Contacts of the helix formed by residues 350 - 355 (chain A) in PDB entry 3W6R
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 MET 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A GLY* 1.3 73.9 - - - -
351A LEU* 1.3 66.7 + - - +
352A ALA* 4.2 8.3 - - + +
353A ASP* 3.0 37.4 + - - +
354A PHE* 3.3 8.5 - - - -
429A LEU* 4.2 1.6 - - - -
430A LYS* 3.6 29.2 - - + +
431A GLU* 3.5 40.6 - - + +
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Residues in contact with LEU 351 (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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350A MET* 1.3 74.1 - - - +
352A ALA* 1.3 58.2 + - - +
354A PHE* 2.9 26.7 + - - +
355A VAL* 3.8 6.0 + - + +
363A PRO* 3.6 30.7 - - + -
425A PHE* 4.7 3.6 - - + -
426A LEU* 5.2 0.2 - - + -
429A LEU* 3.9 38.0 - - + +
431A GLU* 5.6 4.6 + - + +
433A LEU* 3.8 11.4 - - + -
468A ALA* 3.5 30.7 - - + +
469A ASN* 3.5 37.2 - - - +
472A THR* 3.9 11.4 - - + +
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Residues in contact with ALA 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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350A MET* 3.2 7.0 - - + +
351A LEU* 1.3 78.3 - - - +
353A ASP* 1.3 61.5 + - - +
354A PHE 3.1 1.3 + - - -
355A VAL* 3.1 37.9 + - + +
468A ALA* 4.7 8.2 - - + +
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Residues in contact with ASP 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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348A GLU 5.5 0.4 - - - +
349A GLY* 4.1 5.2 - - - -
350A MET* 3.0 39.2 + - - +
352A ALA* 1.3 80.3 - - - +
354A PHE* 1.3 69.3 + - + +
355A VAL 3.5 2.0 - - - +
404A LYS* 5.4 7.8 - - - +
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Residues in contact with PHE 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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348A GLU* 3.2 42.2 - - + -
350A MET 3.3 26.5 - - - -
351A LEU 2.9 9.4 + - - +
353A ASP* 1.3 86.4 - - + +
355A VAL* 1.3 59.1 + - - +
363A PRO* 3.4 35.1 - - + +
364A SER 4.4 2.4 + - - -
400A PHE* 3.7 36.3 - + - -
401A LEU* 4.0 8.1 - - + -
404A LYS* 5.2 14.1 - - + -
425A PHE* 3.8 17.9 - + - -
429A LEU* 4.0 11.4 - - + -
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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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351A LEU* 4.0 7.4 - - + +
352A ALA* 3.1 35.1 - - + +
353A ASP 4.6 1.6 - - - +
354A PHE* 1.3 85.7 + - - +
356A SER* 1.3 69.8 + - - +
361A MET* 3.8 25.6 - - + +
362A ILE 3.8 7.9 - - - +
363A PRO* 3.7 26.0 - - + -
468A ALA* 3.9 17.5 - - + -
472A THR* 5.0 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