Contacts of the helix formed by residues 338 - 352 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B THR 4.6 0.7 - - - +
220B ASP 4.0 16.8 - - - +
221B THR* 4.2 17.5 - - - +
224B PHE* 3.6 45.5 - - + -
330B HIS* 3.5 8.8 + - - -
334B ASP 4.9 0.2 - - - +
336B ILE 4.1 0.7 - - - +
337B VAL* 1.3 92.7 - - + +
339B TYR* 1.3 63.7 - - - +
340B GLN 4.7 0.4 - - - +
341B PRO* 3.6 30.4 - - + +
342B ALA* 4.1 5.2 + - - +
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Residues in contact with TYR 339 (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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18A ASP* 4.6 4.2 + - - +
330B HIS* 3.6 28.9 - - + -
331B ALA 3.6 7.0 - - - +
332B ILE* 3.4 54.2 - - + +
334B ASP* 4.7 2.6 + - + +
337B VAL 3.4 3.0 + - - -
338B PRO* 1.3 72.2 - - - +
340B GLN* 1.3 91.0 + - + +
342B ALA* 3.2 5.0 + - + +
343B ALA* 3.0 37.3 + - + +
358B PHE* 3.4 30.5 - + - -
360B PRO* 3.4 27.7 - - + +
397B PRO* 5.6 0.2 - - - +
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Residues in contact with GLN 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASP* 2.9 28.3 + - - +
270A ARG* 3.4 32.8 - - - +
332B ILE* 5.4 0.2 - - - +
338B PRO* 4.6 0.8 - - - +
339B TYR* 1.3 93.4 - - - +
341B PRO* 1.4 64.5 - - + +
343B ALA* 3.1 16.2 + - - +
344B THR* 2.8 36.3 + - - +
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Residues in contact with PRO 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B VAL* 3.3 25.3 - - + +
217B SER* 4.8 2.0 - - - +
220B ASP* 3.9 31.9 - - + +
311B VAL* 4.1 6.7 - - + +
338B PRO* 3.6 33.4 - - + +
339B TYR 3.6 2.9 - - - -
340B GLN* 1.4 93.7 - - + +
342B ALA* 1.3 55.4 + - - +
344B THR* 3.4 8.1 + - - -
345B TYR* 2.9 24.1 + - - +
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Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B THR* 4.0 14.6 - - - +
216B VAL* 3.6 14.8 - - + +
328B ILE* 5.6 6.7 - - + -
330B HIS* 3.7 34.8 - - + +
338B PRO 4.1 2.5 + - - +
339B TYR* 3.2 10.1 + - + +
341B PRO* 1.3 75.3 - - - +
343B ALA* 1.3 66.4 + - - +
345B TYR* 3.4 3.2 + - - +
346B VAL* 3.1 29.5 + - - +
358B PHE* 5.2 2.0 - - + -
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Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B TYR* 3.0 44.3 + - + +
340B GLN* 3.1 17.0 + - - +
342B ALA* 1.3 74.8 - - - +
344B THR* 1.3 56.8 + - - +
346B VAL* 3.4 3.5 + - - +
347B LYS* 3.0 28.3 + - - +
358B PHE* 4.2 14.0 - - + -
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Residues in contact with THR 344 (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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311B VAL* 4.0 14.4 - - + -
313B ALA* 5.5 3.1 - - + -
340B GLN* 2.8 20.6 + - - +
341B PRO* 3.6 8.8 - - - +
343B ALA* 1.3 72.9 - - - +
345B TYR* 1.3 66.4 + - - +
347B LYS* 3.3 9.2 + - + +
348B GLU* 2.8 49.0 + - + +
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Residues in contact with TYR 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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191B VAL* 3.3 25.1 - - + +
195B SER* 4.4 6.9 + - - -
211B HIS* 4.9 1.1 - + - -
216B VAL* 4.0 22.0 - - + -
310B VAL* 3.2 45.5 - - + -
311B VAL* 4.7 3.1 - - + +
319B VAL* 4.8 1.8 - - + -
320B SER 4.9 0.2 + - - -
322B PRO* 4.4 2.6 - - - +
