Contacts of the helix formed by residues 373 - 407 (chain B) in PDB entry 4RNP
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 373 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B GLU* 3.8 23.8 - - - +
374B LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ALA* 3.8 29.2 - - - +
375B THR* 3.8 28.0 - - - +
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Residues in contact with THR 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 3.8 25.1 - - - +
376B ALA* 3.8 29.2 - - - +
378B LYS* 4.7 13.9 - - - +
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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
----------------------------------------------------------
375B THR* 3.8 29.6 - - - +
377B TRP* 3.8 26.7 - - - +
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Residues in contact with TRP 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ALA* 3.8 25.1 - - - +
378B LYS* 3.8 29.2 - - - +
380B ALA* 4.6 16.8 - - - +
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Residues in contact with LYS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B THR* 4.7 17.7 - - - +
377B TRP* 3.8 26.5 - - - +
379B ARG* 3.8 28.9 - - - +
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Residues in contact with ARG 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LYS* 3.8 29.4 - - - +
380B ALA* 3.8 26.7 - - - +
382B ALA* 4.6 16.6 - - - +
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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
----------------------------------------------------------
377B TRP* 4.6 16.2 - - - +
379B ARG* 3.8 29.2 - - - +
381B ALA* 3.8 26.0 - - - +
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ALA* 3.8 27.6 - - - +
382B ALA* 3.8 28.7 - - - +
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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
----------------------------------------------------------
379B ARG* 4.6 16.4 - - - +
381B ALA* 3.8 28.9 - - - +
383B ALA* 3.8 27.4 - - - +
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Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ALA* 3.8 29.4 - - - +
384B VAL* 3.8 27.4 - - - +
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ALA* 3.8 24.7 - - - +
385B TYR* 3.8 29.4 - - - +
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Residues in contact with TYR 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 3.8 29.6 - - - +
386B ARG* 3.8 26.0 - - - +
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Residues in contact with ARG 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B TYR* 3.8 28.0 - - - +
387B LYS* 3.8 26.0 - - - +
389B LYS* 4.5 15.7 - - - +
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Residues in contact with LYS 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ARG* 3.8 27.6 - - - +
388B ASP* 3.8 29.4 - - - +
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Residues in contact with ASP 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LYS* 3.8 28.7 - - - +
389B LYS* 3.8 24.5 - - - +
391B ARG* 4.4 19.1 - - - +
----------------------------------------------------------
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Residues in contact with LYS 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ARG* 4.5 19.1 - - - +
388B ASP* 3.8 24.9 - - - +
390B ALA* 3.8 28.5 - - - +
----------------------------------------------------------
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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
----------------------------------------------------------
389B LYS* 3.8 28.5 - - - +
391B ARG* 3.8 26.9 - - - +
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Residues in contact with ARG 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ASP* 4.4 16.2 - - - +
390B ALA* 3.8 29.2 - - - +
392B LYS* 3.8 28.9 - - - +
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Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ARG* 3.8 24.0 - - - +
393B SER* 3.8 29.6 - - - +
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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
----------------------------------------------------------
127B THR* 4.1 26.2 - - - +
392B LYS* 3.8 29.2 - - - +
394B ARG* 3.8 26.2 - - - +
396B ILE* 4.5 18.4 - - - +
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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
----------------------------------------------------------
354B ALA* 4.6 16.6 - - - +
393B SER* 3.8 29.2 - - - +
395B ARG* 3.8 23.8 - - - +
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Residues in contact with ARG 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ARG* 3.8 26.9 - - - +
396B ILE* 3.8 28.9 - - - +
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Residues in contact with ILE 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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393B SER* 4.5 14.4 - - - +
395B ARG* 3.8 28.5 - - - +
397B SER* 3.8 25.1 - - - +
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Residues in contact with SER 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ILE* 3.8 28.7 - - - +
398B LEU* 3.8 27.6 - - - +
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B SER* 3.8 24.2 - - - +
399B GLU* 3.8 29.2 - - - +
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Residues in contact with GLU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LEU* 3.8 28.9 - - - +
400B PHE* 3.8 26.9 - - - +
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Residues in contact with PHE 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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399B GLU* 3.8 29.2 - - - +
401B MET* 3.8 25.1 - - - +
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Residues in contact with MET 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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400B PHE* 3.8 26.2 - - - +
402B LEU* 3.8 28.3 - - - +
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Residues in contact with LEU 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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401B MET* 3.8 27.6 - - - +
403B GLU* 3.8 29.4 - - - +
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Residues in contact with GLU 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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402B LEU* 3.8 28.9 - - - +
404B GLN* 3.8 24.5 - - - +
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Residues in contact with GLN 404 (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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403B GLU* 3.8 29.6 - - - +
405B ALA* 3.8 27.6 - - - +
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Residues in contact with ALA 405 (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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404B GLN* 3.8 26.2 - - - +
406B ASN* 3.8 29.6 - - - +
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Residues in contact with ASN 406 (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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405B ALA* 3.8 29.4 - - - +
407B LYS* 3.8 24.2 - - - +
409B ALA* 4.6 12.3 - - - +
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Residues in contact with LYS 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ASN* 3.8 26.9 - - - +
408B PHE* 3.8 28.9 - - - +
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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