Contacts of the helix formed by residues 373 - 407 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C GLU* 3.8 23.8 - - - +
374C LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C ALA* 3.8 29.4 - - - +
375C THR* 3.8 28.0 - - - +
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Residues in contact with THR 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C LEU* 3.8 24.2 - - - +
376C ALA* 3.8 28.5 - - - +
378C LYS* 4.7 14.1 - - - +
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Residues in contact with ALA 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C THR* 3.8 29.2 - - - +
377C TRP* 3.8 26.7 - - - +
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Residues in contact with TRP 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ALA* 3.8 24.9 - - - +
378C LYS* 3.8 28.9 - - - +
380C ALA* 4.6 17.0 - - - +
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Residues in contact with LYS 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C THR* 4.7 17.0 - - - +
377C TRP* 3.8 26.0 - - - +
379C ARG* 3.8 28.9 - - - +
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Residues in contact with ARG 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C LYS* 3.8 28.7 - - - +
380C ALA* 3.8 26.0 - - - +
382C ALA* 4.6 16.8 - - - +
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Residues in contact with ALA 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C TRP* 4.6 16.2 - - - +
379C ARG* 3.8 28.9 - - - +
381C ALA* 3.8 25.4 - - - +
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Residues in contact with ALA 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C ALA* 3.8 26.2 - - - +
382C ALA* 3.8 29.6 - - - +
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Residues in contact with ALA 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C ARG* 4.6 16.4 - - - +
381C ALA* 3.8 28.7 - - - +
383C ALA* 3.8 27.1 - - - +
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Residues in contact with ALA 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C ALA* 3.8 28.9 - - - +
384C VAL* 3.8 26.9 - - - +
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Residues in contact with VAL 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C ALA* 3.8 25.6 - - - +
385C TYR* 3.8 28.9 - - - +
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Residues in contact with TYR 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C VAL* 3.8 29.2 - - - +
386C ARG* 3.8 26.9 - - - +
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Residues in contact with ARG 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C TYR* 3.8 28.0 - - - +
387C LYS* 3.8 26.0 - - - +
389C LYS* 4.5 16.4 - - - +
----------------------------------------------------------
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Residues in contact with LYS 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C ARG* 3.8 27.6 - - - +
388C ASP* 3.8 28.9 - - - +
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Residues in contact with ASP 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C LYS* 3.8 28.0 - - - +
389C LYS* 3.8 24.5 - - - +
391C ARG* 4.4 18.6 - - - +
----------------------------------------------------------
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Residues in contact with LYS 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C ARG* 4.5 18.2 - - - +
388C ASP* 3.8 25.1 - - - +
390C ALA* 3.8 29.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C LYS* 3.8 28.9 - - - +
391C ARG* 3.8 26.0 - - - +
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Residues in contact with ARG 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ASP* 4.4 16.2 - - - +
390C ALA* 3.8 28.3 - - - +
392C LYS* 3.8 28.5 - - - +
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Residues in contact with LYS 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C ARG* 3.8 23.3 - - - +
393C SER* 3.8 29.4 - - - +
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Residues in contact with SER 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C THR* 4.1 25.4 - - - +
392C LYS* 3.8 28.9 - - - +
394C ARG* 3.8 27.4 - - - +
396C ILE* 4.5 18.2 - - - +
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Residues in contact with ARG 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C ALA* 4.6 17.3 - - - +
393C SER* 3.8 29.2 - - - +
395C ARG* 3.8 23.8 - - - +
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Residues in contact with ARG 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ARG* 3.8 28.0 - - - +
396C ILE* 3.8 28.5 - - - +
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Residues in contact with ILE 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C SER* 4.5 14.6 - - - +
395C ARG* 3.8 28.7 - - - +
397C SER* 3.8 25.4 - - - +
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Residues in contact with SER 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C ILE* 3.8 28.7 - - - +
398C LEU* 3.8 26.9 - - - +
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Residues in contact with LEU 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397C SER* 3.8 25.1 - - - +
399C GLU* 3.8 29.2 - - - +
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Residues in contact with GLU 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C LEU* 3.8 28.0 - - - +
400C PHE* 3.8 28.0 - - - +
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Residues in contact with PHE 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C GLU* 3.8 29.2 - - - +
401C MET* 3.8 25.4 - - - +
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Residues in contact with MET 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C PHE* 3.8 26.2 - - - +
402C LEU* 3.8 28.5 - - - +
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Residues in contact with LEU 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C MET* 3.8 27.8 - - - +
403C GLU* 3.8 29.8 - - - +
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Residues in contact with GLU 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C LEU* 3.8 29.4 - - - +
404C GLN* 3.8 24.7 - - - +
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Residues in contact with GLN 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403C GLU* 3.8 28.3 - - - +
405C ALA* 3.8 27.6 - - - +
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Residues in contact with ALA 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C GLN* 3.8 26.0 - - - +
406C ASN* 3.8 28.9 - - - +
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Residues in contact with ASN 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C ALA* 3.8 28.5 - - - +
407C LYS* 3.8 24.5 - - - +
409C ALA* 4.6 12.6 - - - +
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Residues in contact with LYS 407 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C ASN* 3.8 26.9 - - - +
408C PHE* 3.8 28.7 - - - +
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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