Contacts of the helix formed by residues 373 - 407 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A GLU* 3.8 24.0 - - - +
374A LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A ALA* 3.8 29.4 - - - +
375A THR* 3.8 28.0 - - - +
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Residues in contact with THR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 3.8 24.9 - - - +
376A ALA* 3.8 28.7 - - - +
378A LYS* 4.7 14.6 - - - +
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Residues in contact with ALA 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A THR* 3.8 29.2 - - - +
377A TRP* 3.8 27.1 - - - +
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Residues in contact with TRP 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ALA* 3.8 25.1 - - - +
378A LYS* 3.8 29.2 - - - +
380A ALA* 4.6 17.0 - - - +
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Residues in contact with LYS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A THR* 4.7 17.7 - - - +
377A TRP* 3.8 26.2 - - - +
379A ARG* 3.8 29.2 - - - +
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Residues in contact with ARG 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LYS* 3.8 29.2 - - - +
380A ALA* 3.8 26.7 - - - +
382A ALA* 4.6 16.4 - - - +
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TRP* 4.6 16.6 - - - +
379A ARG* 3.8 28.9 - - - +
381A ALA* 3.8 25.8 - - - +
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA* 3.8 26.7 - - - +
382A ALA* 3.8 28.9 - - - +
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ARG* 4.6 16.2 - - - +
381A ALA* 3.8 28.9 - - - +
383A ALA* 3.8 27.6 - - - +
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Residues in contact with ALA 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ALA* 3.8 29.2 - - - +
384A VAL* 3.8 26.2 - - - +
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ALA* 3.8 25.4 - - - +
385A TYR* 3.8 29.4 - - - +
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Residues in contact with TYR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A VAL* 3.8 29.2 - - - +
386A ARG* 3.8 26.2 - - - +
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A TYR* 3.8 28.9 - - - +
387A LYS* 3.8 25.4 - - - +
389A LYS* 4.5 15.9 - - - +
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Residues in contact with LYS 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A ARG* 3.8 28.3 - - - +
388A ASP* 3.8 28.5 - - - +
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Residues in contact with ASP 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LYS* 3.8 28.7 - - - +
389A LYS* 3.8 24.5 - - - +
391A ARG* 4.4 18.8 - - - +
----------------------------------------------------------
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Residues in contact with LYS 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ARG* 4.5 18.6 - - - +
388A ASP* 3.8 24.5 - - - +
390A ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LYS* 3.8 29.2 - - - +
391A ARG* 3.8 26.5 - - - +
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Residues in contact with ARG 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ASP* 4.4 16.4 - - - +
390A ALA* 3.8 28.7 - - - +
392A LYS* 3.8 28.9 - - - +
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Residues in contact with LYS 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ARG* 3.8 24.2 - - - +
393A SER* 3.8 28.3 - - - +
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Residues in contact with SER 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A THR* 4.1 26.0 - - - +
392A LYS* 3.8 29.2 - - - +
394A ARG* 3.8 27.1 - - - +
396A ILE* 4.5 18.2 - - - +
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Residues in contact with ARG 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ALA* 4.6 17.7 - - - +
393A SER* 3.8 29.2 - - - +
395A ARG* 3.8 24.2 - - - +
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Residues in contact with ARG 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A ARG* 3.8 27.6 - - - +
396A ILE* 3.8 29.8 - - - +
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Residues in contact with ILE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A SER* 4.5 15.0 - - - +
395A ARG* 3.8 28.7 - - - +
397A SER* 3.8 25.4 - - - +
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Residues in contact with SER 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ILE* 3.8 28.9 - - - +
398A LEU* 3.8 26.9 - - - +
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A SER* 3.8 24.7 - - - +
399A GLU* 3.8 28.9 - - - +
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Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LEU* 3.8 29.2 - - - +
400A PHE* 3.8 27.8 - - - +
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Residues in contact with PHE 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A GLU* 3.8 29.2 - - - +
401A MET* 3.8 24.7 - - - +
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Residues in contact with MET 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A PHE* 3.8 26.0 - - - +
402A LEU* 3.8 28.7 - - - +
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A MET* 3.8 27.6 - - - +
403A GLU* 3.8 29.4 - - - +
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Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A LEU* 3.8 29.2 - - - +
404A GLN* 3.8 24.9 - - - +
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Residues in contact with GLN 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A GLU* 3.8 28.7 - - - +
405A ALA* 3.8 26.9 - - - +
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Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A GLN* 3.8 26.2 - - - +
406A ASN* 3.8 29.4 - - - +
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Residues in contact with ASN 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A ALA* 3.8 29.6 - - - +
407A LYS* 3.8 24.0 - - - +
409A ALA* 4.6 12.8 - - - +
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Residues in contact with LYS 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A ASN* 3.8 27.4 - - - +
408A 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