Contacts of the helix formed by residues 351 - 359 (chain A) in PDB entry 2W8D
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 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A PHE* 3.0 25.1 + - - +
318A VAL* 3.7 25.1 + - + +
321A ALA* 3.7 2.4 - - - +
348A THR 2.8 22.8 + - - -
350A TRP* 1.3 71.1 - - - +
352A ARG* 1.3 62.7 + - - +
353A ASN* 3.3 8.4 - - - +
354A GLU* 3.1 39.1 + - - +
355A MSE 3.2 10.2 + - - +
481B LYS* 3.2 27.9 + - - +
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Residues in contact with ARG 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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297A TPO 3.5 25.1 + - - +
298A SER 4.7 0.2 - - - +
301A GLU* 2.8 29.5 + - - -
317A PHE* 3.9 23.5 - - + -
341A THR* 5.6 0.2 - - - -
343A HIS* 3.5 29.6 + - - -
346A THR 5.3 1.1 + - - -
347A GLN 3.6 5.5 + - - +
349A PHE* 3.2 31.1 + - - +
350A TRP* 3.0 28.0 + - + +
351A ASN* 1.3 76.5 - - - +
353A ASN* 1.3 63.1 + - - +
354A GLU 3.1 0.2 + - - -
356A TYR* 3.0 47.8 + - + +
364A PHE* 3.6 28.0 - - + -
407A ILE* 3.9 9.7 - - - +
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Residues in contact with ASN 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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347A GLN* 3.0 59.0 + - + +
348A THR* 4.0 18.6 - - - +
351A ASN* 4.2 9.7 - - - +
352A ARG* 1.3 74.8 - - - +
354A GLU* 1.3 65.3 + - - +
357A LYS* 3.2 34.8 + - - +
364A PHE* 4.0 2.6 - - - -
632A TYR* 3.6 15.9 - - + -
481B LYS* 5.7 0.3 + - - -
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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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318A VAL 5.0 1.6 - - - +
321A ALA* 3.7 17.3 - - + +
322A GLN* 4.0 21.5 - - - +
351A ASN* 3.1 35.5 + - - +
353A ASN* 1.3 83.5 + - - +
355A MSE 1.3 64.0 + - - +
357A LYS* 3.3 23.7 + - + +
358A ALA* 3.5 6.4 + - - +
481B LYS* 3.3 20.1 + - - +
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Residues in contact with MSE 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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302A PHE* 4.0 19.7 - - + -
316A VAL* 3.3 30.1 - - + +
317A PHE* 3.5 55.2 - - + +
320A LYS 3.7 21.1 - - - +
321A ALA* 3.8 17.5 - - + +
325A LEU* 3.6 23.6 - - + -
351A ASN 3.2 9.2 + - - +
354A GLU* 1.3 72.8 - - - +
356A TYR* 1.3 65.9 + - - +
357A LYS 3.1 2.0 - - - -
358A ALA* 3.2 4.5 + - - +
359A GLU* 3.1 28.8 + - - +
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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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301A GLU* 2.5 29.9 + - - -
317A PHE* 3.7 22.0 - + - -
341A THR* 3.4 39.9 - - + +
352A ARG* 3.0 34.5 + - + +
355A MSE 1.3 73.1 - - - +
357A LYS* 1.3 64.7 + - - +
359A GLU* 3.1 25.4 + - - -
361A ILE* 3.0 39.2 + - + -
364A PHE* 3.7 37.5 - + + -
405A LYS* 4.0 6.1 - - - -
407A ILE* 4.5 0.2 - - - +
632A TYR* 3.4 16.2 - - + +
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Residues in contact with LYS 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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347A GLN* 5.6 1.0 - - - +
353A ASN* 3.2 29.3 + - - +
354A GLU* 3.3 12.5 + - + +
355A MSE 3.1 0.8 - - - -
356A TYR* 1.3 77.1 - - - +
358A ALA* 1.3 65.0 + - - +
360A GLY 3.2 9.0 + - - -
625A VAL* 3.6 5.4 - - - +
627A PRO* 3.7 27.2 - - + +
628A SER* 5.9 0.7 - - - +
630A TYR* 3.2 50.4 + - + -
631A ASP* 4.8 1.0 + - - +
632A TYR* 3.6 32.1 - - + +
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Residues in contact with ALA 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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321A ALA 3.4 26.0 - - - +
323A ASN 4.1 14.1 - - - +
325A LEU* 3.9 28.7 + - + +
354A GLU 3.5 2.5 + - - +
355A MSE 3.2 12.7 + - - +
357A LYS* 1.3 80.7 - - - +
359A GLU* 1.3 59.7 + - - +
360A GLY 3.3 1.1 + - - -
625A VAL* 3.7 14.2 - - - +
627A PRO* 4.2 16.1 - - + +
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Residues in contact with GLU 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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302A PHE* 3.9 14.9 - - - -
305A GLU* 3.5 24.7 - - - +
306A ASN* 2.9 22.3 + - - -
317A PHE* 4.2 2.9 - - - -
325A LEU* 3.8 12.1 - - + -
327A SER* 3.4 35.5 - - - +
329A PRO* 3.6 9.2 - - + +
330A ALA* 3.8 10.1 - - - +
355A MSE 3.1 25.2 + - - +
356A TYR* 3.1 31.7 + - - +
358A ALA* 1.3 78.8 - - - +
360A GLY* 1.3 60.4 + - - +
361A ILE* 3.4 9.5 - - + +
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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