Contacts of the helix formed by residues 318 - 336 (chain B) in PDB entry 1G9Z
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 SER 318 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B PHE* 3.6 4.7 - - - -
314B SER 3.8 1.8 + - - -
315B ALA 3.2 7.6 + - - +
317B GLU* 1.3 83.0 - - - +
319B PRO* 1.3 68.5 - - - +
320B ASP* 3.1 18.7 + - - +
321B LYS* 3.3 29.2 + - - +
322B PHE* 2.8 26.2 + - - +
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Residues in contact with PRO 319 (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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234B LYS* 5.5 1.3 - - - +
235B PHE* 3.6 28.5 - - + -
317B GLU 4.5 1.8 - - - +
318B SER* 1.3 90.7 - - - +
320B ASP* 1.3 62.3 + - - +
322B PHE* 3.6 4.0 - - + +
323B LEU* 3.0 29.8 + - - +
351B VAL* 4.4 21.6 - - + +
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Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B SER* 3.1 8.5 + - - +
319B PRO* 1.3 81.2 - - - +
321B LYS* 1.3 61.4 + - + +
323B LEU* 3.3 7.5 + - - +
324B GLU* 2.8 29.5 + - - +
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B SER* 2.9 50.5 + - - +
315B ALA* 3.9 3.8 - - - +
317B GLU* 4.4 12.2 + - + +
318B SER* 3.3 24.5 + - - +
320B ASP* 1.3 79.1 - - + +
322B PHE* 1.3 62.3 + - - +
324B GLU* 3.4 15.3 + - - +
325B VAL* 3.1 29.7 + - + +
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Residues in contact with PHE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B PHE* 3.6 36.8 - + + -
237B HIS* 3.8 34.5 - - + -
239B LEU* 3.5 39.5 - - + -
315B ALA* 3.6 20.6 + - + +
316B LYS* 5.1 4.9 - - + -
318B SER 2.8 17.7 + - - +
319B PRO* 3.6 5.6 - - + +
320B ASP 3.2 0.2 - - - -
321B LYS* 1.3 78.5 - - - +
323B LEU* 1.3 57.7 + - - +
325B VAL* 3.3 4.9 + - - +
326B CYS* 2.9 50.5 + - - -
348B VAL* 3.8 21.1 - - + -
351B VAL* 5.6 1.1 - - + -
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Residues in contact with LEU 323 (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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319B PRO 3.0 18.8 + - - +
320B ASP* 3.3 8.0 + - - +
322B PHE* 1.3 74.6 - - + +
324B GLU* 1.3 65.2 + - - +
326B CYS* 3.2 5.1 + - + +
327B THR* 3.0 24.3 + - + +
345B SER* 3.8 33.4 - - - +
348B VAL* 3.8 26.7 - - + +
349B ARG* 3.6 42.6 - - - +
351B VAL* 5.2 5.2 - - + -
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Residues in contact with GLU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ASP 2.8 17.1 + - - +
321B LYS* 3.6 16.7 - - - +
322B PHE 3.2 0.2 - - - -
323B LEU* 1.3 77.4 - - - +
325B VAL* 1.3 62.2 + - - +
327B THR* 2.4 31.3 + - - +
328B TRP* 3.4 38.0 + - + +
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LEU* 3.7 22.2 - - + -
308B ILE* 3.5 36.8 - - + +
311B GLN* 4.1 22.4 - - + +
312B LEU* 4.9 0.4 - - + -
315B ALA* 3.6 17.0 - - + -
321B LYS 3.1 15.2 + - - +
322B PHE 3.6 7.0 - - - +
324B GLU* 1.3 76.9 - - + +
326B CYS* 1.3 58.1 + - - +
328B TRP* 2.9 32.8 + - + +
329B VAL* 3.2 10.7 + - - +
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Residues in contact with CYS 326 (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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227B ILE* 3.6 21.3 - - + -
239B LEU* 4.0 10.3 - - - -
322B PHE* 2.9 47.5 + - - -
323B LEU* 3.3 12.1 - - + +
324B GLU 3.1 0.4 - - - -
325B VAL* 1.3 78.4 - - - +
327B THR* 1.3 59.1 + - - +
329B VAL* 2.7 32.8 - - - +
330B ASP* 3.2 6.8 + - - +
345B SER* 3.6 17.0 - - - -
348B VAL* 3.8 11.7 - - - -
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Residues in contact with THR 327 (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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323B LEU* 3.0 22.9 + - + +
324B GLU* 2.4 27.0 + - - +
326B CYS* 1.3 75.7 - - - +
328B TRP* 1.3 71.2 + - - +
330B ASP* 3.2 25.3 - - - +
331B GLN* 3.3 17.4 + - - +
345B SER* 3.9 14.4 - - - +
346B GLU* 5.9 0.9 - - - +
349B ARG* 5.9 1.3 - - - +
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Residues in contact with TRP 328 (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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304B LEU* 4.5 10.2 - - + +
