Contacts of the helix formed by residues 411 - 433 (chain B) in PDB entry 4U04
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 VAL 411 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU* 3.9 15.0 - - + -
357B TYR* 4.1 16.8 - - + -
406B ALA* 4.0 25.4 - - + +
409B GLY 4.2 1.3 + - - +
410B ASP* 1.4 72.3 + - - +
412B ARG* 1.3 68.7 + - + +
413B PRO 3.5 0.7 - - - -
414B PHE* 3.2 9.5 + - + +
415B ILE* 3.0 37.8 + - + +
501B PG4 4.1 24.2 - - - -
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Residues in contact with ARG 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASP* 2.7 31.3 + - - +
161B TYR* 4.5 4.6 - - - +
164B THR* 3.4 22.0 + - - +
184B LEU* 5.7 4.0 - - - +
187B VAL* 3.3 21.2 - - - +
188B GLU* 6.1 1.0 - - - +
191B ASP* 4.5 8.3 - - - +
410B ASP* 3.0 30.1 + - - +
411B VAL* 1.3 78.5 - - + +
413B PRO* 1.3 69.5 - - + +
415B ILE* 3.0 15.0 + - + +
416B ARG* 2.9 51.9 + - - +
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Residues in contact with PRO 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B TYR* 4.0 27.6 - - + -
402B VAL* 3.5 22.2 - - + +
405B ALA* 4.5 10.1 - - + -
410B ASP* 3.4 23.6 - - - +
412B ARG* 1.3 91.4 - - + +
414B PHE* 1.4 53.9 + - - +
416B ARG* 3.4 19.5 + - + +
417B PHE* 2.9 27.7 + - - +
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Residues in contact with PHE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ALA* 3.2 30.3 - - + -
356B HIS* 3.8 21.5 - + - -
357B TYR* 4.1 16.4 - + + -
399B TYR* 3.8 15.5 - + - -
402B VAL* 3.5 35.4 + - + +
403B LEU* 3.3 36.3 - - + -
406B ALA* 4.6 6.1 - - + -
411B VAL* 3.2 13.3 + - + +
412B ARG 3.2 0.6 - - - -
413B PRO* 1.4 74.7 - - - +
415B ILE* 1.3 69.0 + - + +
417B PHE* 3.2 3.3 + + - +
418B ILE* 3.0 50.2 + - + +
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Residues in contact with ILE 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B PHE* 3.9 28.3 - - + -
349B VAL* 4.5 1.5 - - - +
350B GLU* 4.0 39.0 - - + +
353B ALA* 4.1 19.1 - - + -
354B LEU* 4.1 12.1 - - + +
411B VAL* 3.0 39.3 + - + +
412B ARG* 3.0 15.1 + - + +
414B PHE* 1.3 75.3 - - + +
416B ARG* 1.3 60.1 + - + +
418B ILE* 3.5 2.9 + - - +
419B ALA* 3.0 26.2 + - - +
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Residues in contact with ARG 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 3.4 45.5 + - - +
160B ASP* 6.2 0.2 - - - +
161B TYR* 5.9 2.8 - - - +
187B VAL* 4.6 7.1 - - - +
191B ASP* 2.9 40.9 + - - +
194B TYR* 4.8 5.5 - - + -
410B ASP* 5.8 0.2 + - - -
412B ARG* 2.9 43.1 + - + +
413B PRO* 3.6 39.6 - - + +
415B ILE* 1.3 76.7 - - + +
417B PHE* 1.3 57.9 + - - +
419B ALA* 3.6 6.9 - - - +
420B LYS* 3.0 29.5 + - - +
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Residues in contact with PHE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ILE* 3.8 23.3 - - + -
395B GLN* 3.3 38.4 - - + -
398B ASP* 3.7 26.7 - - + -
399B TYR* 3.8 29.2 - + + -
402B VAL* 3.8 26.9 - - + -
413B PRO 2.9 15.3 + - - +
414B PHE* 3.2 8.3 + + - +
416B ARG* 1.3 75.7 - - - +
418B ILE* 1.4 70.3 + - + +
420B LYS* 3.3 14.9 - - + +
