Contacts of the helix formed by residues 354 - 361 (chain A) in PDB entry 3C0M
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 SER 354 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A PHE* 4.7 0.2 - - - -
344A VAL 5.2 1.8 - - - -
348A TYR* 4.1 17.5 - - - -
349A LYS 5.8 0.2 - - - -
350A ASP 3.4 13.3 + - - -
351A LYS 3.1 4.6 + - - -
352A ALA 3.4 0.4 - - - -
353A SER* 1.3 77.4 - - - +
355A ILE* 1.3 66.3 + - - +
356A ARG* 3.6 7.3 + - - +
357A TYR* 2.7 39.3 + - - +
358A GLN* 3.2 24.3 + - - +
45B TRP* 4.3 2.6 - - - -
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Residues in contact with ILE 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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85A ILE* 4.6 0.9 - - + -
119A LEU* 3.8 30.1 - - + -
343A PHE* 3.3 42.0 - - + -
344A VAL 5.4 1.4 + - - -
345A ILE* 4.5 3.4 - - + -
353A SER 3.6 3.2 + - - -
354A SER* 1.3 72.5 - - - +
356A ARG* 1.3 63.9 + - - +
358A GLN* 3.6 1.4 + - - +
359A TRP* 3.0 23.8 + - + +
373A TRP* 4.1 12.8 + - + -
389A LEU* 3.9 34.1 - - + -
392A VAL* 4.2 17.0 - - + -
393A LEU* 4.2 25.3 - - + +
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Residues in contact with ARG 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 6.2 0.2 - - - +
85A ILE* 3.3 54.3 + - + +
86A PRO 3.6 4.6 + - - -
87A THR* 3.4 21.9 + - - +
354A SER* 3.1 5.3 + - - +
355A ILE* 1.3 82.7 - - - +
357A TYR* 1.3 66.2 + - - +
359A TRP* 3.9 4.1 - - - +
360A ASP* 3.1 32.1 + - - +
393A LEU* 3.8 29.6 + - + +
44B GLN* 4.6 23.7 + - - +
45B TRP* 4.1 10.0 - - + -
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Residues in contact with TYR 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TYR* 4.4 4.0 - + + -
351A LYS* 2.9 55.1 + - + -
354A SER* 2.7 33.7 + - - +
356A ARG* 1.3 71.3 - - - +
358A GLN* 1.3 72.2 + - + +
360A ASP* 2.8 15.8 + - - +
361A LYS* 3.1 40.7 + - + +
367A GLU* 2.8 29.1 + - + -
370A TRP* 4.9 3.6 - + - -
45B TRP* 3.8 29.3 - + + -
61B TYR* 3.4 30.9 + + - -
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Residues in contact with GLN 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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343A PHE* 4.2 2.0 - - - -
351A LYS 3.1 15.3 + - - +
352A ALA* 2.7 34.4 + - - +
354A SER 3.2 13.8 + - - +
355A ILE 4.0 0.2 - - - +
357A TYR* 1.3 86.4 - - + +
359A TRP* 1.3 63.1 + - - +
361A LYS* 3.3 3.0 + - - +
362A ARG* 3.0 24.6 + - - +
367A GLU 5.7 0.9 - - - +
370A TRP* 3.7 30.9 - - + +
371A TRP* 3.3 21.5 - - - +
373A TRP* 2.8 35.5 + - + +
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Residues in contact with TRP 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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83A GLY 3.1 23.7 + - - -
84A GLU* 4.4 0.4 - - - +
85A ILE* 3.6 32.5 - - + +
355A ILE 3.0 19.9 + - - +
356A ARG 3.9 2.7 - - - +
358A GLN* 1.3 76.6 - - - +
360A ASP* 1.3 76.6 + - - +
362A ARG* 3.1 52.8 + - - +
373A TRP* 3.7 37.4 - + + -
376A THR* 4.5 1.3 - - - -
377A ILE* 3.8 21.8 - - + -
382A LEU* 4.0 12.1 - - + -
385A MET* 3.6 30.7 - - + -
386A GLN* 4.2 10.1 - - + -
389A LEU* 3.4 22.4 - - + -
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Residues in contact with ASP 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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7A ASP* 4.6 4.0 - - - +
81A VAL* 4.6 21.8 - - - +
84A GLU* 5.0 17.6 - - - +
85A ILE* 5.2 1.6 + - - +
356A ARG* 3.1 23.5 + - - +
357A TYR 2.8 8.4 + - - +
359A TRP* 1.3 89.9 + - - +
361A LYS* 1.3 64.3 + - + +
362A ARG* 3.4 2.5 + - - +
363A TYR 5.2 0.3 + - - -
364A ILE* 4.8 3.3 - - - +
44B GLN* 3.4 10.9 + - - -
45B TRP* 2.9 36.8 + - + +
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Residues in contact with LYS 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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357A TYR* 3.1 57.9 + - + +
358A GLN* 3.6 4.0 - - - +
360A ASP* 1.3 82.2 - - + +
362A ARG* 1.3 52.9 + - - +
363A TYR 2.6 19.2 + - - -
364A ILE* 2.9 34.8 + - + +
367A GLU* 3.9 23.9 - - + +
368A VAL* 5.1 1.8 + - - -
45B TRP* 3.8 30.6 + - + +
61B TYR* 3.9 8.9 + - - -
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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