Contacts of the helix formed by residues 368 - 384 (chain B) in PDB entry 1B70
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 GLY 368 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B ARG* 5.6 0.5 - - - -
258B GLN* 4.0 8.7 - - - -
365B ASP* 2.9 28.8 + - - -
367B LEU* 1.3 78.3 - - - +
369B GLN* 1.3 66.1 + - - +
371B PRO* 3.0 11.3 - - - +
372B ALA* 3.0 24.4 + - - +
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Residues in contact with GLN 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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212B HIS* 3.3 20.6 - - + +
214B THR* 3.8 18.8 - - + -
258B GLN* 2.7 25.4 - - - +
335B VAL* 3.5 28.6 - - - +
336B ALA* 3.3 19.2 + - - -
337B CYS* 3.6 5.7 - - - +
364B VAL* 3.2 11.7 - - - +
365B ASP 3.1 10.9 + - - +
366B PRO 3.0 24.5 - - - +
367B LEU 3.3 0.6 - - - -
368B GLY* 1.3 76.1 + - - +
370B VAL* 1.3 59.5 + - - +
372B ALA* 3.1 3.5 + - - +
373B GLN* 2.9 31.5 + - - +
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Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B HIS* 4.9 2.9 - - - +
214B THR* 4.5 8.5 - - + -
367B LEU 4.5 2.5 + - - +
369B GLN* 1.3 70.5 - - + +
371B PRO* 1.3 75.9 - - + +
373B GLN* 3.1 16.8 + - - +
374B ARG* 3.1 24.5 + - + +
392B LEU* 4.3 17.5 - - + -
394B GLU* 3.6 30.3 - - - +
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Residues in contact with PRO 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ARG* 4.3 16.9 + - - +
367B LEU 3.5 12.8 - - - +
368B GLY* 3.0 31.0 - - - +
370B VAL* 1.3 90.9 - - + +
372B ALA* 1.3 54.4 + - - +
374B ARG* 3.4 9.2 + - + +
375B ARG* 3.0 27.0 + - - +
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B VAL* 4.4 2.9 - - - +
256B ARG* 4.2 23.1 - - - +
258B GLN* 3.8 27.1 - - + -
260B MET* 4.5 7.3 - - + +
335B VAL* 4.1 3.8 - - + -
368B GLY 3.0 20.1 + - - +
369B GLN 3.2 4.9 - - - +
371B PRO* 1.3 76.5 - - - +
373B GLN* 1.3 59.4 + - - +
375B ARG* 3.2 3.6 + - - +
376B ALA* 2.9 30.0 + - - +
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Residues in contact with GLN 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B THR* 2.9 29.9 + - - +
215B LEU 3.7 0.6 - - - +
216B GLY* 3.5 26.8 + - - +
333B LEU* 3.1 31.2 + - - +
335B VAL* 3.4 19.0 - - + +
369B GLN 2.9 17.6 + - - +
370B VAL 3.1 7.6 + - - +
372B ALA* 1.3 72.1 - - - +
374B ARG* 1.3 62.5 + - - +
376B ALA* 3.8 4.2 - - - +
377B LEU* 2.9 50.5 + - + +
392B LEU* 4.1 20.8 - - + +
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Residues in contact with ARG 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA* 3.7 11.7 - - + +
191B LEU* 4.0 27.7 - - + +
193B ALA* 4.6 4.9 - - - +
370B VAL* 3.1 24.1 + - + +
371B PRO* 3.6 10.5 - - + +
372B ALA 3.3 0.2 - - - -
373B GLN* 1.3 78.1 - - - +
375B ARG* 1.3 63.9 + - - +
377B LEU* 4.8 5.9 - - - +
378B SER* 3.0 27.4 + - - -
388B VAL* 5.3 0.2 - - - +
389B ALA 4.2 10.7 + - - -
390B GLU* 2.7 34.1 + - - +
392B LEU* 3.6 33.4 - - - +
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Residues in contact with ARG 375 (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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11B TYR* 5.0 1.4 + - - -
187B PRO* 3.5 27.1 - - - +
188B GLU 4.3 12.5 + - - -
189B ALA* 3.8 15.2 - - + +
229B TRP* 6.1 0.6 - - - -
251B TYR* 3.9 18.2 + - - -
252B VAL* 4.0 13.9 - - + +
255B GLU* 2.8 42.0 + - - +
256B ARG* 3.9 21.3 - - - +
371B PRO 3.0 14.0 + - - +
372B ALA* 3.4 8.5 - - - +
373B GLN 3.2 0.2 - - - -
374B ARG* 1.3 78.8 - - - +
376B ALA* 1.3 56.9 + - - +
378B SER* 3.4 5.8 + - - -
379B LEU* 3.1 53.0 + - - +
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Residues in contact with ALA 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B VAL* 4.0 9.0 - - + +
