Contacts of the helix formed by residues 332 - 347 (chain A) in PDB entry 3PE3
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 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A LYS* 3.0 34.5 + - + +
330A GLN* 3.2 9.4 + - + +
331A GLY* 1.3 74.1 - - - +
333A ILE* 1.3 63.1 + - - +
334A GLU* 3.2 7.8 + - - +
335A GLU* 3.1 35.2 + - - +
336A ALA* 3.3 13.5 + - - +
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Residues in contact with ILE 333 (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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328A ARG* 4.3 26.5 - - + +
331A GLY* 3.1 12.0 + - - +
332A ASN* 1.3 73.3 - - - +
334A GLU* 1.3 62.4 + - - +
336A ALA* 3.4 7.0 + - - +
337A VAL* 3.3 21.5 + - - +
360A VAL* 4.5 14.8 - - + +
363A GLN* 3.4 29.4 - - - +
364A GLN* 3.5 35.2 - - + +
523A ASP* 3.8 22.4 - - + +
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Residues in contact with GLU 334 (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 ASN* 3.2 7.3 + - - +
333A ILE* 1.3 82.2 - - - +
335A GLU* 1.3 60.9 + - - +
337A VAL* 3.7 6.0 + - - +
338A ARG* 3.4 51.8 + - - +
364A GLN* 4.7 12.0 + - - +
526A ASN* 5.0 9.2 - - - +
527A VAL* 5.7 2.6 - - - +
529A HIS* 3.3 30.1 + - - -
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Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LYS* 4.1 23.6 - - + -
332A ASN* 3.1 31.0 + - - +
334A GLU* 1.3 76.1 - - - +
336A ALA* 1.3 66.4 + - - +
338A ARG* 3.0 40.3 + - - +
339A LEU* 3.1 36.6 + - + +
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Residues in contact with ALA 336 (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 ALA* 3.6 24.0 - - - +
327A LYS* 4.0 8.4 - - - +
328A ARG* 4.1 14.8 - - + +
332A ASN 3.3 11.2 + - - +
333A ILE* 3.5 11.0 - - - +
335A GLU* 1.3 77.6 - - - +
337A VAL* 1.3 62.7 + - - +
339A LEU* 3.0 4.7 + - - +
340A TYR* 2.9 39.5 + - + -
360A VAL* 5.1 3.4 - - + -
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Residues in contact with VAL 337 (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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333A ILE 3.3 13.6 + - - +
334A GLU* 3.8 9.0 - - - +
335A GLU 3.3 0.2 - - - -
336A ALA* 1.3 75.2 - - - +
338A ARG* 1.3 63.6 + - + +
340A TYR* 3.5 7.5 + - - +
341A ARG* 3.0 58.1 + - - +
357A LEU* 3.8 9.4 - - + -
360A VAL* 3.6 28.3 - - + -
361A LEU* 5.2 2.9 - - + +
364A GLN* 4.0 23.6 - - - +
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Residues in contact with ARG 338 (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 GLU* 3.4 47.4 + - - +
335A GLU* 3.0 42.2 + - - +
337A VAL* 1.3 80.1 - - + +
339A LEU* 1.3 60.0 + - + +
341A ARG* 3.6 7.9 + - - +
342A LYS* 3.2 26.2 + - - +
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Residues in contact with LEU 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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320A LEU* 4.1 27.1 - - + +
323A LEU* 3.8 15.5 - - + -
324A ALA* 3.5 31.2 - - + +
327A LYS* 3.7 33.2 - - + -
335A GLU* 3.1 26.9 + - + +
336A ALA 3.0 2.7 + - - +
338A ARG* 1.3 77.8 - - - +
340A TYR* 1.3 64.8 + - - +
341A ARG 3.2 0.2 - - - -
342A LYS* 3.0 16.2 + - + +
343A ALA* 3.0 22.2 + - - +
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Residues in contact with TYR 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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321A ASN* 3.3 31.4 - - - -
324A ALA* 3.2 24.7 - - + -
325A ASN* 2.9 28.8 + - - -
328A ARG* 3.9 13.7 + - - -
