Contacts of the helix formed by residues 327 - 331 (chain M) in PDB entry 4WQS
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 HIS 327 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324M ASP* 2.6 34.5 + - + +
325M ILE 2.6 9.3 + - - +
326M ASP* 1.3 67.4 - - - +
328M LEU* 1.3 55.2 + - - +
329M GLY* 2.8 33.1 + - - -
330M ASN* 3.0 24.5 + - - +
331M ARG* 4.1 2.3 + - - +
431M HIS* 3.4 12.3 + + - +
433M THR* 3.8 10.5 + - + -
488M ALA* 3.3 28.0 - - + -
489M THR* 3.5 20.0 - - + +
492M ASP* 3.1 25.9 + - - +
518M LYS* 6.0 1.6 - - - -
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Residues in contact with LEU 328 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326M ASP 2.9 17.3 - - - +
327M HIS* 1.3 69.1 - - - +
329M GLY* 1.3 54.8 + - - +
330M ASN 3.2 4.1 + - - -
331M ARG* 3.5 13.6 - - - +
433M THR* 2.9 42.5 - - + +
434M HIS* 3.0 30.5 - - + +
437M ARG* 3.1 26.9 - - + -
438M ILE* 4.8 6.3 - - + -
466M PHE* 3.0 23.9 - - - -
467M ILE* 5.6 6.5 - - + +
488M ALA* 3.1 15.3 - - + -
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Residues in contact with GLY 329 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275M TYR* 2.9 23.3 + - - -
280M LYS* 3.6 4.7 + - - -
327M HIS* 2.8 14.6 + - - -
328M LEU* 1.3 72.4 - - - +
330M ASN* 1.4 68.9 + - - +
466M PHE* 3.5 11.1 - - - -
487M THR* 4.5 1.8 - - - -
488M ALA* 3.4 4.3 - - - +
489M THR* 3.3 27.5 - - - +
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Residues in contact with ASN 330 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142M ARG* 3.1 10.8 - - - +
143M SER* 2.9 13.0 + - - -
147M TYR* 2.8 48.5 + - + -
280M LYS* 3.2 22.7 + - - +
323M ASP* 3.5 17.7 + - - +
324M ASP 4.3 5.5 + - - +
325M ILE* 4.4 7.8 - - - +
327M HIS* 3.0 31.2 + - - +
329M GLY* 1.4 87.1 - - - +
331M ARG* 1.3 63.9 + - - +
489M THR* 4.7 3.1 - - - +
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Residues in contact with ARG 331 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140M ILE* 3.0 33.9 - - + +
141M HIS 2.7 23.9 + - - +
142M ARG* 3.9 9.3 - - - +
325M ILE* 3.4 33.3 - - - +
326M ASP* 3.1 37.3 + - - +
327M HIS 4.5 2.9 - - - +
328M LEU* 3.5 10.3 + - - +
330M ASN* 1.3 84.8 - - - +
332M ARG* 1.3 62.4 + - - +
333M ILE* 3.7 10.4 - - + +
419M THR* 6.3 0.6 - - - -
427M VAL* 3.7 27.0 + - - +
434M HIS* 5.8 3.2 + - - -
465M GLY 3.9 0.2 - - - +
466M PHE* 3.4 14.3 - - - -
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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