Contacts of the helix formed by residues 376 - 397 (chain B) in PDB entry 3F9C
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 ASP 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ASN* 4.8 0.4 - - - -
363B LYS* 6.1 7.6 - - + +
374B ASP 3.7 1.6 + - - -
375B ILE* 1.3 80.8 - - - +
377B SER* 1.3 55.7 + - - +
378B ASN* 2.7 19.0 + - - -
379B VAL* 2.6 40.3 + - + +
380B ALA* 2.9 30.4 + - - +
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Residues in contact with SER 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ASN* 3.8 12.3 + - - +
358B THR* 2.7 30.7 + - - +
359B PHE* 3.9 21.0 - - - -
372B LYS* 3.3 29.4 + - - +
375B ILE 3.7 1.6 + - - -
376B ASP* 1.3 70.2 + - - +
378B ASN* 1.3 67.2 + - - -
379B VAL 3.1 1.1 - - - -
380B ALA* 3.3 1.4 + - - +
381B ILE* 3.1 24.9 + - - +
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Residues in contact with ASN 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS 4.8 2.3 - - - +
57B PRO* 4.1 16.7 - - + +
58B ARG* 5.2 4.3 + - - -
359B PHE* 3.6 19.2 - - - -
376B ASP* 2.7 19.0 + - - +
377B SER* 1.3 74.2 - - - +
379B VAL* 1.3 56.6 + - + +
381B ILE* 3.5 7.8 - - - +
382B ASP* 3.0 42.9 + - - +
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Residues in contact with VAL 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ILE* 3.9 24.0 - - + -
376B ASP* 2.6 33.0 + - + +
378B ASN* 1.3 74.4 - - + +
380B ALA* 1.3 61.1 + - - +
382B ASP* 3.4 7.6 + - - +
383B LEU* 3.1 29.3 + - + +
415B ASN* 4.5 10.1 - - - +
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 3.4 28.3 - - + +
349B SER* 5.1 0.2 - - - -
353B ASN* 4.0 22.7 - - + +
375B ILE* 3.8 21.1 - - + -
376B ASP 2.9 16.5 + - - +
377B SER 3.3 2.0 + - - +
379B VAL* 1.3 78.4 - - - +
381B ILE* 1.3 61.7 + - - +
383B LEU* 3.3 2.5 + - - -
384B SER* 3.2 21.4 + - - -
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO* 4.5 10.1 - - + -
162B ALA* 4.6 8.3 - - + -
163B ILE* 3.7 30.1 - - + -
353B ASN 3.8 19.7 + - - +
354B PHE* 4.0 11.0 - - + +
359B PHE* 3.7 24.9 - - + -
377B SER 3.1 15.0 + - - +
378B ASN* 3.5 14.8 - - + +
380B ALA* 1.3 73.9 - - - +
382B ASP* 1.3 66.4 + - - +
384B SER* 3.7 8.3 + - - -
385B ASN* 2.8 57.4 + - - +
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Residues in contact with ASP 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO* 6.0 1.2 - - - +
60B ASN* 3.4 23.5 - - - +
378B ASN* 3.0 29.4 + - - +
379B VAL* 3.5 7.8 - - - +
381B ILE* 1.3 83.7 - - - +
383B LEU* 1.3 63.1 + - - +
385B ASN* 3.8 7.3 + - - +
386B LYS* 3.0 46.3 + - + +
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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
----------------------------------------------------------
344B ILE* 6.0 0.2 - - - -
346B ILE* 3.9 25.6 - - + -
375B ILE* 4.1 4.7 - - + -
379B VAL* 3.1 22.7 + - + +
380B ALA* 3.5 6.5 - - - +
381B ILE 3.2 0.4 - - - -
382B ASP* 1.3 77.3 - - - +
384B SER* 1.3 54.9 + - - +
386B LYS* 3.6 4.8 - - - +
387B ALA* 2.7 37.1 + - - +
408B LEU* 3.7 16.4 - - + +
413B ASP* 3.9 12.8 - - - +
415B ASN* 3.5 31.0 - - + +
416B LEU* 3.5 34.5 - - + -
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Residues in contact with SER 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 5.1 1.7 - - - +
295B LEU* 3.7 14.4 - - - +
