Contacts of the helix formed by residues 345 - 363 (chain B) in PDB entry 3DYQ
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 345 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B ASN 4.0 5.6 - - - +
344B ILE* 1.3 96.1 - - + +
346B PRO* 1.3 76.1 - - + +
347B ASP* 4.5 5.8 - - + +
348B GLY* 3.0 9.1 + - - +
349B PHE* 2.9 18.1 + - - -
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Residues in contact with PRO 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ARG* 4.2 17.3 - - - +
344B ILE 4.6 0.4 - - - +
345B PRO* 1.3 88.7 - - + +
347B ASP* 1.3 56.0 + - - +
349B PHE* 3.1 8.7 + - + +
350B LYS* 2.7 53.7 + - - +
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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
----------------------------------------------------------
345B PRO* 3.3 4.6 - - + +
346B PRO* 1.3 81.8 - - - +
348B GLY* 1.3 64.2 + - - +
350B LYS* 3.5 14.3 + - - +
351B GLN* 3.1 24.3 + - - +
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Residues in contact with GLY 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B THR* 6.0 1.8 - - - -
344B ILE* 3.7 15.7 - - - -
345B PRO* 3.0 12.7 + - - +
347B ASP* 1.3 75.4 - - - +
349B PHE* 1.3 64.8 + - - +
351B GLN* 3.0 12.7 + - - +
352B ILE* 2.9 29.5 + - - +
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Residues in contact with PHE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ARG* 3.4 52.5 - - + +
330B PHE* 4.2 26.2 - + - -
333B LEU* 5.7 3.4 - - + -
339B ASN* 5.2 5.4 - - - -
341B PHE* 4.0 37.7 - + + +
344B ILE* 3.6 10.6 - - + +
345B PRO 2.9 13.5 + - - +
346B PRO* 3.1 11.6 + - + +
348B GLY* 1.3 75.0 - - - +
350B LYS* 1.3 67.7 + - + +
352B ILE* 3.1 6.7 + - - +
353B ARG* 2.8 50.2 + - + +
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Residues in contact with LYS 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ILE* 5.5 9.2 - - + -
306A ASN* 3.6 31.1 + - - +
308A ARG* 5.5 5.0 - - - +
437A PRO* 5.5 7.4 - - - +
346B PRO* 2.7 38.7 + - - +
347B ASP* 3.7 13.7 + - - +
349B PHE* 1.3 82.4 - - + +
351B GLN* 1.3 61.8 + - - +
353B ARG* 3.8 6.3 - - - +
354B GLN* 3.0 26.7 + - - +
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Residues in contact with GLN 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B THR* 3.6 28.2 + - + +
281B ASP* 5.5 2.6 - - - +
284B ILE* 3.9 8.7 - - + +
347B ASP 3.1 14.6 + - - +
348B GLY* 3.0 14.4 + - - +
350B LYS* 1.3 77.1 - - - +
352B ILE* 1.3 62.0 + - - +
354B GLN* 3.8 4.5 - - - +
355B GLY 3.2 16.3 + - - -
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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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228B PHE* 4.9 2.9 - - + -
280B THR* 3.8 22.9 - - + -
283B LEU* 3.7 19.7 - - + -
284B ILE* 3.9 17.7 - - + +
341B PHE* 3.7 30.7 - - + -
344B ILE* 3.4 35.0 - - + -
348B GLY* 2.9 25.1 + - - +
349B PHE* 3.7 5.2 - - - +
351B GLN* 1.3 72.5 - - - +
353B ARG* 1.3 67.6 + - - +
355B GLY* 3.2 2.3 + - - -
356B MET* 2.9 34.1 + - - +
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Residues in contact with ARG 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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305A ILE 5.9 0.4 + - - -
308A ARG* 6.1 2.8 - - - +
312A ALA* 3.2 22.8 + - - +
313A VAL* 4.0 9.8 - - - +
316A ASN* 3.5 12.9 + - - +
317A ASP* 2.7 43.9 + - - +
330B PHE* 3.1 63.9 - - + +
349B PHE* 2.8 41.3 + - + +
350B LYS* 3.8 6.7 - - - +
352B ILE* 1.3 75.8 - - - +
354B GLN* 1.3 63.6 + - - +
356B MET* 3.1 2.9 + - - +
357B ILE* 2.9 37.9 + - + +
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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
----------------------------------------------------------
317A ASP* 5.9 3.7 - - - +
350B LYS 3.0 18.6 + - - +
351B GLN* 3.8 6.3 - - - +
353B ARG* 1.3 77.9 - - - +
355B GLY* 1.3 63.0 + - - +
357B ILE* 3.4 15.1 + - - +
358B THR* 3.0 35.8 + - - +
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Residues in contact with GLY 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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284B ILE* 3.6 24.9 - - - -
