Contacts of the helix formed by residues 354 - 364 (chain A) in PDB entry 3EA4
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 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A LEU 3.0 12.5 + - - -
347A HIS* 3.9 15.9 - - + -
348A MET* 2.8 15.3 + - + +
353A GLY* 1.3 75.0 - - - -
355A VAL* 1.3 66.7 + - - +
356A TYR* 3.3 33.1 - - + +
357A ALA* 3.0 18.4 + - - +
358A ASN* 3.1 20.9 + - - -
451A PHE 5.5 0.2 - - - -
453A LEU* 4.0 24.5 - - + -
494A GLN* 6.0 1.1 - - + +
649A PRO* 4.5 5.2 - - - -
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Residues in contact with VAL 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 GLY 3.8 1.4 + - - -
354A THR* 1.3 72.3 - - - +
356A TYR* 1.3 58.7 + - - +
358A ASN* 3.4 3.0 + - - +
359A TYR* 2.8 26.9 + - - +
447A GLN* 4.3 6.7 - - - +
451A PHE* 3.6 48.9 + - + +
649A PRO* 3.7 23.6 - - + +
657A PHE* 3.6 24.9 - - + -
660A VAL* 4.8 8.7 - - + -
662A THR* 3.9 22.9 - - + -
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Residues in contact with TYR 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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346A LEU* 3.2 41.3 - - + +
347A HIS* 2.7 30.3 + - - -
354A THR* 3.3 27.9 - - + +
355A VAL* 1.3 78.2 - - - +
357A ALA* 1.3 60.6 + - - +
359A TYR* 3.6 6.5 - - - +
360A ALA* 2.9 30.1 + - - +
444A LEU* 4.3 7.2 - - + +
447A GLN* 4.1 10.8 - - + -
448A LYS* 3.7 54.5 - - + +
451A PHE 3.5 22.9 - - - -
452A PRO* 4.2 10.3 - - + +
453A LEU* 4.5 10.3 + - - +
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Residues in contact with ALA 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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329A ALA* 4.3 4.1 - - + +
346A LEU* 3.3 29.4 - - + +
347A HIS 4.3 1.1 - - - +
348A MET 3.5 17.5 - - - +
349A LEU* 3.9 13.5 - - + -
354A THR* 3.0 22.5 + - - +
356A TYR* 1.3 77.4 - - - +
358A ASN* 1.3 63.4 + - - +
360A ALA* 3.4 4.3 + - - +
361A VAL* 3.2 25.6 + - - +
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Residues in contact with ASN 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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349A LEU* 3.5 7.8 - - - +
350A GLY* 2.9 46.4 + - - +
353A GLY 3.9 8.5 + - - -
354A THR 3.1 18.3 + - - +
355A VAL* 3.9 3.4 - - - +
357A ALA* 1.3 73.6 - - - +
359A TYR* 1.3 58.7 + - - +
361A VAL* 3.3 5.6 + - - +
362A GLU* 2.9 30.8 + - - +
378A VAL 4.9 3.5 - - - +
649A PRO* 6.0 0.2 - - - +
651A ILE* 3.8 17.8 - - + +
657A PHE* 3.7 22.9 - - + +
660A VAL* 5.6 3.6 - - - +
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Residues in contact with TYR 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 VAL 2.8 22.5 + - - +
356A TYR* 3.6 8.3 - - - +
358A ASN* 1.3 72.2 - - - +
360A ALA* 1.3 66.9 + - - +
362A GLU* 3.1 5.3 + - - +
363A HIS* 3.0 52.3 + + - +
440A TRP* 4.5 2.7 - + - -
443A GLU* 2.7 34.0 + - + +
444A LEU* 3.6 20.6 - - + -
447A GLN* 3.6 42.0 + - + +
657A PHE* 3.5 24.1 - + + -
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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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303A VAL* 3.8 13.2 - - + -
346A LEU* 3.6 25.4 - - + -
356A TYR 2.9 17.9 + - - +
357A ALA 3.4 5.8 - - - +
359A TYR* 1.3 76.5 - - - +
361A VAL* 1.3 57.8 + - - +
364A SER* 2.9 30.8 + - - -
440A TRP* 3.5 7.2 - - - -
444A LEU* 3.7 22.4 - - + -
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Residues in contact with VAL 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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303A VAL* 4.0 19.5 - - + -
305A TYR* 5.3 0.4 - - + -
329A ALA* 4.7 2.0 - - + -
349A LEU* 3.6 26.9 - - + -
357A ALA 3.2 11.4 + - - +
358A ASN* 3.8 7.9 - - - +
359A TYR 3.3 0.2 - - - -
360A ALA* 1.3 73.6 - - - +
362A GLU* 1.3 66.8 + - - +
364A SER* 2.8 23.8 + - - +
367A LEU* 4.1 12.6 - - + -
385A PHE* 3.6 37.5 - - + -
386A ALA* 3.7 20.9 - - + +
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Residues in contact with GLU 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 ASN 2.9 17.9 + - - +
359A TYR 3.4 6.1 - - - +
361A VAL* 1.3 79.4 - - - +
363A HIS* 1.3 75.5 + - + +
364A SER 3.9 1.9 + - - +
384A ALA* 3.4 23.0 - - - +
385A PHE* 5.0 1.0 - - - -
386A ALA* 4.7 5.5 + - - +
387A SER* 4.6 16.7 + - - -
388A ARG* 4.8 7.1 - - - +
656A THR* 4.2 10.7 - - - +
657A PHE* 3.5 41.8 + - + +
658A ASN* 5.8 2.4 + - - +
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Residues in contact with HIS 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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301A LYS* 3.3 28.6 + - - +
359A TYR* 3.0 59.2 + + + +
360A ALA 3.7 1.3 - - - -
362A GLU* 1.3 94.5 + - + +
364A SER* 1.3 66.8 + - - +
365A ASP* 5.2 0.2 - - - +
388A ARG* 5.4 3.9 - - - +
440A TRP* 4.0 15.5 - - + -
443A GLU* 5.1 1.6 - - - +
657A PHE* 4.7 5.1 - - - -
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Residues in contact with SER 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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301A LYS* 3.3 18.2 - - - -
303A VAL* 3.7 14.4 - - - -
360A ALA 2.9 17.1 + - - -
361A VAL* 2.8 21.0 + - - +
362A GLU 4.8 0.2 - - - +
363A HIS* 1.3 81.6 - - - +
365A ASP* 1.3 59.0 + - - +
366A LEU 4.2 8.3 - - - -
367A LEU* 4.3 7.4 - - - +
386A ALA* 4.5 0.2 - - - +
388A ARG* 3.4 14.9 + - - +
389A ALA* 3.4 23.0 - - - +
440A TRP* 4.4 0.4 - - - -
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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