Contacts of the helix formed by residues 385 - 404 (chain B) in PDB entry 3RFU
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 ALA 385 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B LEU* 5.2 0.4 - - - -
383B PRO 3.2 0.6 - - - -
384B CYS* 1.3 80.4 - - - +
386B LEU* 1.3 52.4 + - - +
387B GLY 3.0 5.4 - - - -
388B LEU* 2.7 38.0 + - + +
389B ALA* 3.3 8.8 + - - +
685B ALA* 3.9 13.9 - - + +
720B SER* 3.6 42.2 - - - +
721B SER* 4.2 6.1 - - - +
724B VAL* 4.2 7.2 - - + +
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 3.3 37.0 - - + +
151B LEU* 3.8 13.9 - - + -
152B ILE* 3.8 18.2 - - + -
336B ALA* 5.0 6.6 - - + +
340B SER* 3.8 22.4 - - - +
383B PRO* 3.5 34.4 + - + +
385B ALA* 1.3 76.8 - - - +
387B GLY* 1.3 65.4 + - - +
388B LEU 3.2 0.7 + - - -
389B ALA* 3.8 14.4 + - - +
390B THR* 4.6 3.6 + - - -
391B PRO* 5.0 1.0 - - - +
682B LEU* 4.4 16.1 - - + +
685B ALA* 3.8 16.3 - - + +
686B PHE* 3.9 8.7 - - + -
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Residues in contact with GLY 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 4.6 8.1 - - - -
198B VAL* 4.6 12.8 - - - -
201B GLY* 2.9 30.4 - - - -
202B GLN* 5.6 2.1 + - - -
384B CYS 3.6 7.4 + - - -
385B ALA 2.8 1.6 + - - -
386B LEU* 1.3 90.5 - - - +
388B LEU* 1.3 59.4 + - - +
391B PRO* 3.1 13.5 - - - +
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 3.5 42.2 - - + +
200B LEU* 3.8 26.7 - - + -
201B GLY* 3.7 15.7 - - - +
204B LEU* 4.5 9.6 - - + -
384B CYS 4.8 2.0 - - - +
385B ALA* 2.7 16.9 + - + +
387B GLY* 1.3 80.2 - - - +
389B ALA* 1.3 66.4 + - - +
391B PRO* 3.1 4.8 - - - +
392B MET* 2.9 42.9 + - + +
721B SER* 5.8 5.8 - - - +
724B VAL* 4.5 7.0 - - + -
725B ILE* 5.2 13.2 - - + -
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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
----------------------------------------------------------
385B ALA 3.3 7.5 + - - +
386B LEU* 3.8 11.4 + - - +
387B GLY 3.7 0.2 - - - -
388B LEU* 1.3 81.6 - - - +
390B THR* 1.3 68.6 + - - +
392B MET* 3.0 8.1 + - - +
393B SER* 3.1 13.4 + - - -
678B ILE* 4.8 0.7 - - - +
681B ASN* 3.5 35.4 + - + +
682B LEU* 4.0 22.4 - - + +
685B ALA* 5.2 0.2 - - + -
724B VAL* 4.1 10.7 - - + +
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Residues in contact with THR 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ARG* 4.1 16.6 - - - +
334B ARG* 5.6 10.2 - - + +
335B LEU* 5.8 1.0 + - - +
336B ALA* 4.5 17.9 + - - +
386B LEU 4.6 2.4 + - - -
389B ALA* 1.3 76.8 - - - +
391B PRO* 1.3 74.7 - - + +
393B SER* 3.1 2.4 + - - -
394B ILE* 3.0 33.4 + - + +
415B GLU* 4.5 4.7 - - - +
678B ILE* 3.9 37.3 - - + +
682B LEU* 4.7 5.9 - - - +
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Residues in contact with PRO 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLY* 4.2 7.0 - - - +
204B LEU* 3.9 25.0 - - + +
205B GLU* 4.0 18.6 - - + +
208B ALA* 5.3 3.4 - - + +
209B ARG* 4.9 5.4 - - - +
386B LEU 5.0 0.7 - - - +
387B GLY 3.1 24.7 - - - +
388B LEU* 3.1 22.0 - - - +
389B ALA 3.9 0.2 - - - +
390B THR* 1.3 96.3 - - + +
392B MET* 1.3 55.0 + - + +
394B ILE* 3.3 9.5 + - + +
395B MET* 3.0 31.6 + - - +
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Residues in contact with MET 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 4.5 16.6 - - + -
388B LEU* 2.9 41.1 + - + +
389B ALA* 3.6 2.9 - - - +
391B PRO* 1.3 73.0 - - - +
393B SER* 1.3 67.4 + - - +
395B MET* 3.4 22.9 - - + +
396B VAL* 3.0 28.1 + - - +
724B VAL* 4.6 4.3 - - + -
725B ILE* 4.0 46.4 - - + +
728B ALA* 4.0 16.7 - - + +
729B LEU* 5.4 6.5 - - + -
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Residues in contact with SER 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ALA 3.1 5.7 + - - -
390B THR 3.6 2.2 - - - -
392B MET* 1.3 75.6 - - - +
394B ILE* 1.3 60.2 + - - +
396B VAL* 3.1 10.8 - - - +
397B GLY* 3.0 25.8 + - - -
674B THR* 4.2 15.3 - - - -
677B ASN* 2.9 13.4 + - - -
678B ILE* 3.3 33.4 + - - +
681B ASN* 2.6 31.4 + - - +
728B ALA* 4.4 0.9 - - - +
731B LEU* 5.5 0.4 - - - -
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Residues in contact with ILE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ALA* 4.5 16.6 - - + +
209B ARG* 4.2 9.9 - - - +
390B THR* 3.0 23.5 + - + +
391B PRO* 3.5 9.4 - - + +
392B MET 3.1 0.2 - - - -
393B SER* 1.3 75.8 - - - +
395B MET* 1.3 66.8 + - - +
397B GLY* 3.3 1.3 + - - -
