Contacts of the helix formed by residues 360 - 374 (chain B) in PDB entry 3BWE
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 THR 360 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 3.6 20.0 - - + +
345B ARG* 3.3 52.7 - - + +
355B SER* 3.0 21.6 + - - -
356B ARG* 3.4 4.1 + - + -
357B GLY 2.8 28.0 + - - +
359B GLY* 1.3 77.4 - - - +
361B SER* 1.3 54.1 + - - +
362B PHE 3.2 3.1 - - - -
363B GLU* 3.0 7.9 + - - +
364B PHE* 2.8 33.6 + - - +
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Residues in contact with SER 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B MSE 4.6 0.4 - - - -
218B GLU* 3.7 22.7 + - - +
221B ILE* 3.6 31.0 - - - +
222B PRO* 4.7 3.3 - - - +
305B ILE* 3.7 22.3 - - - +
357B GLY 3.4 1.6 + - - -
358B PRO* 3.2 17.3 + - - +
359B GLY 3.6 0.4 - - - -
360B THR* 1.3 77.7 - - - +
362B PHE* 1.3 57.7 + - - +
364B PHE* 3.4 2.8 - - - +
365B ALA* 2.7 31.9 + - - +
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Residues in contact with PHE 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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17A MSE 3.7 30.7 - - - -
21A ILE* 4.3 4.5 - - + -
158A PRO* 3.5 33.4 - - + -
159A GLY* 4.7 1.1 - - - -
162A PHE* 4.2 19.7 - + - -
221B ILE* 3.8 29.8 - - + -
225B VAL* 4.4 3.6 - - + -
358B PRO 5.7 0.4 - - - -
359B GLY 5.3 3.3 + - - +
360B THR 3.2 1.4 - - - -
361B SER* 1.3 79.6 - - - +
363B GLU* 1.3 62.9 + - + +
365B ALA* 3.8 2.0 - - - +
366B LEU* 2.9 37.7 + - - +
385B LEU* 3.9 24.7 - - + -
387B LEU* 3.7 36.8 - - + -
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Residues in contact with GLU 363 (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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188A LYS* 5.3 4.5 + - - +
345B ARG* 2.3 59.7 + - - +
346B VAL* 3.7 15.5 - - + +
359B GLY 3.9 4.7 - - - +
360B THR* 3.0 7.8 + - - +
362B PHE* 1.3 77.7 - - + +
364B PHE* 1.3 61.3 + - - +
366B LEU* 4.1 7.1 - - + +
367B ALA* 2.9 31.0 + - - +
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Residues in contact with PHE 364 (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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218B GLU 5.3 0.2 - - - -
222B PRO* 4.2 21.3 - - + -
271B VAL* 4.9 7.0 - - + -
272B LEU 5.2 0.7 - - - -
303B ALA* 3.6 32.1 - - + -
304B ALA* 3.4 24.9 - - - -
305B ILE* 3.8 26.2 - - + -
346B VAL* 3.7 7.1 - - + +
353B LEU* 3.6 32.3 - - + +
355B SER* 3.4 26.0 - - - +
360B THR 2.8 15.6 + - - +
361B SER 3.4 3.1 - - - +
363B GLU* 1.3 78.4 - - - +
365B ALA* 1.3 61.9 + - - +
367B ALA* 3.4 4.7 + - - +
368B ILE* 3.2 35.8 + - + +
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Residues in contact with ALA 365 (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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221B ILE* 4.3 1.3 - - + +
222B PRO* 3.6 31.2 - - + +
225B VAL* 3.9 20.2 - - + -
226B MSE 4.8 1.7 - - + +
361B SER 2.7 20.8 + - - +
362B PHE 3.9 2.7 - - - +
364B PHE* 1.3 73.5 - - - +
366B LEU* 1.3 65.1 + - - +
368B ILE* 3.1 15.4 + - - +
369B VAL* 3.1 25.7 + - - +
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Residues in contact with LEU 366 (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 VAL* 4.2 19.3 - - + -
362B PHE* 2.9 25.3 + - + +
363B GLU* 4.1 6.7 - - + +
365B ALA* 1.3 76.1 - - - +
367B ALA* 1.3 63.7 + - - +
369B VAL* 3.2 8.4 + - + +
370B GLU* 2.9 24.1 + - - +
378B ALA* 3.8 28.6 - - + +
381B VAL* 4.2 9.4 - - + -
382B LYS* 4.1 23.3 - - + +
385B LEU* 4.5 4.9 - - + -
387B LEU* 3.7 30.1 - - + -
