Contacts of the helix formed by residues 419 - 438 (chain A) in PDB entry 2P0F
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 HIS 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A ASN* 4.0 1.8 - - - -
417A SER* 3.0 17.7 + - - +
418A ASP* 1.3 92.1 + - + +
420A GLU* 1.3 66.5 + - - +
421A THR* 3.3 2.7 - - - +
422A GLU* 3.0 30.6 + - + +
423A LEU* 3.1 9.9 + - - +
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Residues in contact with GLU 420 (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 ARG* 3.3 28.4 + - - +
401A ASN* 3.5 32.4 - - + +
418A ASP 3.7 1.4 + - - -
419A HIS* 1.3 70.7 - - - +
421A THR* 1.3 59.0 + - - +
423A LEU* 3.3 2.4 + - - +
424A ARG* 2.8 62.2 + - + +
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Residues in contact with THR 421 (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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419A HIS* 3.3 1.9 - - - -
420A GLU* 1.3 79.9 - - - +
422A GLU* 1.3 66.4 + - - +
424A ARG* 3.5 25.5 + - + +
425A ALA* 3.1 23.9 + - + +
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Residues in contact with GLU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS* 4.4 13.6 + - - -
329A LEU* 5.3 2.2 - - + -
417A SER* 4.2 8.7 - - - +
419A HIS* 3.0 28.8 + - + +
421A THR* 1.3 83.1 - - - +
423A LEU* 1.3 64.2 + - - +
425A ALA* 3.2 7.4 + - - +
426A TRP* 3.2 37.6 + - + -
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Residues in contact with LEU 423 (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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329A LEU* 4.2 13.5 - - + -
401A ASN* 2.8 48.5 - - + +
402A VAL* 3.3 9.9 - - - +
403A LEU* 3.8 33.0 - - + -
415A LEU* 3.9 18.8 - - + +
416A GLN* 4.1 6.3 - - - +
417A SER* 4.1 10.9 - - - +
419A HIS 3.1 10.0 + - - +
420A GLU 4.0 5.2 - - - +
422A GLU* 1.3 79.2 - - - +
424A ARG* 1.3 61.5 + - - +
426A TRP* 3.1 8.2 + - + +
427A HIS* 2.9 22.6 + - - +
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Residues in contact with ARG 424 (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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420A GLU* 2.8 63.0 + - + +
421A THR* 3.5 28.1 + - - +
423A LEU* 1.3 73.3 - - - +
425A ALA* 1.3 63.5 + - - +
427A HIS* 3.2 9.1 + - - +
428A ARG* 3.0 40.0 + - + +
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Residues in contact with ALA 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS* 3.7 23.5 - - - +
421A THR* 3.1 18.5 + - + +
422A GLU* 3.2 8.5 + - - +
424A ARG* 1.3 77.1 - - - +
426A TRP* 1.3 57.8 + - - +
428A ARG* 3.3 7.4 + - - +
429A ALA* 2.9 31.0 + - - +
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Residues in contact with TRP 426 (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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325A LYS* 3.6 34.8 - - + +
326A SER* 3.6 12.7 + - - -
327A GLY* 3.5 33.2 - - - -
328A LEU 5.3 0.2 + - - -
329A LEU* 3.6 40.6 - - + +
350A VAL* 3.6 37.9 - - + -
352A LEU* 3.9 22.0 - - + -
357A LEU* 4.2 4.3 - - + -
403A LEU* 4.6 4.9 - - + -
415A LEU* 5.1 0.7 - - + -
422A GLU* 3.2 31.1 + - - -
423A LEU* 3.1 17.1 + - + +
425A ALA* 1.3 72.6 - - - +
427A HIS* 1.3 61.3 + - - +
429A ALA* 3.3 0.5 + - - +
430A LEU* 2.8 50.4 + - + +
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Residues in contact with HIS 427 (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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390A LEU* 3.6 27.0 - - + +
391A ALA* 5.0 12.1 - - - -
392A HIS* 5.1 8.2 + - + +
403A LEU* 3.3 36.7 - - + +
423A LEU 2.9 11.9 + - - +
424A ARG* 3.4 12.3 - - + +
426A TRP* 1.3 78.3 - - - +
428A ARG* 1.3 63.5 + - + +
431A ARG* 3.1 51.2 + - - +
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Residues in contact with ARG 428 (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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424A ARG* 3.0 30.3 + - + +
425A ALA* 3.8 9.4 - - - +
427A HIS* 1.3 77.0 - - + +
429A ALA* 1.3 58.8 + - - +
431A ARG* 3.4 36.0 + - - +
432A THR* 3.0 32.8 + - - +
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Residues in contact with ALA 429 (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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324A GLU* 5.8 3.1 - - + +