336A ALA* 2.9 34.7 + - + +
337A VAL* 3.8 7.9 - - - +
339A LEU* 1.3 75.2 - - - +
341A ARG* 1.3 63.3 + - - +
343A ALA* 3.1 16.7 + - - +
344A LEU* 3.1 19.3 + - - +
353A ALA* 4.5 5.9 - - - +
356A ASN* 3.4 28.6 - - + +
357A LEU* 3.9 31.2 - - + -
360A VAL* 4.3 11.7 - - + -
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Residues in contact with ARG 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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337A VAL* 3.0 37.9 + - - +
338A ARG* 3.8 8.3 - - - +
339A LEU 3.2 0.4 - - - -
340A TYR* 1.3 75.4 - - - +
342A LYS* 1.3 57.6 + - - +
344A LEU* 3.5 10.0 + - - +
345A GLU* 3.2 26.2 + - - +
357A LEU* 4.2 22.4 - - + +
361A LEU* 3.8 19.6 - - - +
366A LYS* 5.7 2.8 - - - +
369A GLU* 3.1 33.1 + - - -
373A HIS* 4.4 7.3 + - - -
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Residues in contact with LYS 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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316A HIS* 6.4 0.4 - - - -
320A LEU* 3.6 26.1 - - + +
338A ARG 3.2 13.8 + - - +
339A LEU* 3.0 22.0 + - + +
341A ARG* 1.3 76.2 - - - +
343A ALA* 1.3 64.5 + - - +
345A GLU* 3.3 16.4 + - - +
346A VAL* 3.2 30.0 + - + +
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Residues in contact with ALA 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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317A ALA* 3.2 36.5 - - + +
320A LEU* 3.5 18.8 - - + +
321A ASN* 4.1 6.3 - - - +
339A LEU 3.0 8.9 + - - +
340A TYR* 3.4 11.0 - - - +
342A LYS* 1.3 77.6 - - - +
344A LEU* 1.3 57.2 + - - +
346A VAL 3.4 0.3 + - - -
347A PHE 2.9 25.6 + - - +
350A PHE* 4.3 10.3 - - + -
353A ALA* 4.4 6.1 - - + -
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Residues in contact with LEU 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 TYR 3.1 16.2 + - - +
341A ARG* 4.0 6.5 - - - +
342A LYS 3.2 0.4 - - - -
343A ALA* 1.3 73.6 - - - +
345A GLU* 1.3 64.1 + - - +
346A VAL 3.2 0.7 - - - -
347A PHE 3.9 4.7 - - - +
348A PRO* 3.2 30.1 - - + +
350A PHE* 3.8 12.3 - - + +
353A ALA* 3.5 25.4 - - + -
354A HIS* 3.5 54.7 - - + +
357A LEU* 4.0 25.8 - - + -
373A HIS* 4.0 5.8 - - + +
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Residues in contact with GLU 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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341A ARG 3.2 16.6 + - - +
342A LYS* 3.3 18.4 + - - +
344A LEU* 1.3 78.7 - - - +
346A VAL* 1.3 63.8 + - + +
348A PRO* 4.5 5.2 - - - +
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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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312A SER* 3.1 34.0 + - - +
313A CYS 3.1 35.9 - - - +
316A HIS* 3.7 33.2 - - + +
317A ALA* 4.0 5.4 - - + -
320A LEU* 3.9 7.2 - - + -
342A LYS* 3.2 16.5 + - + +
343A ALA 3.7 6.5 - - - +
345A GLU* 1.3 81.5 - - + +
347A PHE* 1.3 57.1 + - - +
348A PRO* 3.6 5.9 - - - +
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Residues in contact with PHE 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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312A SER* 4.7 9.6 - - - -
313A CYS 4.0 6.7 - - - +
314A PRO* 3.8 33.2 - - + -
317A ALA* 3.4 17.5 - - + -
343A ALA 2.9 9.0 + - - +
344A LEU* 3.6 3.9 - - - -
346A VAL* 1.3 78.5 - - - +
348A PRO* 1.3 63.7 - - + +
349A GLU* 3.6 35.7 - - + -
350A PHE* 3.0 49.1 - + + +
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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