Contacts of the helix formed by residues 333 - 346 (chain A) in PDB entry 3PEI
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 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ASN* 3.1 19.4 + - + +
332A ASP* 1.3 75.7 - - - +
334A GLU* 1.3 58.3 + - - +
335A GLY 3.2 3.4 - - - -
336A ARG* 2.9 48.9 - - - +
337A LEU* 4.2 0.9 - - - +
419A ASN* 3.1 28.6 + - - +
420A CYS* 4.4 4.0 - - + -
496A CL 3.8 9.0 - - - -
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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
----------------------------------------------------------
219A ALA 4.7 1.0 - - - +
220A VAL* 3.3 56.4 - - + +
252A LEU* 4.2 8.7 - - + -
305A ASN* 4.1 19.1 + - - +
312A TYR* 4.1 29.8 - - - +
328A VAL* 5.1 6.0 - - + +
330A ASN 5.0 0.9 - - - +
331A THR* 3.0 26.4 - - - +
332A ASP 3.2 4.3 + - - +
333A ALA* 1.3 75.6 - - - +
335A GLY* 1.3 63.4 + - - +
337A LEU* 3.1 27.6 + - + +
338A VAL* 3.5 3.3 + - - +
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Residues in contact with GLY 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LYS* 3.9 19.0 - - - +
252A LEU* 3.8 21.0 - - - +
255A ASP* 4.4 1.9 + - - -
332A ASP 4.7 1.0 + - - -
333A ALA 3.2 1.8 - - - -
334A GLU* 1.3 79.0 - - - +
336A ARG* 1.3 61.3 + - - +
338A VAL* 3.3 7.4 + - - +
339A LEU* 3.2 22.3 + - - +
360A LEU* 4.4 5.2 - - - -
496A CL 3.8 9.6 - - - +
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Residues in contact with ARG 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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333A ALA* 2.9 34.2 + - - +
335A GLY* 1.3 75.7 - - - +
337A LEU* 1.3 58.3 + - - +
339A LEU* 3.3 6.8 + - - +
340A CYS* 2.9 30.1 + - - +
360A LEU* 4.1 12.1 + - + +
361A THR* 3.7 15.6 - - - +
419A ASN* 2.9 35.5 + - + +
420A CYS* 4.0 16.6 - - - +
427A GLY 5.0 1.6 + - - -
430A VAL* 4.9 3.0 - - - +
431A ALA* 3.6 36.7 - - - +
434A PHE* 3.7 26.3 - - + -
435A LEU* 3.7 8.9 - - + +
496A CL 3.3 27.1 - - + +
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A CYS* 3.4 27.9 - - + +
217A ALA 3.6 3.5 + - - -
219A ALA* 5.7 0.2 - - + -
220A VAL* 3.7 23.1 - - + +
318A LEU* 4.1 10.1 - - + -
326A VAL* 4.1 16.4 - - + -
328A VAL* 4.1 29.4 - - + -
333A ALA 4.2 6.7 - - - +
334A GLU* 3.1 21.2 + - - +
336A ARG* 1.3 73.7 - - + +
338A VAL* 1.3 67.2 + - - +
340A CYS* 3.2 20.5 + - - -
341A ASP 3.6 1.6 + - - -
419A ASN* 4.1 24.9 - - + +
434A PHE* 4.2 7.9 - - + -
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Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ALA* 3.9 20.0 - - + +
220A VAL* 3.9 35.2 - - + -
228A ASN* 5.7 0.7 - - - +
250A LYS* 5.7 6.1 - - + -
251A GLY 5.6 2.5 - - - +
252A LEU* 4.6 9.0 - - + +
301A GLY* 4.0 34.8 - - - +
302A LEU 4.8 0.9 - - - +
303A ALA* 4.4 14.6 - - + +
334A GLU 3.5 4.0 + - - +
335A GLY* 3.3 8.2 + - - +
336A ARG 3.3 0.4 - - - -
337A LEU* 1.3 78.7 - - - +
339A LEU* 1.3 60.7 + - + +
341A ASP 3.7 0.5 + - - -
342A THR* 2.8 29.4 + - - +
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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
----------------------------------------------------------
248A VAL* 3.7 29.4 - - + +
249A GLY 4.6 0.9 - - - +
250A LYS* 3.8 26.9 - - + +
335A GLY 3.2 6.1 + - - +
336A ARG 3.3 7.6 + - - +
338A VAL* 1.3 79.8 - - + +
340A CYS* 1.3 59.4 + - - +
342A THR* 3.5 3.8 + - - -
343A LEU* 2.9 38.6 + - + +
356A ASP* 4.1 17.5 - - + +
357A LEU 5.2 0.7 - - - +
358A ALA* 3.6 31.0 - - + -
360A LEU* 4.1 15.3 - - + -
435A LEU* 3.9 22.9 - - + -