326B ARG* 2.8 30.2 + - - -
328B ILE* 4.3 13.9 - - + -
341B PRO 2.9 17.2 + - - +
342B ALA* 3.6 4.7 - - - +
344B THR* 1.3 76.5 - - - +
346B VAL* 1.3 66.4 + - + +
348B GLU* 3.6 9.9 + - - +
349B GLN* 2.8 69.9 + - + +
356B ILE* 5.1 0.4 - - + -
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Residues in contact with VAL 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ILE* 4.1 28.7 - - + -
342B ALA 3.1 20.2 + - - +
343B ALA 3.7 4.7 - - - +
345B TYR* 1.3 76.4 - - + +
347B LYS* 1.3 59.0 + - - +
349B GLN* 3.7 0.7 - - - +
350B CYS* 2.8 40.2 + - - -
356B ILE* 4.0 14.1 - - + -
358B PHE* 3.9 38.6 - - + -
395B GLY* 3.8 28.0 - - - -
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Residues in contact with LYS 347 (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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343B ALA 3.0 17.9 + - - +
344B THR* 3.6 8.1 - - + +
346B VAL* 1.3 78.4 - - - +
348B GLU* 1.4 63.1 + - - +
350B CYS* 3.7 5.0 - - - +
351B ALA* 3.0 24.8 + - + +
395B GLY* 6.4 0.2 - - - -
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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
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310B VAL 4.1 3.5 - - - +
311B VAL* 3.5 16.1 - - - +
312B GLN* 2.6 36.7 + - + +
313B ALA* 3.0 32.7 + - - +
321B VAL* 5.9 0.2 - - - -
344B THR* 2.8 31.7 + - + +
345B TYR* 3.6 5.9 - - - +
347B LYS* 1.4 70.7 - - + +
349B GLN* 1.3 67.0 + - + +
351B ALA* 3.3 8.8 + - - +
352B LYS* 3.2 29.6 + - + +
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Residues in contact with GLN 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B VAL 4.8 1.0 + - - -
319B VAL* 4.2 6.9 - - - +
320B SER 3.1 19.6 + - - -
321B VAL* 3.2 33.6 - - - +
322B PRO* 3.4 1.9 - - - +
326B ARG* 2.9 22.1 + - - +
345B TYR* 2.8 64.4 + - + +
346B VAL 3.7 3.1 - - - +
348B GLU* 1.3 76.1 - - + +
350B CYS* 1.3 61.2 + - - +
352B LYS* 3.2 11.3 + - - -
353B GLY 3.4 0.5 + - - -
354B ALA* 3.0 24.8 + - + +
356B ILE* 3.8 15.5 - - + -
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Residues in contact with CYS 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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346B VAL* 2.8 33.1 + - - +
347B LYS* 3.7 5.2 - - - +
349B GLN* 1.3 69.6 - - - +
351B ALA* 1.3 65.1 + - - +
352B LYS 3.0 2.0 - - - -
353B GLY* 3.1 14.0 + - - -
354B ALA* 4.2 1.0 - - - +
356B ILE* 4.1 4.9 - - - -
394B CYS* 2.1 58.5 - - + +
395B GLY* 3.4 21.3 - - - -
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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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347B LYS* 3.0 18.5 + - + +
348B GLU* 3.3 7.6 + - - +
350B CYS* 1.3 75.7 - - - +
352B LYS* 1.3 61.3 + - + +
353B GLY 3.5 0.6 + - - -
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Residues in contact with LYS 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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312B GLN* 4.6 17.7 + - + +
318B THR* 4.4 19.8 - - - +
319B VAL 4.7 2.2 + - - -
321B VAL* 4.0 27.2 - - + +
323B LYS* 3.8 18.4 + - - -
348B GLU* 3.2 16.5 + - + +
349B GLN 3.2 7.6 + - - +
350B CYS 3.0 1.0 - - - -
351B ALA* 1.3 80.5 - - + +
353B GLY* 1.3 56.8 + - - -
354B ALA 3.7 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