351B GLN 3.2 4.8 + - - -
352B ILE 3.2 6.9 + - - -
354B GLN* 1.3 79.7 - - - +
356B MET* 1.3 57.0 + - - +
358B THR* 3.3 6.1 + - - -
359B LEU* 2.9 33.7 + - - +
394B LYS* 5.6 4.0 - - - -
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Residues in contact with MET 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ILE* 4.2 23.1 - - + +
287B THR* 3.5 44.2 - - + +
288B ALA* 4.1 8.1 - - + +
291B CYS* 4.5 10.1 - - + -
329B ALA* 4.8 1.6 - - + -
330B PHE* 3.8 29.8 - - + -
333B LEU* 4.5 6.7 - - + -
341B PHE* 4.1 5.4 - - - -
352B ILE* 2.9 38.7 + - + +
353B ARG 3.7 3.4 - - - +
355B GLY* 1.3 72.3 - - - +
357B ILE* 1.3 62.7 + - - +
360B ILE* 2.8 44.9 + - + +
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Residues in contact with ILE 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASN* 3.1 55.2 - - + +
317A ASP* 4.4 4.3 - - + +
318A ILE* 4.5 4.0 - - + -
326B CYS* 3.6 22.4 - - - -
330B PHE* 4.5 3.1 - - + -
353B ARG* 2.9 45.6 + - + +
354B GLN* 3.7 14.8 - - - +
356B MET* 1.3 77.1 - - - +
358B THR* 1.3 64.9 + - - +
360B ILE* 3.9 0.3 - - - +
361B LEU* 2.9 43.1 + - + +
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Residues in contact with THR 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B GLN* 3.0 30.8 + - - +
355B GLY* 3.6 9.7 - - - -
357B ILE* 1.3 77.5 - - - +
359B LEU* 1.3 60.1 + - + +
361B LEU* 3.5 6.8 + - - +
362B ALA* 3.0 25.8 + - - +
367B ARG* 5.1 1.3 + - - +
391B THR* 3.7 29.5 - - + +
395B MET* 3.9 18.6 - - + +
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Residues in contact with LEU 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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284B ILE* 3.5 26.0 - - + -
285B LEU* 3.9 31.4 - - + -
288B ALA* 4.0 15.7 - - + -
355B GLY* 2.9 18.6 + - - +
356B MET 4.0 0.2 - - - +
358B THR* 1.3 78.8 - - + +
360B ILE* 1.3 65.3 + - - +
362B ALA* 3.1 18.2 + - - +
363B THR* 3.5 10.9 - - - +
391B THR* 4.3 2.5 - - + +
394B LYS* 3.4 15.0 - - + +
395B MET* 3.4 42.6 - - + +
398B ILE* 3.7 13.4 - - + +
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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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288B ALA* 4.0 26.5 - - + +
291B CYS* 4.3 22.0 - - + -
292B HIS* 3.8 25.6 - - - +
322B GLU* 3.7 25.8 - - - +
325B HIS* 4.1 3.6 - - + -
326B CYS* 3.8 30.1 - - + -
329B ALA* 4.6 2.2 - - + -
356B MET* 2.8 35.9 + - + +
357B ILE 4.1 1.1 - - - +
359B LEU* 1.3 70.9 - - - +
361B LEU* 1.3 61.1 + - - +
363B THR* 2.6 32.4 + - - +
398B ILE* 5.0 0.2 - - - -
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Residues in contact with LEU 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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316A ASN* 4.9 2.5 - - - +
318A ILE* 3.7 30.3 - - + -
319B SER* 4.8 7.7 + - - -
322B GLU* 3.9 11.8 - - + +
323B ASN* 3.7 43.5 - - - +
326B CYS* 5.2 2.0 - - + -
357B ILE* 2.9 32.3 + - + +
358B THR* 3.9 5.8 - - - +
360B ILE* 1.3 77.1 - - + +
362B ALA* 1.3 62.1 + - - +
363B THR 3.1 1.7 + - - -
364B ASP* 3.4 18.0 + - - +
367B ARG* 3.3 21.0 + - - +
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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 THR 3.0 18.9 + - - +
359B LEU* 3.1 9.6 + - - +
361B LEU* 1.3 76.3 - - - +
363B THR* 1.3 61.3 + - - +
364B ASP 3.2 5.8 + - - +
367B ARG* 3.9 3.8 - - - +
371B ILE* 3.5 27.6 - - + +
395B MET* 3.8 28.3 - - + -
398B ILE* 4.7 2.9 - - + -
399B LYS* 3.4 21.4 - - + +
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Residues in contact with THR 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B HIS* 4.2 25.8 + - + -
293B ASP* 5.3 0.7 + - - -
322B GLU* 3.6 12.0 + - - +
359B LEU 3.5 15.7 - - - +
360B ILE* 2.6 19.5 + - - +
362B ALA* 1.3 78.4 - - - +
364B ASP* 1.3 64.2 + - - +
365B MET* 3.1 13.2 + - - +
398B ILE* 4.2 29.4 - - + +
399B LYS* 4.6 6.9 - - - +
402B ASP* 3.8 23.9 - - + +
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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
------------------------------------------------------------
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