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Residues in contact with CYS 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A CYS* 3.6 25.6 - - - -
336A ARG 2.9 15.3 + - - +
337A LEU* 3.2 24.5 - - - -
338A VAL 3.3 0.8 - - - -
339A LEU* 1.3 77.3 - - - +
341A ASP* 1.3 68.3 + - - +
343A LEU* 3.3 5.6 + - - +
344A THR* 3.0 26.4 + - - -
434A PHE* 4.0 9.9 - - + -
435A LEU* 4.2 4.5 - - + +
438A PHE* 3.5 46.9 - - + -
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Residues in contact with ASP 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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214A MSE 3.0 37.3 - - + +
216A CYS* 2.6 36.9 + - - -
217A ALA* 2.9 19.2 + - + -
320A SER* 3.5 10.0 - - - -
321A MSE 2.9 27.2 + - - +
322A LYS 4.6 0.2 + - - -
337A LEU 3.6 2.0 + - - -
339A LEU 3.5 0.2 - - - -
340A CYS* 1.3 79.1 - - - +
342A THR* 1.3 56.2 + - - +
344A THR* 3.4 6.3 + - - -
345A TYR* 3.0 27.9 + - - +
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Residues in contact with THR 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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209A MSE 5.9 0.2 - - - +
214A MSE 4.1 13.7 - - - +
217A ALA* 5.2 0.5 - - - +
230A THR* 4.2 12.0 + - + +
248A VAL* 3.7 18.8 - - + -
299A VAL* 3.7 29.6 - - + -
301A GLY* 4.2 19.3 - - - +
338A VAL* 2.8 21.1 + - - +
339A LEU* 3.8 5.2 - - - -
340A CYS 3.2 0.4 - - - -
341A ASP* 1.3 76.4 - - - +
343A LEU* 1.3 58.4 + - - +
345A TYR* 3.1 4.2 + - - +
346A ILE* 3.1 30.9 + - + +
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 4.1 15.0 - - + -
339A LEU* 2.9 33.9 + - + +
340A CYS* 3.6 6.5 - - - +
342A THR* 1.3 74.4 - - - +
344A THR* 1.3 55.3 + - - +
346A ILE* 3.2 12.4 - - + +
354A VAL* 3.8 29.6 - - + -
356A ASP* 3.9 19.7 - - + +
435A LEU* 4.3 21.1 - - + +
438A PHE* 4.5 5.2 - - + -
439A THR* 3.8 30.5 - - + -
442A TYR* 2.5 32.6 + - + -
444A TRP* 4.2 4.9 - - - +
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Residues in contact with THR 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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321A MSE 3.7 36.0 - - + +
322A LYS* 3.9 20.3 + - + +
340A CYS 3.0 14.6 + - - -
341A ASP* 3.6 9.4 + - - -
343A LEU* 1.3 76.8 - - - +
345A TYR* 1.3 63.8 + - - +
347A GLY* 3.3 11.6 + - - -
438A PHE* 3.6 25.3 + - - +
442A TYR* 3.5 5.6 + - - -
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Residues in contact with TYR 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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202A ASP* 4.3 8.3 + - - -
204A LEU* 3.8 28.7 - - + +
212A LEU* 3.8 33.0 - - + -
214A MSE 4.2 6.5 - - + -
230A THR* 4.2 16.2 - - + -
232A CYS* 4.2 23.0 - - - -
321A MSE 3.9 22.2 - - + +
341A ASP 3.0 17.4 + - - +
342A THR 3.1 4.9 + - - +
344A THR* 1.3 78.6 - - - +
346A ILE* 1.3 68.9 + - + +
347A GLY 3.0 5.6 + - - -
348A LYS* 3.3 53.8 + - + +
349A TYR* 5.1 0.9 - + - -
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Residues in contact with ILE 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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246A VAL* 4.1 13.5 - - + -
248A VAL* 4.3 6.3 - - + -
299A VAL* 3.8 39.5 - - + -
342A THR 3.1 16.0 + - - +
343A LEU* 3.2 23.1 - - - +
345A TYR* 1.3 81.9 - - + +
347A GLY* 1.3 59.6 + - - +
348A LYS 3.0 6.5 - - - -
349A TYR* 3.1 33.1 + - + +
351A PRO* 3.8 6.8 - - + +
354A VAL* 3.6 43.3 - - + -
442A TYR* 3.9 7.4 - - + -
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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