398B VAL* 3.0 40.7 + - + +
411B ALA* 3.7 26.9 - - + +
414B LEU* 4.5 9.5 - - + +
415B GLU* 4.3 18.6 - - + +
674B THR* 4.8 7.9 - - - +
678B ILE* 3.8 22.7 - - + -
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Residues in contact with MET 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 4.4 31.6 - - - +
207B LYS* 6.0 5.8 - - - +
208B ALA* 5.3 10.1 - - + +
391B PRO 3.0 19.3 + - - +
392B MET* 3.4 25.6 - - + +
394B ILE* 1.3 75.2 - - - +
396B VAL* 1.3 63.1 + - + +
398B VAL* 3.0 25.4 - - + +
399B GLY* 3.0 7.3 + - - -
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Residues in contact with VAL 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B MET 3.0 20.8 + - - +
393B SER* 3.1 14.8 - - - +
395B MET* 1.3 81.2 - - + +
397B GLY* 1.3 66.5 + - - +
399B GLY* 3.2 3.7 + - - -
400B LYS* 3.1 20.1 + - - +
728B ALA* 3.7 24.9 - - + +
729B LEU* 4.9 2.9 - - + -
731B LEU* 3.5 28.7 - - + +
732B LYS* 3.8 24.0 - - + -
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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
----------------------------------------------------------
393B SER 3.0 11.9 + - - -
394B ILE 3.7 0.4 - - - -
395B MET 3.2 0.2 - - - -
396B VAL* 1.3 80.7 - - - +
398B VAL* 1.3 59.6 + - - +
399B GLY 3.0 1.6 - - - -
400B LYS* 2.8 20.1 + - - +
401B GLY* 3.0 11.8 + - - -
414B LEU* 4.4 6.7 - - - -
670B LEU* 4.1 5.7 - - - +
674B THR* 4.1 12.8 - - - -
731B LEU* 3.9 16.2 - - - -
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Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ALA* 6.5 0.2 - - + -
394B ILE* 3.0 25.5 + - + +
395B MET* 3.0 26.7 - - - +
397B GLY* 1.3 75.0 - - - +
399B GLY* 1.3 57.2 + - - +
402B ALA* 2.8 32.2 + - - +
406B VAL 4.7 0.2 - - - +
408B ILE* 3.6 47.1 + - + +
410B ASN 5.8 0.2 - - - -
411B ALA* 5.7 0.2 - - - -
414B LEU* 4.0 9.9 - - + -
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Residues in contact with GLY 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B MET 3.0 13.8 + - - -
396B VAL* 3.5 6.5 - - - -
397B GLY 3.0 1.0 - - - -
398B VAL* 1.3 80.4 - - - +
400B LYS* 1.3 55.6 + - - +
402B ALA* 4.0 4.0 - - - +
403B GLN* 3.0 27.6 + - - +
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Residues in contact with LYS 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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396B VAL 3.1 10.7 + - - +
397B GLY* 2.8 12.1 + - - +
399B GLY* 1.3 74.9 - - - +
401B GLY* 1.3 65.8 + - - +
403B GLN* 2.8 46.0 + - - +
404B SER* 3.1 7.8 + - - -
670B LEU* 4.3 9.0 - - + -
731B LEU* 5.2 5.4 - - + +
732B LYS* 3.3 48.9 + - + +
733B ARG 4.1 1.6 - - - +
734B VAL* 3.9 33.6 - - - +
736B LEU* 4.1 20.5 - - + +
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Residues in contact with GLY 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B GLY 3.0 11.5 + - - -
398B VAL 4.3 0.4 - - - -
400B LYS* 1.3 77.1 - - - +
402B ALA* 1.3 53.8 + - - +
404B SER* 2.6 29.3 + - - -
406B VAL* 2.9 38.7 + - - -
408B ILE* 4.7 3.4 - - - -
670B LEU* 4.5 10.4 - - - +
736B LEU* 4.5 5.8 - - - -
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Residues in contact with ALA 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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398B VAL 2.8 23.1 + - - +
399B GLY* 4.1 4.9 - - - +
401B GLY* 1.3 75.0 - - - +
403B GLN* 1.3 62.1 + - - +
404B SER 3.2 0.9 + - - -
405B GLY* 3.4 8.3 + - - -
406B VAL 2.9 13.2 + - - +
407B LEU* 3.6 22.4 - - + +
408B ILE 5.5 0.7 - - - +
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Residues in contact with GLN 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B GLY 3.0 18.4 + - - +
400B LYS* 2.8 45.1 + - - +
402B ALA* 1.3 78.8 - - - +
404B SER* 1.3 56.4 + - - +
405B GLY 3.6 0.7 + - - -
734B VAL* 5.9 0.7 - - - +
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Residues in contact with SER 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LYS 3.1 2.2 + - - -
401B GLY 2.6 14.3 + - - -
403B GLN* 1.3 74.4 - - - +
405B GLY* 1.3 54.6 + - - +
406B VAL* 3.2 11.2 + - - +
666B LYS* 3.0 35.8 + - - -
734B VAL* 5.9 2.5 - - - -
736B LEU* 3.0 31.1 - - - +
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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
------------------------------------------------------------
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