Contacts of the helix formed by residues 351 - 369 (chain A) in PDB entry 4P22
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 ASN 351 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A ARG* 3.0 58.5 + - + +
349A PRO 3.0 3.9 - - - +
350A ARG* 1.3 79.9 + - - +
352A ASP* 1.3 57.8 + - - +
353A GLU* 2.9 27.6 + - - +
354A ASP* 3.2 26.9 + - - +
355A ALA 3.4 7.4 + - - -
388A TYR* 3.8 11.2 - - - -
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Residues in contact with ASP 352 (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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350A ARG 4.1 1.1 - - - +
351A ASN* 1.3 71.4 - - - +
353A GLU* 1.3 72.7 + - - +
355A ALA* 4.0 3.2 - - - +
356A ALA* 3.3 23.7 + - - +
384A ARG* 6.2 0.2 - - - -
388A TYR* 3.3 24.9 + - - +
258B GLU* 4.1 25.5 - - - +
261B GLY* 3.9 18.3 - - - -
262B ASN* 3.2 23.7 + - - +
283B PHE* 5.8 1.4 - - - -
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Residues in contact with GLU 353 (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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348A ARG* 6.1 0.2 - - - +
351A ASN* 2.9 13.6 + - - +
352A ASP* 1.3 92.4 + - - +
354A ASP* 1.3 62.4 + - - +
355A ALA 3.1 1.6 - - - -
356A ALA* 3.0 10.7 + - - +
357A GLU* 2.9 28.5 + - - +
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Residues in contact with ASP 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 3.6 15.8 - - + -
345A ARG* 2.7 33.7 + - - -
347A PRO* 3.6 19.4 - - + +
348A ARG* 3.1 33.5 + - - +
351A ASN* 3.2 22.1 + - - +
353A GLU* 1.3 77.2 - - - +
355A ALA* 1.3 57.9 + - - +
357A GLU* 3.3 8.7 + - - +
358A LEU* 2.9 26.7 + - - +
387A ALA* 4.4 1.7 - - - +
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Residues in contact with ALA 355 (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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351A ASN 3.4 3.9 + - - +
352A ASP 4.1 2.7 - - - +
353A GLU 3.1 0.4 - - - -
354A ASP* 1.3 77.5 - - - +
356A ALA* 1.3 61.9 + - - +
358A LEU* 3.8 2.1 - - - +
359A VAL* 3.1 28.2 + - - +
384A ARG* 3.9 16.5 - - + +
387A ALA* 3.5 25.2 - - + +
388A TYR* 3.8 36.8 - - + +
261B GLY 5.4 0.2 - - - +
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Residues in contact with ALA 356 (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 ASP 3.3 14.5 + - - +
353A GLU* 3.0 17.1 + - - +
355A ALA* 1.3 74.9 - - - +
357A GLU* 1.3 66.3 + - - +
359A VAL* 3.1 8.4 + - - +
360A ALA* 3.0 22.2 + - - +
384A ARG* 5.5 2.2 - - - +
261B GLY* 6.5 0.7 - - - -
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Residues in contact with GLU 357 (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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339A PHE* 3.7 14.7 - - + -
342A GLN* 4.6 6.8 - - - +
343A HIS* 2.7 39.6 + - - -
353A GLU 2.9 12.0 + - - +
354A ASP* 3.5 13.4 - - - +
356A ALA* 1.3 77.0 - - - +
358A LEU* 1.3 58.3 + - - +
360A ALA* 3.0 10.5 + - + +
361A LEU* 2.9 40.1 + - + +
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Residues in contact with LEU 358 (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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332A GLY 4.7 1.3 - - - +
335A ALA* 3.7 16.4 - - + +
336A LEU* 3.7 34.3 - - + -
339A PHE* 3.9 17.6 - - + -
347A PRO* 4.6 1.3 - - + -
354A ASP 2.9 16.6 + - - +
355A ALA 3.8 5.4 - - - +
356A ALA 3.3 0.2 - - - -
357A GLU* 1.3 74.3 - - - +
359A VAL* 1.3 57.7 + - - +
361A LEU* 3.2 5.3 + - + +
362A ALA* 2.8 27.9 + - - +
383A ILE* 3.5 32.8 - - + +
386A LEU* 4.1 18.6 - - + -
387A ALA* 3.8 24.0 - - + +
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Residues in contact with VAL 359 (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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355A ALA 3.1 19.3 + - - +
356A ALA* 3.1 11.2 + - - +
358A LEU* 1.3 73.3 - - - +
360A ALA* 1.3 60.9 + - - +
362A ALA* 3.2 2.5 + - + +
363A GLN* 2.8 41.1 + - + +
378A LEU* 5.6 0.4 - - + -
380A GLU* 3.8 41.5 - - + +
383A ILE* 3.9 18.6 - - + -
384A ARG* 3.5 27.6 - - + +
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Residues in contact with ALA 360 (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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356A ALA 3.0 12.4 + - - +