421B CYS* 3.1 33.3 + - - -
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Residues in contact with ILE 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B VAL* 4.0 13.7 - - + +
352B ALA* 5.2 2.7 - - + -
353B ALA* 3.5 33.0 - - + +
356B HIS* 4.3 1.3 - - - +
377B MET* 3.2 40.2 - - + -
381B LEU* 5.4 1.1 - - + -
391B ILE* 3.9 19.7 - - + -
414B PHE* 3.0 43.0 + - + +
415B ILE 3.8 1.3 - - - +
417B PHE* 1.4 82.3 - - + +
419B ALA* 1.3 61.9 + - - +
421B CYS* 3.1 7.4 + - - +
422B THR* 3.0 35.3 + - + +
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Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B TYR* 3.8 22.2 - - + -
195B PHE* 4.1 9.0 - - + -
198B ILE* 3.4 13.3 - - + +
349B VAL* 3.6 21.1 - - + +
415B ILE 3.0 17.7 + - - +
416B ARG* 3.6 8.5 - - - +
417B PHE 3.4 0.2 - - - -
418B ILE* 1.3 76.7 - - - +
420B LYS* 1.4 57.8 + - - +
422B THR* 3.0 20.5 + - - -
423B GLU* 3.0 10.2 + - - +
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Residues in contact with LYS 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B TYR* 3.3 23.9 - - + +
395B GLN* 5.3 4.9 - - - +
416B ARG 3.0 16.4 + - - +
417B PHE* 3.3 26.0 - - + +
419B ALA* 1.4 75.1 - - - +
421B CYS* 1.4 58.2 + - - +
423B GLU* 3.4 2.0 + - - +
424B THR* 3.0 36.4 + - + +
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Residues in contact with CYS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ILE* 4.2 12.6 - - + -
390B THR 4.2 11.6 - - - +
391B ILE* 4.0 13.7 - - + -
395B GLN* 3.6 34.3 - - - +
417B PHE* 3.1 36.4 + - - +
418B ILE* 3.1 12.8 + - - +
420B LYS* 1.4 76.6 - - - +
422B THR* 1.4 57.6 + - - +
424B THR* 2.7 20.7 + - - -
425B THR* 3.1 18.4 + - - -
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Residues in contact with THR 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ILE* 3.6 23.4 - - - +
349B VAL* 3.8 24.3 - - + +
381B LEU* 4.6 7.4 - - + -
386B TYR* 5.1 3.4 - - + -
389B ILE* 3.5 29.8 - - + +
418B ILE* 3.0 25.0 + - + +
419B ALA 3.0 8.6 + - - +
421B CYS* 1.4 73.6 - - - +
423B GLU* 1.3 61.6 + - - +
425B THR* 3.3 2.6 + - - -
426B LEU* 2.9 38.5 + - - +
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Residues in contact with GLU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B TYR* 2.7 41.8 + - - +
197B ILE* 3.6 18.2 - - - +
198B ILE* 4.2 9.9 - - + -
201B LYS* 2.9 36.9 + - + +
419B ALA 3.0 5.8 + - - +
420B LYS* 3.9 3.8 - - - +
422B THR* 1.3 82.0 + - - +
424B THR* 1.3 55.0 + - + +
426B LEU* 3.2 10.0 + - - +
427B ASP* 2.8 46.0 + - - +
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Residues in contact with THR 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B THR 5.4 1.2 + - - -
395B GLN* 5.7 0.9 + - - -
420B LYS* 3.0 20.9 + - + +
421B CYS* 2.7 26.0 + - - -
423B GLU* 1.3 76.6 - - + +
425B THR* 1.3 55.2 + - - +
427B ASP* 3.3 11.1 + - - +
428B THR* 3.0 33.2 + - - -
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Residues in contact with THR 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B PRO* 4.2 2.9 - - + -
388B PRO 3.5 23.6 - - - +
389B ILE* 3.8 18.6 - - + +
390B THR* 3.9 16.5 + - - +
