Contacts of the helix formed by residues 371 - 375 (chain A) in PDB entry 3IML
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 PHE 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A ILE* 4.0 12.6 - - + -
357A LYS* 3.8 32.5 - - + -
358A THR* 3.6 20.9 - - + -
362A GLY 5.1 0.2 - - - -
363A HIS 4.7 8.1 - - - -
366A ARG* 3.3 45.8 - - + +
368A GLU* 3.0 39.7 + - + +
369A PRO 3.2 2.5 - - - +
370A GLU* 1.3 87.3 - - + +
372A SER* 1.3 64.8 + - - +
373A TRP* 3.2 35.0 - + + +
374A GLU* 3.1 18.4 + - + +
375A ALA* 4.0 2.9 + - - +
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TYR* 3.7 9.9 - - - -
347A MET 4.6 1.7 + - - -
348A LEU* 3.2 45.3 + - - +
349A ASP* 5.1 1.4 - - - +
352A ARG* 4.1 9.6 + - - -
369A PRO 5.1 2.5 - - - -
370A GLU 3.0 6.6 + - - -
371A PHE* 1.3 72.8 - - - +
373A TRP* 1.3 67.2 + - - +
374A GLU 3.1 1.6 + - - -
375A ALA* 3.2 21.4 + - - +
377A ASP* 5.2 0.3 - - - +
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Residues in contact with TRP 373 (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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280A TYR* 3.2 67.5 - + + +
283A ARG* 4.1 6.8 - - + +
284A TYR* 3.3 36.7 + - + +
287A LYS* 4.5 3.5 - - - +
348A LEU* 3.7 6.5 - - + +
350A LEU* 3.9 21.5 - - + -
354A ILE* 3.9 21.1 - - + -
355A TYR* 4.8 0.4 - + - -
358A THR* 3.9 14.8 - - + -
363A HIS 2.9 22.5 + - - -
364A PHE* 3.6 23.8 - + - -
371A PHE* 3.5 36.3 - + + +
372A SER* 1.3 89.4 - - - +
374A GLU* 1.3 71.9 + - + +
375A ALA 3.5 1.0 - - - +
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Residues in contact with GLU 374 (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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136A GLU 4.2 0.2 - - - +
283A ARG* 2.8 41.3 + - - +
287A LYS* 2.6 52.4 + - - +
363A HIS 5.0 0.9 - - - +
364A PHE* 3.2 8.3 - - - -
365A GLY* 2.8 27.9 + - - +
366A ARG 3.7 20.8 + - - +
367A GLU* 4.5 12.8 - - + +
371A PHE* 3.1 13.4 + - + +
372A SER 3.1 1.2 - - - -
373A TRP* 1.3 91.2 - - + +
375A ALA* 1.3 59.9 + - - +
376A ALA* 3.6 1.4 + - - +
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Residues in contact with ALA 375 (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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284A TYR* 3.4 8.0 - - - -
287A LYS* 5.3 1.2 - - - +
288A ASN* 3.2 16.6 + - - -
371A PHE 4.0 2.1 + - - +
372A SER* 3.2 18.2 + - - +
373A TRP 4.6 0.2 - - - +
374A GLU* 1.3 77.1 - - - +
376A ALA* 1.3 57.9 + - - +
377A ASP* 3.2 29.8 + - + +
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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