325A LYS* 4.0 18.8 - - + -
352A LEU* 3.9 16.6 - - + -
425A ALA 2.9 17.7 + - - +
426A TRP* 3.8 3.1 - - - +
428A ARG* 1.3 74.7 - - - +
430A LEU* 1.3 63.7 + - - +
432A THR* 3.4 6.5 + - - -
433A VAL* 3.0 28.6 + - - +
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Residues in contact with LEU 430 (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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352A LEU* 4.0 28.3 - - + -
357A LEU* 4.1 16.2 - - + -
385A LEU* 4.3 11.7 - - + -
390A LEU* 3.6 18.2 - - + -
403A LEU* 3.9 21.5 - - + -
405A ILE* 3.6 31.4 - - + -
415A LEU* 4.0 10.1 - - + -
426A TRP* 2.8 32.9 + - + +
429A ALA* 1.3 70.8 - - - +
431A ARG* 1.3 67.3 + - - +
433A VAL* 3.3 2.8 + - - +
434A ILE* 2.9 31.9 + - + +
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Residues in contact with ARG 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 3.7 12.7 - - + +
427A HIS* 3.1 44.4 + - - +
428A ARG* 3.7 51.9 - - - +
429A ALA 3.2 0.2 - - - -
430A LEU* 1.3 77.7 - - - +
432A THR* 1.3 59.7 + - - +
434A ILE* 3.3 6.0 + - - +
435A GLU* 2.9 57.3 + - + +
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Residues in contact with THR 432 (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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324A GLU* 5.3 1.3 - - - +
428A ARG* 3.0 18.1 + - - +
429A ALA* 3.6 7.8 - - - +
430A LEU 3.2 0.2 - - - -
431A ARG* 1.3 79.0 - - - +
433A VAL* 1.3 63.7 + - - +
435A GLU* 3.8 10.6 + - - +
436A ARG* 3.1 64.6 + - + +
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Residues in contact with VAL 433 (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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324A GLU* 3.8 27.8 - - + +
352A LEU* 3.8 10.8 - - + -
353A THR 3.4 27.6 - - - +
354A GLY* 3.5 20.4 - - - +
385A LEU* 3.9 20.4 - - + -
429A ALA 3.0 20.4 + - - +
430A LEU 3.8 3.4 - - - +
432A THR* 1.3 75.3 - - - +
434A ILE* 1.3 63.5 + - - +
436A ARG* 3.3 20.6 + - - +
437A LEU* 3.4 18.5 + - + +
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Residues in contact with ILE 434 (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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385A LEU* 3.9 38.1 - - + +
387A GLY* 5.0 4.1 + - - +
388A ALA* 3.4 40.2 - - + +
389A ALA 5.0 0.2 - - - -
390A LEU* 3.8 32.3 - - + +
430A LEU* 2.9 25.1 + - + +
431A ARG* 3.8 4.7 - - - +
433A VAL* 1.3 77.7 - - - +
435A GLU* 1.3 64.5 + - + +
437A LEU* 3.1 18.7 + - - +
438A VAL* 3.6 11.8 + - + +
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Residues in contact with GLU 435 (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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431A ARG* 2.9 49.9 + - + +
432A THR* 3.8 9.8 + - - +
434A ILE* 1.3 74.3 - - + +
436A ARG* 1.3 63.9 + - + +
437A LEU 3.2 0.9 + - - -
438A VAL* 3.3 25.8 + - + +
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Residues in contact with ARG 436 (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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324A GLU* 3.1 36.6 + - - -
354A GLY* 6.1 1.9 - - - +
432A THR* 3.1 41.7 + - + +
433A VAL* 3.7 12.3 - - - +
434A ILE 3.3 0.2 - - - -
435A GLU* 1.3 77.3 - - + +
437A LEU* 1.3 62.4 + - + +
438A VAL 3.4 3.0 - - - -
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Residues in contact with LEU 437 (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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320A SER 6.3 0.4 - - - +
354A GLY 3.4 26.7 - - - +
355A ASN* 3.9 15.3 - - + -
385A LEU* 3.8 13.5 - - + +
386A ARG* 3.7 67.1 - - + +
387A GLY 5.1 0.4 - - - +
433A VAL* 3.4 15.0 + - + +
434A ILE* 3.1 10.2 + - - +
436A ARG* 1.3 79.4 - - + +
438A VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLY* 6.0 5.8 - - - +
434A ILE* 3.9 13.2 - - + +
435A GLU* 3.3 21.4 + - + +
436A ARG 4.8 2.7 - - - -
437A LEU* 1.3 83.0 - - - +
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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
------------------------------------------------------------
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