Contacts of the helix formed by residues 338 - 354 (chain A) in PDB entry 4PKO
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 GLU 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A GLY* 1.3 72.5 - - - -
339A GLU* 1.3 63.5 + - - +
340A ALA* 3.8 22.1 - - + +
341A ALA* 3.9 14.4 + - + +
342A ILE* 2.9 31.2 + - - +
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Residues in contact with GLU 339 (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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337A GLY 4.0 7.5 - - - +
338A GLU* 1.3 78.9 - - - +
340A ALA* 1.3 61.2 + - - +
341A ALA 3.4 0.2 - - - -
342A ILE* 4.2 12.0 - - + +
343A GLN* 2.8 50.3 + - + +
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Residues in contact with ALA 340 (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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338A GLU* 3.2 19.2 - - + +
339A GLU* 1.3 80.1 - - - +
341A ALA* 1.3 61.7 + - - +
343A GLN* 4.1 1.8 - - - +
344A GLY* 3.3 17.5 + - - -
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Residues in contact with ALA 341 (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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294A THR* 4.7 19.6 - - + +
338A GLU* 3.9 17.8 + - + +
340A ALA* 1.3 76.4 - - - +
342A ILE* 1.3 67.3 + - - +
344A GLY* 3.3 10.2 + - - -
345A ARG* 3.3 16.6 + - - +
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Residues in contact with ILE 342 (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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294A THR* 4.1 21.5 - - - +
295A LEU* 4.8 13.2 - - + +
335A GLY 5.9 0.7 - - - +
337A GLY* 3.6 17.9 - - - +
338A GLU 2.9 24.7 + - - +
339A GLU* 4.1 11.9 - - + +
341A ALA* 1.3 77.1 - - - +
343A GLN* 1.3 68.2 + - + +
345A ARG* 3.1 17.9 + - - +
346A VAL* 3.4 17.0 + - + +
372A LEU 5.2 9.9 - - - +
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Residues in contact with GLN 343 (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 GLU* 2.8 40.2 + - + +
340A ALA* 4.1 2.0 - - - +
342A ILE* 1.3 77.5 - - + +
344A GLY* 1.3 60.1 + - - +
345A ARG 3.3 0.4 - - - -
346A VAL* 3.6 15.3 + - + +
347A ALA* 3.5 18.5 + - - +
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Residues in contact with GLY 344 (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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340A ALA 3.3 11.7 + - - -
341A ALA* 3.3 8.8 + - - -
342A ILE 3.1 1.4 - - - -
343A GLN* 1.3 77.4 - - - +
345A ARG* 1.3 62.2 + - - +
347A ALA* 3.3 15.6 + - - +
348A GLN* 3.4 12.3 + - - +
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Residues in contact with ARG 345 (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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287A ALA 4.2 8.5 + - - -
290A GLN* 4.1 22.8 + - - +
291A ASP* 2.2 37.4 + - - +
294A THR* 3.5 35.9 - - + +
341A ALA 3.3 7.4 + - - +
342A ILE* 3.1 11.0 + - - +
344A GLY* 1.3 75.0 - - - +
346A VAL* 1.3 64.8 + - + +
348A GLN* 2.9 54.2 - - - +
349A ILE* 3.3 16.9 + - + +
368A ARG* 4.2 6.5 - - - +
372A LEU* 6.0 3.8 - - + -
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Residues in contact with VAL 346 (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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342A ILE* 3.5 21.1 - - + +
343A GLN* 3.7 17.7 - - + +
344A GLY 3.2 0.4 - - - -
345A ARG* 1.3 80.4 - - + +
347A ALA* 1.3 57.4 + - - +
349A ILE* 3.5 5.6 + - - +
350A ARG* 3.0 65.0 + - + +
369A VAL* 6.3 0.2 - - + -
372A LEU* 5.9 6.3 - - + +
373A ALA* 5.2 16.2 - - + -
