Contacts of the helix formed by residues 342 - 362 (chain B) in PDB entry 2AG1
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 ARG 342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B LEU 3.1 22.8 + - - -
202B ARG 3.5 12.3 + - - -
204B ALA 2.7 29.9 + - - -
205B GLU* 4.0 9.8 + - - +
207B PRO* 3.6 29.4 - - + +
231B THR 3.9 12.8 + - - +
232B GLY 3.4 23.1 - - - +
233B VAL* 3.9 6.6 - - + +
339B TRP* 5.0 4.6 - - - -
340B PRO* 3.7 27.1 + - - +
341B ASP* 1.3 78.2 - - - +
343B GLY* 1.3 57.6 + - - +
344B ASP* 3.4 2.5 - - - +
345B TRP* 3.2 15.9 + - + +
346B CYS* 2.9 33.8 + - - -
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Residues in contact with GLY 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASP* 2.9 23.0 + - - +
342B ARG* 1.3 76.8 - - - +
344B ASP* 1.3 62.0 + - - +
346B CYS* 3.5 6.5 + - - +
347B ALA* 3.0 23.0 + - - +
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Residues in contact with ASP 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASP* 4.5 1.0 + - - -
342B ARG* 3.4 0.4 - - - -
343B GLY* 1.3 74.0 - - - +
345B TRP* 1.3 64.3 + - - +
347B ALA* 3.2 8.0 + - - +
348B LYS* 3.0 22.1 + - - +
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Residues in contact with TRP 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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205B GLU 4.3 8.7 - - - +
206B ARG* 3.5 46.5 - - + -
207B PRO* 2.6 37.5 + - + -
208B VAL* 3.8 17.7 - - + -
234B PRO* 3.3 22.8 - - + +
263B PHE* 3.7 18.4 - + - -
268B ALA* 3.2 39.3 - - + -
270B PRO* 4.5 4.0 - - + -
342B ARG* 3.2 20.1 + - - +
344B ASP* 1.3 78.1 - - - +
346B CYS* 1.3 57.6 - - - +
348B LYS* 3.1 16.1 + - + +
349B VAL* 2.9 39.8 + - + +
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Residues in contact with CYS 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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232B GLY* 3.3 24.9 - - - -
234B PRO* 4.1 15.3 - - - -
251B ALA* 3.1 34.9 - - + +
252B MSE 4.5 9.0 - - - -
342B ARG* 2.9 25.1 + - - +
343B GLY* 3.7 6.5 - - - +
345B TRP* 1.3 72.9 - - - +
347B ALA* 1.3 60.2 + - - +
349B VAL* 3.3 9.9 + - - +
350B THR* 2.9 31.2 + - - -
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Residues in contact with ALA 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 GLY 3.0 17.8 + - - +
344B ASP* 3.2 8.3 + - - +
346B CYS* 1.3 76.6 - - - +
348B LYS* 1.3 57.1 + - - +
350B THR* 3.3 7.4 + - + -
351B ASP* 2.9 41.8 + - - +
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Residues in contact with LYS 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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266B ALA* 4.4 14.7 + - - +
268B ALA* 4.2 20.2 - - + -
344B ASP 3.0 11.9 + - - +
345B TRP* 3.3 21.1 - - + +
347B ALA* 1.3 74.5 - - - +
349B VAL* 1.3 66.0 + - - +
351B ASP* 3.2 8.7 + - + +
352B LEU* 3.0 60.2 + - + +
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Residues in contact with VAL 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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234B PRO* 3.9 19.1 - - + -
236B PHE* 3.5 30.1 - - + -
253B ARG 4.9 2.2 - - - +
254B GLY* 3.7 18.8 - - - +
263B PHE* 3.9 17.1 - - + -
345B TRP* 2.9 48.3 + - + +
346B CYS* 3.5 8.5 - - - +
348B LYS* 1.3 77.5 - - - +
350B THR* 1.3 61.9 + - - +
352B LEU* 3.4 2.6 + - - +
353B ALA* 3.2 22.9 + - + +
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Residues in contact with THR 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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250B ASP 4.3 13.3 + - - -
251B ALA* 4.3 9.2 + - - -
253B ARG 4.8 6.6 + - - -
346B CYS 2.9 16.3 + - - -
347B ALA* 3.5 8.1 - - + +
348B LYS 3.2 0.2 - - - -
349B VAL* 1.3 79.9 - - - +
351B ASP* 1.3 70.8 - - - +
353B ALA* 3.5 5.6 + - - +
354B GLN* 3.0 31.1 + - + +
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Residues in contact with ASP 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 ALA* 2.9 29.7 + - - +
348B LYS* 3.8 10.2 - - + +
350B THR* 1.3 82.7 - - - +
352B LEU* 1.3 63.7 + - + +
354B GLN* 3.7 8.0 - - - +
355B GLU* 2.9 32.5 + - - +
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Residues in contact with LEU 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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259B ASN* 5.3 1.8 - - - +
262B SER* 4.8 14.8 + - - +
263B PHE* 3.5 50.3 - - + -
266B ALA* 3.9 23.3 - - + -
268B ALA* 4.2 7.6 - - + -
348B LYS* 3.0 42.3 + - + +