307B LYS* 3.5 56.0 - - + +
308B ILE* 3.8 27.1 - - + -
311B GLN* 3.5 39.9 - - + -
324B GLU* 3.6 42.4 + - + +
325B VAL* 2.9 20.4 + - + +
327B THR* 1.3 86.7 + - - +
329B VAL* 1.3 62.9 + - - +
330B ASP 3.1 1.6 - - - -
331B GLN* 3.1 33.9 + - - +
332B ILE* 3.2 17.3 + - - +
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Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ALA* 3.8 30.4 - - + +
226B GLN 4.9 3.6 - - - +
227B ILE* 3.2 30.5 - - + +
239B LEU* 4.3 17.3 - - + -
241B LEU* 5.4 2.0 - - + -
308B ILE* 3.8 17.7 - - + -
325B VAL 3.2 12.3 + - - +
326B CYS* 2.7 24.5 - - - +
328B TRP* 1.3 76.3 - - - +
330B ASP* 1.3 62.4 + - - +
332B ILE* 3.3 3.7 + - - +
333B ALA* 3.1 22.0 + - - +
341B ARG* 3.4 10.7 + - - +
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Residues in contact with ASP 330 (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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326B CYS 3.2 8.1 + - - +
327B THR* 3.2 14.3 - - - +
328B TRP 3.1 0.2 - - - -
329B VAL* 1.3 84.4 - - - +
331B GLN* 1.3 57.3 + - + +
333B ALA* 3.4 3.8 + - - +
334B ALA* 3.0 28.1 + - - +
341B ARG* 2.6 41.6 + - - +
344B THR* 3.7 2.7 - - - -
345B SER* 2.6 40.9 + - - -
346B GLU* 5.7 0.2 - - - +
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Residues in contact with GLN 331 (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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304B LEU* 3.8 27.5 - - + +
307B LYS* 5.7 1.8 + - - +
327B THR* 3.5 19.1 + - - +
328B TRP* 3.1 31.3 + - - +
330B ASP* 1.3 76.7 - - + +
332B ILE* 1.3 64.3 + - - +
334B ALA* 3.3 7.3 + - - +
335B LEU* 3.2 29.0 + - + +
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Residues in contact with ILE 332 (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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223B ILE 3.6 24.5 - - - +
225B ALA* 3.4 32.3 - - + +
301B GLN* 4.0 11.7 - - + +
304B LEU* 3.5 33.2 - - + -
305B VAL* 3.6 26.2 - - + -
308B ILE* 3.9 13.9 - - + -
328B TRP 3.2 5.6 + - - +
329B VAL 3.3 6.7 + - - +
331B GLN* 1.3 76.3 - - - +
333B ALA* 1.3 63.5 + - - +
335B LEU* 3.1 8.8 + - - +
336B ASN* 3.0 26.7 + - - +
617F C 5.2 0.2 - - - +
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Residues in contact with ALA 333 (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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225B ALA 5.4 3.8 + - - +
329B VAL 3.1 7.2 + - - +
330B ASP 3.7 7.6 - - - +
332B ILE* 1.3 79.4 - - - +
334B ALA* 1.3 63.1 + - - +
336B ASN* 3.2 17.7 + - - +
338B SER* 3.4 15.5 - - - +
341B ARG* 3.5 39.7 - - - +
617F C 3.6 21.3 - - - +
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Residues in contact with ALA 334 (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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330B ASP 3.0 15.6 + - - +
331B GLN* 3.6 9.0 - - - +
332B ILE 3.2 0.4 - - - -
333B ALA* 1.3 78.3 - - - +
335B LEU* 1.3 62.6 + - + +
336B ASN 3.6 5.2 - - - +
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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
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50A GLN* 5.6 0.9 - - - +
51A ARG* 5.3 4.3 + - - -
300B LYS* 3.7 48.2 - - + -
301B GLN* 3.5 24.9 + - - +
304B LEU* 3.8 20.0 - - + -
331B GLN* 3.2 16.2 - - + +
332B ILE* 3.1 8.3 + - - +
334B ALA* 1.3 75.9 - - + +
336B ASN* 1.3 65.2 + - - +
337B ASP* 4.9 2.4 - - - +
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Residues in contact with ASN 336 (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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222B SER* 4.9 0.8 + - - -
223B ILE 3.1 27.5 + - - +
224B ILE* 4.6 2.0 - - - +
298B LYS* 4.5 2.9 + - - +
301B GLN* 2.9 26.1 + - - +
332B ILE* 3.0 19.6 + - - +
333B ALA 3.2 10.5 + - - +
334B ALA 3.6 5.4 - - - +
335B LEU* 1.3 81.7 - - - +
337B ASP* 1.3 63.2 + - - +
338B SER* 3.0 8.8 + - - +
616F A 3.4 29.9 + - - +
617F C 3.1 27.8 + - - +
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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
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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