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Residues in contact with ALA 347 (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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343A GLN 3.5 9.6 + - - +
344A GLY* 3.3 10.7 + - - +
345A ARG 3.3 0.6 - - - -
346A VAL* 1.3 81.8 - - - +
348A GLN* 1.3 58.9 + - - +
349A ILE 3.3 0.2 - - - -
350A ARG* 3.4 21.1 - - - +
351A GLN* 3.6 8.0 + - - +
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Residues in contact with GLN 348 (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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344A GLY 3.4 6.5 + - - +
345A ARG* 2.9 61.6 - - - +
347A ALA* 1.3 79.0 - - - +
349A ILE* 1.3 84.3 + - - +
351A GLN* 3.6 9.8 + - - +
352A GLN* 2.5 45.2 + - - +
368A ARG* 3.9 0.4 - - - +
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Residues in contact with ILE 349 (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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291A ASP* 4.3 4.0 - - - +
345A ARG* 3.3 14.9 + - - +
346A VAL* 3.5 5.8 + - - +
347A ALA 3.3 0.2 - - - -
348A GLN* 1.3 100.3 - - - +
350A ARG* 1.3 65.8 + - - +
351A GLN 3.2 2.0 - - - -
352A GLN* 3.0 11.5 + - + +
353A ILE* 3.0 24.0 + - + +
365A LEU* 4.7 6.5 - - + +
368A ARG* 3.3 43.3 - - - +
369A VAL* 3.6 28.3 - - + -
372A LEU* 3.6 19.3 - - + -
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Residues in contact with ARG 350 (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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172A GLU* 4.1 20.6 + - - +
346A VAL* 3.0 52.5 + - + +
347A ALA* 3.4 14.4 - - - +
349A ILE* 1.3 79.2 - - - +
351A GLN* 1.3 60.6 + - - +
353A ILE* 3.4 39.2 + - - +
354A GLU* 4.1 7.4 + - - +
369A VAL* 3.9 26.9 - - - +
373A ALA* 5.9 3.8 - - - +
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Residues in contact with GLN 351 (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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347A ALA 3.6 7.7 + - - +
348A GLN* 3.6 12.5 + - - +
349A ILE 3.2 0.2 - - - -
350A ARG* 1.3 80.8 - - - +
352A GLN* 1.3 60.1 + - + +
354A GLU* 2.9 43.5 + - - +
355A GLU* 4.9 1.4 - - - +
209B GLU* 5.5 3.0 - - + +
210B THR* 2.8 57.7 + - + +
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Residues in contact with GLN 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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348A GLN* 2.5 46.4 + - - +
349A ILE* 3.0 16.0 + - + +
351A GLN* 1.3 77.7 - - + +
353A ILE* 1.3 63.2 + - - +
354A GLU 3.3 7.2 + - - +
355A GLU* 4.9 2.8 - - - +
361A ASP* 4.6 5.0 - - - +
362A ARG* 4.6 2.3 + - - -
365A LEU* 4.1 11.8 - - + +
368A ARG* 2.8 33.6 + - - +
327B LYS* 5.9 6.1 - - - +
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Residues in contact with ILE 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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349A ILE* 3.0 22.9 + - + +
350A ARG* 3.5 42.0 - - - +
351A GLN 3.3 0.8 - - - -
352A GLN* 1.3 78.3 - - - +
354A GLU* 1.3 58.0 + - + +
362A ARG* 2.9 32.1 + - - +
365A LEU* 3.4 32.9 - - + +
366A GLN* 5.2 4.7 - - - +
369A VAL* 4.7 6.7 - - + -
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Residues in contact with GLU 354 (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 4.4 6.0 - - - +
351A GLN* 2.9 50.9 + - - +
352A GLN 3.7 2.6 - - - +
353A ILE* 1.3 81.3 - - + +
355A GLU* 1.3 75.0 + - - +
362A ARG* 4.2 2.9 - - - +
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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
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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