317B ILE* 3.8 5.7 - - - +
346B ILE* 3.6 16.1 - - - +
354B PHE* 3.4 28.9 - - - -
380B ALA 3.2 13.7 + - - -
381B ILE* 3.8 11.3 - - - +
383B LEU* 1.3 76.4 - - - +
385B ASN* 1.3 53.8 + - - -
387B ALA* 3.6 7.1 - - - +
388B SER* 2.7 38.4 + - - -
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Residues in contact with ASN 385 (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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162B ALA 4.2 4.2 + - - -
163B ILE* 3.8 28.4 - - - +
166B ASP* 3.2 42.7 + - - +
167B LEU* 5.2 4.8 - - + +
381B ILE* 2.8 47.2 + - - +
382B ASP* 3.8 8.1 + - - +
383B LEU 3.2 0.2 + - - -
384B SER* 1.3 71.0 + - - +
386B LYS* 1.3 56.7 + - + +
388B SER* 3.3 7.8 + - - -
389B LEU* 2.7 42.2 + - + +
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Residues in contact with LYS 386 (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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60B ASN* 5.1 8.3 + - - +
382B ASP* 3.0 39.8 + - + +
383B LEU* 3.7 2.9 - - - +
385B ASN* 1.3 71.1 - - + +
387B ALA* 1.3 69.8 + - - +
388B SER 3.0 1.1 - - - -
389B LEU* 3.2 4.1 + - + +
390B ALA* 3.0 22.5 + - - +
405B TRP* 3.2 67.4 - - + +
408B LEU* 3.7 10.8 - - + -
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Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B PHE* 3.7 20.4 - - + -
317B ILE* 4.0 2.9 - - + -
344B ILE* 3.9 27.6 - - + -
383B LEU 2.7 21.5 + - - +
384B SER 3.6 5.8 - - - +
386B LYS* 1.3 74.0 - - - +
388B SER* 1.4 57.0 + - - +
390B ALA* 3.3 4.7 + - - +
391B PHE 3.0 22.0 + - - -
405B TRP 4.8 0.2 - - - -
408B LEU* 4.0 21.7 - - + +
409B ILE* 3.8 2.7 - - - +
416B LEU* 6.1 0.2 - - + -
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Residues in contact with SER 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 6.2 1.1 - - - +
167B LEU* 5.0 10.8 - - - -
270B ILE* 5.3 4.1 - - - +
293B ILE* 3.8 25.6 - - - +
295B LEU* 4.4 5.2 - - - +
315B PHE* 4.6 2.7 - - - -
317B ILE* 3.5 13.7 - - - +
384B SER* 2.7 25.3 + - - -
385B ASN* 3.4 9.7 + - - -
386B LYS 3.0 0.2 - - - -
387B ALA* 1.4 72.9 - - - +
389B LEU* 1.3 59.8 + - - +
391B PHE* 3.3 1.1 + - - +
392B LEU* 2.9 36.9 + - - +
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Residues in contact with LEU 389 (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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166B ASP* 4.1 5.4 - - - +
167B LEU* 3.8 18.8 - - + -
170B HIS* 3.4 45.1 - - + +
172B PHE* 3.7 28.5 - - + -
385B ASN* 2.7 33.1 + - + +
386B LYS* 3.2 5.8 + - + +
388B SER* 1.3 72.4 - - - +
390B ALA* 1.3 57.0 + - - +
392B LEU* 3.8 3.7 - - - +
393B GLN* 2.9 30.7 + - - +
402B PHE* 3.5 28.0 - - + +
405B TRP* 4.0 15.5 - - + -
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Residues in contact with ALA 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LYS 3.0 9.4 + - - +
387B ALA 3.5 6.5 - - - +
389B LEU* 1.3 77.4 - - - +
391B PHE* 1.3 63.2 + - - +
393B GLN* 3.3 4.7 + - - +
394B LYS* 3.2 21.7 + - - +
402B PHE* 3.4 26.1 - - - +
405B TRP 3.6 15.9 - - - +
406B ASP* 3.7 9.5 - - - +
409B ILE* 3.2 24.6 - - + +
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Residues in contact with PHE 391 (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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291B CYS* 4.1 17.9 - - + -