252B VAL* 4.2 14.4 - - + -
260B MET* 3.6 27.1 - - - -
333B LEU* 3.8 16.2 - - + -
372B ALA 2.9 15.9 + - - +
373B GLN* 3.9 1.3 - - - +
375B ARG* 1.3 75.3 - - - +
377B LEU* 1.3 59.9 + - - +
379B LEU* 3.0 5.1 + - - +
380B LEU* 2.8 33.6 + - + +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU* 3.7 17.4 - - + +
216B GLY* 4.8 2.7 - - - -
217B TYR 4.9 7.4 - - - +
218B ALA* 4.2 12.1 - - + -
331B ILE* 6.0 0.4 - - + -
333B LEU* 4.2 13.7 - - + -
373B GLN* 2.9 46.9 + - + +
374B ARG* 4.6 9.6 - - - +
376B ALA* 1.3 69.1 - - - +
378B SER* 1.3 62.3 + - - +
380B LEU* 3.1 21.5 + - + +
381B GLN* 2.9 30.3 + - - +
388B VAL* 3.6 30.6 - - + +
389B ALA 5.6 0.2 - - - +
392B LEU* 4.5 12.8 - - + -
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Residues in contact with SER 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLU 4.5 1.6 + - - -
189B ALA* 3.5 16.8 - - - -
190B ALA* 3.0 37.1 + - - +
191B LEU* 4.0 9.3 - - - +
374B ARG 3.0 17.9 + - - -
375B ARG* 3.5 7.1 + - - -
377B LEU* 1.3 78.4 - - - +
379B LEU* 1.3 66.2 + - - +
381B GLN* 3.4 3.5 + - - +
382B ALA* 3.2 22.2 + - - +
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Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B TRP* 4.9 14.1 - - + -
230B MET* 5.3 1.8 - - + -
248B VAL* 4.0 17.5 - - + -
251B TYR* 4.5 10.5 - - + -
252B VAL* 3.7 30.1 - - + -
375B ARG* 3.1 50.4 + - - +
376B ALA 3.0 8.5 + - - +
378B SER* 1.3 77.3 - - - +
380B LEU* 1.3 53.2 + - - +
382B ALA* 3.2 6.9 + - + +
383B LEU* 2.7 54.4 + - + +
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Residues in contact with LEU 380 (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 ALA* 4.5 11.4 - - + -
221B LEU* 5.4 2.0 - - + -
244B ASN 5.4 0.2 - - - -
245B VAL* 4.2 31.2 - - + +
248B VAL* 4.1 26.5 - - + -
249B THR* 6.4 0.2 - - + -
331B ILE* 4.8 10.1 - - + -
333B LEU* 4.6 11.0 - - + -
376B ALA* 2.8 21.0 + - + +
377B LEU* 3.1 27.3 + - + +
379B LEU* 1.3 75.2 - - - +
381B GLN* 1.3 62.3 + - - +
383B LEU* 4.4 0.4 - - + +
384B ALA* 2.6 36.4 + - + +
385B GLY 3.1 3.5 + - - -
386B ALA* 3.4 14.6 + - + -
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Residues in contact with GLN 381 (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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190B ALA 4.7 1.0 - - - +
191B LEU* 3.0 25.5 - - + +
192B LYS* 2.7 50.4 + - - +
377B LEU 2.9 14.9 + - - +
378B SER 3.6 5.6 - - - +
380B LEU* 1.3 75.3 - - - +
382B ALA* 1.3 58.6 + - - +
385B GLY* 2.9 25.5 + - - -
386B ALA* 3.1 24.7 + - - +
387B ARG* 4.6 0.6 - - - +
388B VAL* 3.2 21.6 - - + +
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Residues in contact with ALA 382 (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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378B SER* 3.2 10.4 + - - +
379B LEU* 3.5 10.8 - - + +
380B LEU 3.0 0.6 - - - -
381B GLN* 1.3 82.2 - - - +
383B LEU* 1.3 75.0 + - + +
385B GLY* 4.3 1.6 + - - -
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Residues in contact with LEU 383 (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 ARG 4.6 0.3 - - - +
226B SER* 5.1 1.3 - - - +
227B PRO* 3.8 31.2 - - + -
229B TRP* 4.5 11.0 - - + +
230B MET* 3.8 29.6 - - + -
244B ASN* 2.8 29.1 + - + +
248B VAL* 4.2 17.7 - - + -
379B LEU* 2.7 27.6 + - + +
380B LEU* 5.1 0.9 - - + -
382B ALA* 1.3 89.4 - - + +
384B ALA* 1.3 59.0 + - + +
385B GLY 3.5 0.4 - - - -
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 3.8 21.6 - - + -
222B ARG* 3.2 35.1 + - - +
244B ASN* 3.7 15.3 - - - +
245B VAL* 4.1 15.7 - - + -
380B LEU* 2.6 19.9 + - + +
383B LEU* 1.3 73.8 - - + +
385B GLY* 1.3 67.0 + - - +
386B ALA 3.1 1.0 + - - -
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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