349B VAL 3.8 3.4 - - - +
351B ASP* 1.3 77.5 - - + +
353B ALA* 1.3 63.0 + - - +
355B GLU* 3.1 25.5 + - - +
356B ARG* 3.0 22.9 + - - +
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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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253B ARG 5.9 1.3 - - - +
254B GLY 4.3 12.6 - - - +
259B ASN* 4.3 29.0 + - - +
263B PHE* 5.3 2.3 - - + -
349B VAL* 3.2 10.9 + - + +
350B THR* 3.7 9.2 - - - +
352B LEU* 1.3 77.1 - - - +
354B GLN* 1.3 62.3 + - - +
356B ARG* 3.3 7.1 + - - +
357B TYR* 3.2 21.8 + - - +
405B SER* 5.7 4.3 - - - -
406B ARG* 5.7 0.9 - - - -
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Residues in contact with GLN 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 THR* 3.0 21.6 + - + +
351B ASP* 3.7 9.0 - - - +
353B ALA* 1.3 76.3 - - - +
355B GLU* 1.3 58.5 + - - +
357B TYR* 3.4 6.1 + - - +
358B ALA* 3.0 36.3 + - + +
406B ARG* 2.7 47.2 + - - +
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Residues in contact with GLU 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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262B SER* 5.4 2.4 + - - -
351B ASP 2.9 18.6 + - - +
352B LEU* 3.4 26.8 - - - +
354B GLN* 1.3 75.4 - - - +
356B ARG* 1.3 58.9 + - - +
358B ALA* 3.6 5.3 + - - +
359B SER* 3.0 30.4 + - - -
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Residues in contact with ARG 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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258B GLN* 3.5 28.1 + - - +
259B ASN* 3.6 27.4 - - + +
261B TYR* 4.2 14.1 - - - +
262B SER* 5.6 6.8 + - - +
352B LEU 3.0 12.0 + - - +
353B ALA* 3.6 9.9 - - - +
355B GLU* 1.3 74.4 + - - +
357B TYR* 1.3 58.6 + - - +
359B SER* 3.2 7.8 - - - -
360B ILE* 3.0 42.8 + - + +
402B GLU* 2.5 53.2 + - - +
551B PRO* 4.3 10.5 - - + +
552B GLU* 3.2 24.9 + - - -
555B ILE* 6.0 0.8 - - - +
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Residues in contact with TYR 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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353B ALA 3.2 10.6 + - - +
354B GLN* 3.5 12.6 - - - +
356B ARG* 1.3 80.0 - - - +
358B ALA* 1.3 61.7 + - + +
360B ILE* 3.1 10.3 + - - +
361B ALA* 2.9 30.9 + - + +
373B PHE* 3.9 16.9 - + - -
377B GLN* 3.1 37.0 + - - +
402B GLU* 3.4 26.5 - - - +
403B VAL* 4.0 10.4 - - + +
406B ARG* 3.3 54.4 + - - +
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Residues in contact with ALA 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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354B GLN* 3.0 27.0 + - - +
355B GLU* 4.1 6.1 - - - +
357B TYR* 1.3 75.8 - - + +
359B SER* 1.3 65.6 + - - +
361B ALA* 3.4 9.1 + - - +
362B ALA* 3.0 24.6 + - - +
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Residues in contact with SER 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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355B GLU* 3.0 19.8 + - - -
356B ARG* 3.2 10.1 - - - -
358B ALA* 1.3 76.7 - - - +
360B ILE* 1.3 66.6 + - - +
362B ALA* 3.3 9.2 + - - +
363B LYS* 3.2 35.4 + - - +
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Residues in contact with ILE 360 (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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356B ARG* 3.0 28.0 + - + +
357B TYR* 3.5 7.0 - - - +
359B SER* 1.3 79.6 - - - +
361B ALA* 1.3 59.5 + - - +
363B LYS* 3.1 28.4 + - - +
364B SER* 3.0 17.9 + - - +
373B PHE* 3.5 35.0 - - + -
399B TRP* 3.8 20.6 - - + -
402B GLU* 4.7 10.5 - - + +
551B PRO* 3.4 31.0 - - + -
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Residues in contact with ALA 361 (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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357B TYR* 2.9 20.6 + - + +
358B ALA* 3.6 11.0 - - - +
359B SER 3.3 0.2 - - - -
360B ILE* 1.3 76.3 - - - +
362B ALA* 1.3 59.6 + - - +
363B LYS 3.1 2.1 + - - -
364B SER* 3.7 13.6 + - - +
373B PHE* 3.6 23.7 - - + -
374B HIS* 4.8 6.1 - - + -
377B GLN* 4.7 6.7 - - - +
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Residues in contact with ALA 362 (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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358B ALA 3.0 17.1 + - - +
359B SER* 3.5 9.4 - - - +
360B ILE 3.2 0.4 - - - -
361B ALA* 1.3 75.7 - - - +
363B LYS* 1.3 65.7 + - + +
364B SER 3.8 0.9 - - - -
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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