292B GLY 3.6 17.7 - - - -
293B ILE* 3.9 11.4 - - + -
313B PRO* 3.7 4.7 - - + -
314B LEU 3.7 23.6 - - - -
315B PHE* 3.4 49.8 - + + -
340B GLU* 4.6 3.6 - - + -
342B LYS* 4.5 11.9 - - + -
387B ALA 3.0 10.1 + - - +
388B SER 3.3 2.9 + - - +
390B ALA* 1.3 76.8 - - - +
392B LEU* 1.3 62.0 + - - +
394B LYS* 3.4 3.8 + - + -
395B HIS* 3.2 62.4 + + - +
409B ILE* 3.7 19.9 - - + +
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Residues in contact with LEU 392 (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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147B VAL* 4.3 1.6 - - + -
167B LEU* 3.9 22.2 - - + -
172B PHE* 3.4 37.0 - - + -
268B ALA* 3.6 31.4 - - + -
270B ILE* 4.2 12.3 - - + -
291B CYS* 3.9 10.3 - - - -
293B ILE* 3.8 17.5 - - + -
388B SER 2.9 28.1 + - - +
389B LEU* 3.8 4.9 - - - +
391B PHE* 1.3 70.5 - - - +
393B GLN* 1.3 60.3 + - - +
396B LEU* 2.8 42.9 + - + +
398B LEU* 4.2 0.9 - - - -
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Residues in contact with GLN 393 (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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389B LEU 2.9 22.1 + - - +
390B ALA* 3.3 5.1 + - - +
392B LEU* 1.3 73.9 - - - +
394B LYS* 1.3 59.4 + - - +
397B GLY* 3.0 22.7 + - - -
398B LEU* 3.0 37.7 + - + +
400B LYS* 2.6 49.5 + - - +
402B PHE* 3.4 13.2 + - + +
403B ASP* 3.1 36.4 + - + +
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Residues in contact with LYS 394 (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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340B GLU* 5.4 3.1 - - - +
390B ALA 3.2 6.2 + - - +
391B PHE* 3.6 9.4 - - + +
392B LEU 3.2 0.6 - - - -
393B GLN* 1.3 81.6 - - - +
395B HIS* 1.3 85.2 + - + +
396B LEU 3.6 0.2 + - - -
397B GLY* 3.6 6.9 + - - -
403B ASP* 4.9 4.6 - - - +
406B ASP* 3.7 37.6 + - - +
409B ILE* 4.5 15.5 - - + -
410B GLU* 5.9 2.5 - - - -
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Residues in contact with HIS 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ARG* 4.1 14.2 - - - +
291B CYS* 4.0 13.2 - - + -
313B PRO* 3.2 28.2 - - + +
340B GLU* 3.4 42.7 + - + -
391B PHE* 3.2 50.9 + + - +
392B LEU 3.8 0.2 - - - -
394B LYS* 1.3 96.4 + - + +
396B LEU* 1.3 67.8 + - - +
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Residues in contact with LEU 396 (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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145B PRO* 4.7 1.8 - - + -
146B LEU 5.1 0.7 - - - +
172B PHE* 4.3 23.3 - - + -
265B GLU 5.3 0.7 - - - +
266B LYS* 3.5 44.9 + - + +
267B ILE 3.7 19.5 - - - +
268B ALA* 4.2 15.9 - - + +
290B ARG* 3.6 31.4 - - + -
291B CYS* 4.0 11.4 - - - -
392B LEU* 2.8 23.0 + - + +
395B HIS* 1.3 80.5 - - - +
397B GLY* 1.3 61.4 + - - +
398B LEU* 4.0 12.1 - - + -
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Residues in contact with GLY 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LYS* 3.5 7.7 + - - -
393B GLN 3.0 9.9 + - - -
394B LYS 3.6 6.0 + - - -
395B HIS 3.6 1.6 - - - -
396B LEU* 1.3 80.1 - - - +
398B LEU* 1.3 65.6 + - - +
399B HIS* 3.4 21.6 + - - -
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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