357A GLU* 3.3 12.6 - - + +
359A VAL* 1.3 76.7 - - - +
361A LEU* 1.3 64.9 + - + +
363A GLN* 3.3 8.3 + - - +
364A ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 361 (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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335A ALA* 3.6 32.1 - - + +
338A GLN* 3.5 32.1 - - + +
339A PHE* 3.7 34.1 - - + +
342A GLN* 6.4 0.4 - - + -
357A GLU* 2.9 28.2 + - + +
358A LEU* 3.5 8.3 - - - +
360A ALA* 1.3 75.1 - - + +
362A ALA* 1.3 61.3 + - - +
364A ALA* 3.3 6.6 + - + +
365A VAL* 2.9 33.6 + - - +
368A ARG* 4.6 0.3 + - - -
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Residues in contact with ALA 362 (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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331A ILE* 3.5 13.3 - - + +
335A ALA* 3.6 11.8 - - + +
358A LEU 2.8 19.6 + - - +
359A VAL 3.2 4.9 + - - +
361A LEU* 1.3 74.1 - - - +
363A GLN* 1.3 52.7 - - - +
365A VAL 3.2 0.9 + - - -
366A ASN* 2.7 35.2 + - - +
378A LEU* 3.6 20.6 - - + -
383A ILE* 3.8 25.8 - - + -
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Residues in contact with GLN 363 (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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359A VAL* 2.8 30.4 + - + +
360A ALA* 3.6 8.5 - - - +
361A LEU 3.3 0.2 - - - -
362A ALA* 1.3 76.4 - - - +
364A ALA* 1.3 58.1 + - - +
366A ASN* 3.3 11.6 + - - +
367A ALA* 2.8 29.7 + - - +
378A LEU* 3.1 25.5 - - + +
380A GLU* 2.2 37.0 + - - -
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Residues in contact with ALA 364 (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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360A ALA 3.1 16.3 + - - +
361A LEU* 3.8 6.1 - - + +
363A GLN* 1.3 73.3 - - - +
365A VAL* 1.3 64.7 + - - +
367A ALA* 3.1 8.0 + - - +
368A ARG* 3.0 51.1 + - - +
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Residues in contact with VAL 365 (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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331A ILE* 3.6 27.8 - - + +
334A GLN* 3.5 38.1 - - + +
335A ALA* 4.1 14.4 - - - +
338A GLN* 4.3 7.2 - - - +
361A LEU 2.9 24.7 + - - +
362A ALA 3.5 4.7 - - - +
364A ALA* 1.3 75.9 - - - +
366A ASN* 1.3 61.3 + - - +
368A ARG* 3.4 22.9 + - - +
369A ALA* 3.1 23.8 + - + +
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Residues in contact with ASN 366 (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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331A ILE* 3.7 20.5 - - + +
362A ALA 2.7 20.3 + - - +
363A GLN* 3.5 13.4 + - - +
364A ALA 3.2 0.2 - - - -
365A VAL* 1.3 74.4 - - - +
367A ALA* 1.3 62.0 + - - +
369A ALA* 3.2 11.5 + - - +
374A GLN* 3.1 24.2 + - - +
375A GLN* 2.8 47.8 + - - -
376A ASN 5.2 0.6 + - - -
378A LEU* 3.9 19.9 - - + +
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Residues in contact with ALA 367 (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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363A GLN 2.8 20.5 + - - +
364A ALA* 3.1 10.1 + - - +
366A ASN* 1.3 72.9 - - - +
368A ARG* 1.3 61.5 + - + +
369A ALA 4.4 0.3 - - - +
374A GLN* 3.3 17.8 + - - +
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Residues in contact with ARG 368 (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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334A GLN* 5.9 2.4 - - - +
338A GLN* 3.9 25.9 + - - +
361A LEU 4.6 0.4 + - - -
364A ALA* 3.0 45.1 + - - +
365A VAL* 3.8 19.2 - - - +
366A ASN 3.2 0.4 - - - -
367A ALA* 1.3 79.7 - - + +
369A ALA* 1.3 64.3 + - - +
370A LEU* 3.8 8.0 + - - +
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Residues in contact with ALA 369 (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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331A ILE* 5.4 1.6 - - + -
365A VAL* 3.1 18.2 + - + +
366A ASN* 3.2 12.4 + - - +
367A ALA 4.4 0.3 - - - +
368A ARG* 1.3 80.4 - - - +
370A LEU* 1.3 70.7 + - - +
371A PRO* 4.6 0.3 - - - +
373A VAL* 4.2 23.1 - - + -
374A GLN* 3.5 21.7 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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