421B CYS 3.1 19.0 + - - -
422B THR 3.6 4.3 - - - -
423B GLU 3.3 0.2 - - - -
424B THR* 1.3 74.6 + - - +
426B LEU* 1.3 63.0 + - - +
428B THR* 3.3 8.5 + - - -
429B LEU* 3.1 37.9 + - + +
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Residues in contact with LEU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ILE* 3.9 23.3 - - + +
201B LYS* 4.0 22.4 - - + +
202B VAL* 3.7 43.5 - - + -
205B VAL* 3.7 15.5 - - + +
386B TYR* 5.1 1.6 - - + -
387B PRO* 4.0 26.5 - - + -
422B THR* 2.9 26.9 + - - +
423B GLU* 3.6 6.5 - - - +
425B THR* 1.3 72.1 - - - +
427B ASP* 1.3 61.4 + - - +
429B LEU* 3.3 4.6 + - - -
430B LEU* 2.8 30.6 + - - +
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Residues in contact with ASP 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LYS* 2.9 37.5 + - - +
423B GLU* 2.8 35.2 + - - +
424B THR* 3.3 11.2 + - - +
426B LEU* 1.3 72.3 - - - +
428B THR* 1.3 57.2 + - - +
430B LEU* 3.8 6.8 - - - +
431B PHE* 3.0 30.8 + - - +
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Residues in contact with THR 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B VAL* 6.5 0.7 - - + -
424B THR 3.0 17.4 + - - -
425B THR* 3.6 7.8 - - - -
426B LEU 3.3 0.2 - - - -
427B ASP* 1.3 76.8 - - - +
429B LEU* 1.3 57.8 + - + +
431B PHE* 3.9 5.1 - - - +
432B ALA* 2.9 36.3 + - + +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 4.0 25.7 - - + +
215B LEU* 5.5 3.1 - - - +
218B VAL* 4.8 16.4 - - + -
219B MET* 5.3 14.1 - - + +
222B THR* 5.9 2.0 - - - +
387B PRO* 3.7 37.7 - - + -
425B THR* 3.1 25.1 + - + +
426B LEU* 3.3 5.4 + - - +
428B THR* 1.3 76.3 - - + +
430B LEU* 1.4 62.0 + - - +
432B ALA* 4.3 4.1 - - - +
433B THR* 3.5 23.9 + - - -
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LYS* 6.4 3.1 - - + -
204B LYS* 4.5 19.7 - - + -
205B VAL* 4.1 13.6 - - + +
426B LEU 2.8 17.9 + - - +
427B ASP* 3.9 8.5 - - - +
428B THR 3.4 0.4 - - - -
429B LEU* 1.4 76.0 - - - +
431B PHE* 1.4 58.6 + - - +
433B THR* 3.8 7.3 - - - +
434B THR* 3.6 15.4 - - - -
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Residues in contact with PHE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ASP 3.0 17.9 + - - +
428B THR* 4.0 5.2 - - - +
430B LEU* 1.4 75.4 - - - +
432B ALA* 1.3 67.1 + - - +
433B THR 3.2 2.0 - - - -
434B THR* 3.3 24.2 + - - +
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Residues in contact with ALA 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA* 5.9 1.6 - - - +
218B VAL* 3.9 37.1 - - + +
428B THR* 2.9 23.3 + - + +
429B LEU* 4.3 3.4 - - - +
430B LEU 3.7 0.2 - - - -
431B PHE* 1.3 79.5 - - - +
433B THR* 1.4 56.8 + - - +
434B THR 3.4 6.3 + - - +
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Residues in contact with THR 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA* 6.4 2.9 - - - -
215B LEU* 5.5 14.8 - - - -
218B VAL* 6.4 1.1 - - - -
429B LEU 3.5 16.5 + - - -
430B LEU* 3.8 6.1 - - - +
431B PHE 3.2 0.6 - - - -
432B ALA* 1.4 75.9 - - - +
434B THR* 1.4 60.6 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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