4.6 0.6 + - - -
319A VAL* 4.3 7.1 + - - +
320A SER 3.2 20.0 + - - -
321A VAL* 3.3 32.2 - - - +
322A PRO* 3.5 1.9 - - - +
326A ARG* 3.1 17.8 + - - -
345A TYR* 3.0 64.3 + - + +
348A GLU* 1.3 78.4 + - + +
350A CYS* 1.3 63.4 + - - +
352A LYS* 3.0 12.8 + - - -
353A GLY 3.4 0.3 + - - -
354A ALA* 3.1 20.9 + - + +
356A ILE* 3.7 18.6 - - + -
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Residues in contact with CYS 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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346A VAL* 2.9 22.9 + - - +
347A LYS* 3.8 5.8 - - - +
349A GLN* 1.3 77.7 - - - +
351A ALA* 1.3 57.7 + - - +
352A LYS 3.4 0.7 + - - -
353A GLY* 3.4 11.3 + - - -
354A ALA* 4.3 0.7 + - - +
356A ILE* 4.0 11.2 - - - -
394A CYS* 2.1 70.8 - - + +
395A GLY* 3.4 10.8 - - - -
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Residues in contact with ALA 351 (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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347A LYS* 3.1 17.9 + - + +
348A GLU* 3.1 9.1 + - - +
350A CYS* 1.3 75.5 - - - +
352A LYS* 1.3 63.3 + - + +
353A GLY 3.6 0.4 - - - -
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Residues in contact with LYS 352 (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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312A GLN* 4.8 10.7 + - + +
318A THR* 4.5 19.2 - - - +
319A VAL 4.9 2.9 + - - -
321A VAL* 3.7 31.3 - - + +
323A LYS* 3.6 17.3 + - - -
348A GLU 3.5 11.7 - - - +
349A GLN 3.0 7.3 + - - +
351A ALA* 1.3 84.1 - - + +
353A GLY* 1.3 57.3 + - - +
354A ALA 3.6 0.2 - - - -
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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