Contacts of the helix formed by residues 348 - 352 (chain A) in PDB entry 4WMB
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 ASP 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A GLU* 5.8 1.2 + - - -
253A ALA* 4.3 2.3 - - - +
346A VAL 3.9 1.2 + - - -
347A LEU* 1.3 76.6 - - - +
349A CYS* 1.3 75.2 + - - +
350A THR* 2.6 41.2 + - - +
351A TRP* 3.0 30.1 + - + +
352A ASN 4.2 0.9 + - - -
375A GLU 4.6 2.9 - - - +
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Residues in contact with CYS 349 (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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253A ALA* 4.9 2.7 - - - -
254A ARG* 5.9 1.3 - - + +
256A MET* 3.3 25.9 - - + +
347A LEU 3.6 2.9 + - - -
348A ASP* 1.3 87.0 + - - +
350A THR* 1.3 61.4 + - - +
351A TRP 3.1 0.9 - - - -
352A ASN 3.2 23.6 + - - +
353A ARG* 3.2 4.3 + - - -
373A ARG 4.8 2.5 - - - +
374A CYS* 2.0 52.2 - - + -
375A GLU 4.1 6.7 - - - -
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Residues in contact with THR 350 (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 ASP* 2.6 24.7 + - - +
349A CYS* 1.3 75.6 - - - +
351A TRP* 1.3 60.5 + - - +
352A ASN 3.2 1.1 + - - -
353A ARG* 4.9 2.9 - - - -
374A CYS* 3.9 10.5 - - - -
375A GLU 3.7 21.3 - - - +
376A GLY* 3.9 13.5 - - - +
377A HIS 3.4 28.0 + - - +
378A VAL* 4.0 7.2 - - + +
379A LYS* 2.9 38.5 + - - +
380A ILE 3.1 11.5 + - - +
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Residues in contact with TRP 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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230A TYR* 6.2 0.2 - + - -
232A THR* 3.7 24.7 - - + -
233A ASN 4.7 1.3 - - - -
234A ILE* 5.2 3.1 - - + -
236A GLU* 4.1 12.8 - - + -
237A LEU* 3.6 58.6 - - + +
239A GLU* 5.4 2.2 - - - -
240A GLU* 4.2 20.6 + - + +
291A VAL* 3.4 12.5 - - + +
347A LEU* 4.3 18.8 - - + -
348A ASP* 3.0 26.2 + - + +
350A THR* 1.3 80.8 + - - +
352A ASN* 1.3 62.1 + - + +
379A LYS* 3.4 40.7 - - + +
380A ILE* 3.3 44.8 - - + +
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Residues in contact with ASN 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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253A ALA* 3.8 21.0 - - + +
256A MET* 2.9 18.5 - - - +
288A ASN* 3.0 37.6 + - - +
291A VAL* 3.7 30.2 + - + +
348A ASP 4.2 0.4 + - - -
349A CYS 3.2 5.5 + - - -
351A TRP* 1.3 81.9 - - - +
353A ARG* 1.3 58.4 + - - +
354A GLN* 3.0 9.4 + - - +
380A ILE* 3.9 4.7 - - - -
382A HIS* 2.9 31.4 + - - +
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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