Contacts of the helix formed by residues 354 - 359 (chain A) in PDB entry 5IWS
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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232A ARG* 3.1 8.0 + - - +
235A LEU* 3.9 1.6 - - - +
310A GLN* 3.8 14.1 - - - +
313A GLY* 5.0 1.3 - - - -
314A SER* 3.8 20.4 - - - +
318A LEU* 3.6 13.0 - - + +
348A VAL* 3.8 10.1 - - + -
352A GLY 3.5 14.4 - - - +
353A VAL* 1.3 71.2 - - - +
355A GLU* 1.3 64.9 + - - +
356A PRO* 3.4 2.0 - - - -
357A ILE 3.4 3.8 + - - -
358A GLU* 2.7 49.4 + - - +
372A TYR* 4.9 1.3 - - - +
2B GLC 2.9 19.6 + - - -
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Residues in contact with GLU 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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20A VAL* 3.7 20.0 - - + -
23A MSE 3.6 18.2 - - + +
235A LEU* 3.6 21.3 - - + +
240A HIS* 4.0 2.6 - - - -
353A VAL* 3.2 7.6 - - + +
354A THR* 1.3 72.7 - - - +
356A PRO* 1.4 70.2 - - + +
357A ILE 2.9 0.2 + - - -
358A GLU* 3.8 4.5 - - - -
359A PHE* 2.9 53.3 + - + +
2B GLC 2.3 54.3 + - - -
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Residues in contact with PRO 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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20A VAL* 4.0 16.4 - - + +
24A PRO* 3.7 22.0 - - + -
344A ALA* 3.9 17.0 - - + +
347A ALA* 4.7 6.7 - - + -
348A VAL* 4.2 9.4 - - + -
353A VAL* 3.6 18.8 - - + +
354A THR 3.6 3.8 - - - -
355A GLU* 1.4 91.2 - - + +
357A ILE* 1.3 57.7 + - - +
359A PHE* 4.6 2.4 - - + +
360A MSE 3.3 28.4 - - - +
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Residues in contact with ILE 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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318A LEU* 3.6 36.6 - - + +
319A MSE 3.6 21.1 - - + -
321A ILE* 4.6 2.0 - - + -
322A ALA* 3.6 26.0 - - + +
325A MSE 5.2 3.6 - - - -
344A ALA* 3.9 13.5 - - + +
345A ALA* 3.6 26.5 - - - -
348A VAL* 3.6 13.7 - - + +
354A THR 3.4 1.2 + - - -
355A GLU 3.1 0.2 - - - -
356A PRO* 1.3 78.6 - - - +
358A GLU* 1.3 67.5 + - - +
359A PHE 3.3 1.6 - - - -
360A MSE 3.1 25.0 + - - +
361A PHE* 3.3 12.6 - - + -
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Residues in contact with GLU 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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232A ARG* 2.5 18.6 + - - -
235A LEU* 3.2 22.6 - - - +
318A LEU* 4.1 7.9 - - + -
354A THR* 2.7 40.8 + - - +
355A GLU* 3.6 2.1 + - - +
357A ILE* 1.3 71.3 - - - +
359A PHE* 1.3 56.2 + - - +
360A MSE 3.0 11.1 + - - -
361A PHE* 3.2 9.9 + - + -
362A MSE 3.0 48.2 + - + +
372A TYR* 2.3 49.4 + - + +
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Residues in contact with PHE 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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13A GLY* 3.8 13.7 - - - -
16A LEU* 3.7 29.8 - - + -
17A LEU* 5.1 2.7 - - + -
20A VAL* 3.6 28.7 - - + -
23A MSE 6.5 0.2 - - + -
68A PHE* 6.3 0.4 - + - -
235A LEU* 4.3 4.7 - - + -
236A PRO* 4.4 6.1 - - + -
355A GLU* 2.9 46.2 + - + +
356A PRO 5.1 2.2 - - - +
357A ILE 3.3 0.2 - - - -
358A GLU* 1.3 74.2 - - - +
360A MSE 1.3 60.2 + - + +
361A PHE 3.5 0.4 - - - -
362A MSE 3.6 22.7 - - + -
363A PHE* 3.5 41.8 + + - +
364A ILE* 5.5 2.6 - - - +
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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