Contacts of the helix formed by residues 353 - 364 (chain A) in PDB entry 3E5A
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 THR 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A GLU* 2.5 36.1 + - - +
351A PHE 3.3 11.2 + - - +
352A VAL* 1.3 76.1 - - - +
354A GLU* 1.3 57.0 + - - +
355A GLY 4.3 1.4 + - - -
356A ALA* 2.8 28.3 + - - +
357A ARG* 2.9 12.2 + - - -
382A TRP* 3.6 12.6 + - - -
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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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352A VAL 3.9 1.4 + - - -
353A THR* 1.3 72.6 - - - +
355A GLY* 1.3 52.4 + - - +
357A ARG* 3.3 17.2 + - + +
358A ASP* 2.8 35.8 + - + +
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Residues in contact with GLY 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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353A THR* 3.3 3.6 + - - -
354A GLU* 1.3 74.9 - - - +
356A ALA* 1.3 64.7 + - - +
358A ASP* 3.5 5.3 + - - -
359A LEU* 3.2 19.9 + - - +
380A HIS* 3.4 15.2 - - - -
382A TRP* 3.7 22.3 - - - +
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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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230A GLU* 4.8 0.4 - - - +
319A CYS* 5.4 0.2 - - - -
323A LEU* 3.8 18.2 - - + -
352A VAL* 3.9 8.7 - - + -
353A THR* 2.8 15.0 + - - +
355A GLY* 1.3 74.8 - - - +
357A ARG* 1.3 64.0 + - - +
359A LEU* 3.5 2.4 + - - +
360A ILE* 3.0 31.7 + - + +
382A TRP* 3.6 42.1 - - + +
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Residues in contact with ARG 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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348A PHE* 3.5 54.5 + - + +
349A PRO 3.1 27.7 + - - -
350A ASP* 4.0 10.9 + - - +
352A VAL* 2.3 37.3 + - + +
353A THR 2.9 16.3 + - - +
354A GLU* 3.5 16.1 - - + +
356A ALA* 1.3 68.7 - - - +
358A ASP* 1.3 67.4 + - - +
360A ILE 3.3 0.5 + - - -
361A SER* 2.8 30.2 + - - +
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Residues in contact with ASP 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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354A GLU* 2.8 23.1 + - - +
355A GLY* 3.8 7.9 - - - +
356A ALA 3.3 0.4 - - - -
357A ARG* 1.3 74.1 - - - +
359A LEU* 1.3 63.4 + - - +
361A SER* 3.2 5.6 + - - -
362A ARG* 2.7 65.9 + - - +
380A HIS* 3.1 18.2 + - + +
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Residues in contact with LEU 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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237A ILE* 5.0 3.4 - - + -
319A CYS* 4.3 9.4 - - - -
355A GLY 3.2 13.8 + - - +
356A ALA 3.7 4.0 - - - +
358A ASP* 1.3 77.9 + - - +
360A ILE* 1.3 64.0 + - - +
362A ARG* 3.1 9.7 + - + +
363A LEU* 3.1 47.2 + - + +
372A PRO* 5.9 0.9 - - + -
377A VAL* 4.4 18.6 - - + -
380A HIS* 3.8 32.9 + - + +
382A TRP* 3.4 36.3 - - + -
383A ILE* 3.7 17.0 - - + -
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Residues in contact with ILE 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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316A GLY 3.9 15.9 - - - +
319A CYS* 4.1 19.5 - - + -
320A TYR* 3.8 28.9 - - + +
323A LEU* 4.2 10.8 - - + -
324A VAL* 6.5 0.2 - - + -
346A PHE* 4.1 4.5 - - + -
348A PHE* 3.8 32.5 - - + -
352A VAL* 5.0 2.0 - - + -
356A ALA* 3.0 22.5 + - + +
359A LEU* 1.3 79.6 - - + +
361A SER* 1.3 58.8 + - - +
363A LEU* 3.2 7.7 + - - +
364A LEU* 2.9 52.5 + - + +
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Residues in contact with SER 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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346A PHE* 4.7 6.8 - - - -
348A PHE* 3.7 18.0 - - - -
357A ARG* 2.8 24.6 + - - +
358A ASP* 3.6 6.3 - - - -
360A ILE* 1.3 79.4 - - - +
362A ARG* 1.3 61.1 + - - +
364A LEU* 3.5 19.9 + - - +
365A LYS* 3.9 15.1 - - - +
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Residues in contact with ARG 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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358A ASP* 2.7 52.8 + - - +
359A LEU* 3.4 8.7 - - + +
361A SER* 1.3 78.4 - - - +
363A LEU* 1.3 59.5 - - - +
365A LYS* 3.3 32.2 - - - +
370A GLN 4.3 1.0 - - - +
371A ARG* 4.0 1.7 - - - -
372A PRO* 3.3 31.0 - - + +
380A HIS* 4.4 15.2 + - - -
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Residues in contact with LEU 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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237A ILE* 5.8 1.1 - - + -
312A LEU* 3.5 44.8 - - + +
313A TRP* 3.8 9.9 - - - -
315A LEU* 4.2 14.4 - - + +
316A GLY* 3.5 29.2 - - - +
319A CYS* 5.0 5.2 - - + -
359A LEU* 3.1 39.7 + - + +
360A ILE* 3.7 4.7 - - - +
362A ARG* 1.3 77.0 - - - +
364A LEU* 1.3 58.9 + - - +
365A LYS 3.2 5.6 + - - -
371A ARG* 3.4 19.6 + - - +
372A PRO* 3.8 16.2 - - + -
377A VAL* 3.9 10.5 - - + -
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Residues in contact with LEU 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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313A TRP* 3.3 55.4 - - + +
316A GLY* 3.9 10.5 - - - -
317A VAL* 3.7 13.0 - - + +
328A PRO* 4.3 17.5 - - + -
329A PHE* 4.4 5.4 - - + -
344A VAL* 3.6 18.0 - - + +
346A PHE* 4.0 26.9 - - + -
360A ILE* 2.9 39.0 + - + +
361A SER* 3.5 9.9 + - - +
362A ARG 3.3 0.6 - - - -
363A LEU* 1.3 76.0 - - - +
365A LYS* 1.3 60.3 + - - +
366A HIS 4.0 0.2 + - - -
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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