Contacts of the helix formed by residues 385 - 404 (chain B) in PDB entry 3RU0
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 MET 385 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B LEU* 3.2 35.0 - - + -
380B GLN* 2.9 28.3 + - + +
383B GLN* 3.2 33.2 - - + +
384B GLY* 1.3 73.5 - - - +
386B PHE* 1.3 57.9 + - - +
387B PRO* 4.4 0.9 - - - -
388B GLN* 3.2 28.9 - - + +
389B ALA* 2.9 28.9 + - - +
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Residues in contact with PHE 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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381B LEU* 3.8 41.1 - - + -
384B GLY* 3.0 30.6 + - - -
385B MET* 1.3 71.9 - - - +
387B PRO* 1.4 66.1 - - + +
389B ALA* 4.3 2.7 - - - -
390B MET* 2.9 30.1 + - - +
420B GLU 5.7 2.0 - - - -
421B CYS* 3.6 19.8 - - - +
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Residues in contact with PRO 387 (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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384B GLY 5.1 0.4 - - - +
385B MET* 4.4 0.7 - - - -
386B PHE* 1.4 92.0 - - + +
388B GLN* 1.3 85.0 + - - +
390B MET* 3.6 6.5 + - + +
391B LYS* 3.2 22.3 + - - +
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Residues in contact with GLN 388 (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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380B GLN* 3.3 25.9 + - - +
385B MET* 3.2 38.1 - - + +
387B PRO* 1.3 88.2 - - - +
389B ALA* 1.3 67.5 + - - +
391B LYS* 3.3 8.4 + - - +
392B ASN* 3.1 21.9 + - - +
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLY 3.4 20.6 - - - +
380B GLN* 3.4 12.0 - - + +
381B LEU* 3.5 22.9 - - + +
385B MET 2.9 19.6 + - - +
386B PHE* 3.7 4.9 - - - +
388B GLN* 1.3 74.6 - - - +
390B MET* 1.3 53.8 + - - +
392B ASN* 3.1 2.4 + - - +
393B LEU* 2.7 41.2 + - + +
421B CYS* 4.1 6.7 - - - -
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Residues in contact with MET 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B PHE 2.9 18.4 + - - +
387B PRO* 3.8 7.4 - - + +
389B ALA* 1.3 74.6 - - - +
391B LYS* 1.3 56.7 + - - +
393B LEU* 3.8 2.2 - - - -
394B ARG* 2.9 35.7 + - + +
418B LEU* 3.8 24.9 - - - +
421B CYS* 3.5 44.6 - - + +
422B ASP* 3.6 17.7 - - + +
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Residues in contact with LYS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B PRO 3.2 12.7 + - - +
388B GLN* 3.6 9.6 - - - +
390B MET* 1.3 77.5 - - - +
392B ASN* 1.3 60.6 + - - +
394B ARG* 3.8 5.4 - - - +
395B LEU* 3.0 27.4 + - - +
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Residues in contact with ASN 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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355B MET* 3.0 29.3 - - - +
373B VAL* 3.1 21.3 - - + +
376B VAL* 4.0 8.0 - - - +
377B GLY* 4.0 10.8 - - - -
380B GLN* 2.8 36.0 + - - +
388B GLN* 3.1 14.1 + - - +
389B ALA 3.8 2.5 - - - +
391B LYS* 1.3 75.8 - - - +
393B LEU* 1.3 60.2 + - - +
395B LEU* 3.1 7.7 + - - +
396B ALA* 2.8 27.5 + - - +
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Residues in contact with LEU 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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374B MET* 4.0 9.9 - - - +
377B GLY* 3.7 30.7 - - - +
378B LYS* 3.8 4.9 - - - +
381B LEU* 4.5 6.1 - - + -
389B ALA* 2.7 28.3 + - + +
390B MET* 4.0 2.9 - - - +
392B ASN* 1.3 70.8 - - - +
394B ARG* 1.3 56.6 + - - +
396B ALA* 3.4 6.2 + - - +
397B PHE* 3.0 27.0 + - - +
414B LEU* 3.9 21.3 - - + +
417B LEU* 3.9 39.7 - - + +
418B LEU* 3.7 19.9 - - + +
421B CYS* 4.1 17.3 - - + -
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B MET* 2.9 21.6 + - + +
391B LYS* 3.8 5.8 - - - +
393B LEU* 1.3 74.1 - - - +
395B LEU* 1.3 59.0 + - - +
397B PHE* 3.4 6.0 + - - +
398B ASP* 3.0 37.3 + - - +
418B LEU* 3.9 11.7 - - + +
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Residues in contact with LEU 395 (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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355B MET* 5.0 3.1 - - + -
369B ARG* 3.7 27.6 - - - +
373B VAL* 4.0 18.2 - - + -
391B LYS 3.0 18.4 + - - +
392B ASN* 3.1 14.8 + - - +
394B ARG* 1.3 72.7 - - - +
396B ALA* 1.3 65.7 + - - +
398B ASP* 3.2 13.8 + - + +
399B ILE* 3.0 38.0 + - + +
