Contacts of the helix formed by residues 389 - 393 (chain B) in PDB entry 4WMJ
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 ASN 389 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLY* 5.7 0.2 - - - -
166A LEU* 6.0 0.2 - - - +
188A SER* 3.3 18.3 + - - +
189A ASN* 3.3 27.8 - - - +
194A HIS* 4.8 1.2 - - - -
346B GLN* 2.9 29.4 + - - +
385B GLU* 5.0 6.7 + - + +
386B PRO* 3.0 21.6 + - + +
388B THR* 1.3 75.6 - - - +
390B GLY* 1.3 64.1 + - - +
392B HIS* 3.0 19.5 + - - +
393B ALA* 3.3 12.8 + - - +
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Residues in contact with GLY 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B GLU* 4.0 9.1 - - - +
386B PRO 2.9 14.4 + - - -
389B ASN* 1.3 75.8 - - - +
391B GLN* 1.3 63.7 + - - +
393B ALA* 3.0 12.8 + - - -
394B PHE* 3.0 41.5 + - - -
395B TYR* 3.3 14.6 - - - -
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Residues in contact with GLN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU* 4.3 0.6 + - - -
361A GLU* 5.1 0.3 - - - +
518A VAL* 4.9 11.1 - - - +
522A LYS* 5.9 5.3 - - - +
344B TYR* 2.7 32.8 + - - +
387B GLY* 5.1 0.2 - - - -
388B THR* 3.0 25.1 - - - +
390B GLY* 1.3 77.8 - - - +
392B HIS* 1.3 75.0 + - + +
393B ALA 3.5 0.3 + - - -
395B TYR* 3.4 44.8 + - + +
396B GLN 5.0 0.2 + - - -
431B ASN* 2.9 29.0 + - - +
435B GLN* 3.5 28.3 - - - +
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Residues in contact with HIS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ILE* 3.7 36.6 - - + +
162A GLY* 3.7 22.8 - - - +
188A SER 5.4 0.7 - - - -
220A GLU* 2.7 39.0 + - - -
357A GLN* 3.3 21.1 + - - -
361A GLU* 3.7 10.8 - - - +
518A VAL* 6.1 0.9 - - - -
522A LYS* 5.1 15.1 - - + -
388B THR* 3.2 30.2 + - - -
389B ASN* 3.0 11.0 + - - +
391B GLN* 1.3 91.8 + - - +
393B ALA* 1.3 57.6 + - - +
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 4.3 12.8 - - + -
353A ALA 5.3 1.3 - - - +
356A GLN* 5.3 1.3 - - - +
357A GLN* 3.4 34.3 - - + +
361A GLU* 3.4 28.2 + - - +
385B GLU* 6.1 1.6 - - + -
389B ASN 3.3 9.3 + - - +
390B GLY* 3.0 10.8 + - - +
392B HIS* 1.3 79.9 - - - +
394B PHE* 1.3 72.5 + - + +
395B TYR 3.9 0.7 - - - -
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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