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Residues in contact with ALA 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B VAL* 3.8 22.9 - - + -
348B LYS* 5.5 2.2 - - + +
353B LEU* 4.0 14.3 - - + +
363B GLU 2.9 21.0 + - - +
364B PHE 3.4 7.0 - - - +
366B LEU* 1.3 77.9 - - - +
368B ILE* 1.3 62.5 + - - +
370B GLU* 3.4 7.3 + - - +
371B ALA* 3.1 23.7 + - - +
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Residues in contact with ILE 368 (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 PRO* 5.1 1.8 - - + -
226B MSE 3.7 29.4 - - + -
269B VAL* 4.1 20.2 - - + -
271B VAL* 4.2 12.1 - - + -
301B LEU* 4.8 1.6 - - + -
303B ALA* 3.8 29.6 - - + -
353B LEU* 4.3 12.8 - - + -
364B PHE* 3.3 32.5 - - + +
365B ALA* 3.1 12.4 + - - +
367B ALA* 1.3 77.8 - - - +
369B VAL* 1.3 61.9 + - - +
371B ALA* 3.4 2.5 + - - +
372B LEU* 3.1 34.0 + - + +
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Residues in contact with VAL 369 (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 VAL* 3.9 24.2 - - + +
226B MSE 4.5 10.1 - - + -
229B ALA* 3.6 31.0 - - + -
231B ILE* 4.7 7.2 - - + -
365B ALA 3.1 14.8 + - - +
366B LEU* 3.4 10.5 - - + +
368B ILE* 1.3 73.8 - - - +
370B GLU* 1.3 59.0 + - - +
372B LEU 3.2 0.3 + - - -
373B ASN* 2.6 35.6 + - + +
374B GLY 3.4 1.6 + - - -
377B VAL* 4.3 7.6 - - + +
378B ALA* 3.8 27.4 - - + +
381B VAL* 4.7 2.5 - - + -
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Residues in contact with GLU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LEU 2.9 16.1 + - - +
367B ALA* 3.7 6.7 - - - +
369B VAL* 1.3 76.2 - - - +
371B ALA* 1.3 65.3 + - - +
374B GLY* 2.9 32.3 + - - -
375B LYS* 3.8 47.0 + - + +
378B ALA* 4.1 9.6 - - + +
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Residues in contact with ALA 371 (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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301B LEU* 3.8 25.4 - - + -
348B LYS* 4.1 21.5 - - + +
353B LEU* 4.9 0.4 - - + -
367B ALA 3.1 17.0 + - - +
368B ILE 3.6 5.4 - - - +
369B VAL 3.3 0.2 - - - -
370B GLU* 1.3 79.6 - - - +
372B LEU* 1.3 62.3 + - + +
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Residues in contact with LEU 372 (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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204B LYS* 3.8 40.5 - - + +
205B ARG 4.6 1.6 - - - +
231B ILE* 3.7 25.4 - - + -
268B ASP* 4.1 14.4 - - + +
269B VAL* 3.8 27.1 - - + -
301B LEU* 3.8 24.9 - - + -
368B ILE* 3.1 24.0 + - + +
369B VAL 4.0 0.9 - - - +
371B ALA* 1.3 84.4 - - - +
373B ASN* 1.3 69.7 + - - +
374B GLY 3.6 0.2 - - - -
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Residues in contact with ASN 373 (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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204B LYS* 3.8 26.3 - - - +
229B ALA* 2.8 28.9 - - - +
230B GLY 4.8 0.7 - - - -
231B ILE* 3.5 16.7 + - - +
369B VAL* 2.6 17.4 + - + +
372B LEU* 1.3 84.6 + - - +
374B GLY* 1.3 57.4 + - - +
377B VAL* 3.6 35.6 - - + +
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Residues in contact with GLY 374 (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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369B VAL 3.4 1.1 + - - +
370B GLU* 2.9 23.1 + - - -
372B LEU 3.6 1.0 - - - -
373B ASN* 1.3 80.6 - - - +
375B LYS* 1.3 64.3 + - - -
376B GLU 3.5 2.2 - - - -
377B VAL 4.3 0.2 - - - -
378B ALA* 3.1 24.9 + - - +
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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