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Residues in contact with ALA 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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370B GLY 3.7 10.3 - - - +
373B VAL* 3.7 5.9 - - + +
374B MET* 3.6 37.7 - - + +
392B ASN 2.8 19.5 + - - +
393B LEU 3.6 5.8 - - - +
395B LEU* 1.3 71.4 - - - +
397B PHE* 1.3 53.4 + - - +
399B ILE* 3.2 4.2 + - - +
400B MET* 2.7 39.8 + - - +
414B LEU* 3.7 11.4 - - + -
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Residues in contact with PHE 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LEU 3.0 15.0 + - - +
394B ARG* 3.6 9.6 - - - +
395B LEU 3.2 0.2 - - - -
396B ALA* 1.3 76.1 - - - +
398B ASP* 1.3 64.7 + - - +
401B ARG* 2.8 62.9 + - + +
411B ILE* 4.3 20.6 - - + -
414B LEU* 3.5 12.3 - - + +
415B ILE* 4.1 25.8 - - + -
418B LEU* 4.1 23.1 - - + -
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Residues in contact with ASP 398 (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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365B SER* 5.1 1.2 + - - -
394B ARG* 3.0 24.0 + - - +
395B LEU* 3.2 18.4 + - + +
397B PHE* 1.3 84.9 - - - +
399B ILE* 1.3 62.7 + - + +
401B ARG* 3.3 30.9 + - - +
402B VAL* 4.2 4.9 + - - +
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Residues in contact with ILE 399 (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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364B GLY 4.7 7.4 - - - +
365B SER* 4.3 8.2 - - - +
366B HIS 3.5 36.1 - - - +
369B ARG* 3.9 41.7 - - + +
370B GLY* 3.6 18.6 - - - -
373B VAL* 4.4 3.8 - - + -
395B LEU* 3.0 33.3 + - + +
396B ALA* 3.8 3.8 - - - +
398B ASP* 1.3 77.1 - - + +
400B MET* 1.3 59.9 + - - +
402B VAL* 3.0 22.0 + - - +
403B THR* 3.0 16.2 + - + +
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Residues in contact with MET 400 (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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370B GLY* 3.6 38.4 - - - +
371B VAL* 4.2 2.5 - - - -
374B MET* 4.0 14.6 - - - +
396B ALA 2.7 19.8 + - - +
399B ILE* 1.3 67.7 - - - +
401B ARG* 1.3 59.9 + - - +
402B VAL 3.1 1.6 - - - -
403B THR* 3.3 8.1 - - - +
404B HIS* 2.9 49.7 + - + +
405B GLY 2.9 9.2 + - - -
410B LEU* 3.7 43.5 - - + +
411B ILE* 3.8 13.7 - - + +
414B LEU* 3.9 19.1 - - + -
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Residues in contact with ARG 401 (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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26B PRO* 4.6 9.3 + - - +
27B GLY* 4.4 6.8 - - - +
397B PHE* 2.8 60.5 + - + +
398B ASP* 3.3 24.3 + - - +
400B MET* 1.3 72.5 - - - +
402B VAL* 1.3 80.9 + - - +
405B GLY* 3.6 16.4 - - - +
411B ILE* 4.0 8.8 - - + +
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Residues in contact with VAL 402 (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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26B PRO* 4.2 14.6 - - + -
27B GLY* 3.4 31.8 - - - +
224B ARG* 3.3 24.7 - - - +
225B ALA 3.9 0.8 - - - +
226B VAL* 3.8 19.3 - - + +
365B SER* 3.7 29.2 - - - +
398B ASP 4.3 4.7 - - - +
399B ILE 3.0 8.9 + - - +
401B ARG* 1.3 105.5 - - - +
403B THR* 1.3 59.3 + - - +
404B HIS 3.5 0.2 - - - -
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Residues in contact with THR 403 (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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213B SER* 5.0 6.8 + - - +
215B VAL* 3.5 20.8 + - - +
224B ARG* 3.8 9.6 - - - +
226B VAL* 4.4 7.9 - - + -
365B SER* 3.5 31.4 - - - +
366B HIS 3.6 2.0 - - - +
367B PRO* 3.5 38.9 - - + +
399B ILE* 3.0 11.1 + - + +
400B MET* 3.3 13.2 - - - +
402B VAL* 1.3 76.2 - - - +
404B HIS* 1.3 81.1 + - - +
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Residues in contact with HIS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ALA 5.3 0.4 + - - -
190B MET* 4.4 1.4 - - - +
215B VAL* 3.5 26.4 - - + +
222B LEU* 3.8 4.5 - - - +
224B ARG* 2.8 27.3 + - - -
367B PRO* 3.6 32.3 - - + -
371B VAL* 3.8 16.4 - - + +
400B MET* 2.9 35.3 + - + +
403B THR* 1.3 104.1 + - - +
405B GLY* 1.3 62.2 + - - +
408B HIS* 3.6 36.9 + + + +
410B LEU* 3.9 7.2 - - + +
411B ILE* 4.2 8.1 - - + -
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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