Contacts of the helix formed by residues 324 - 329 (chain B) in PDB entry 1DGH
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 324 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A ARG* 4.8 2.4 - - - +
396A ASP 3.6 15.0 - - - +
397A ASN* 3.1 38.6 + - - +
399A GLY* 2.8 24.3 + - - +
322B PRO* 4.4 2.5 - - - -
323B VAL* 1.3 78.8 - - + +
325B TYR* 1.3 65.8 + - - +
326B PHE* 3.4 4.9 + - - +
327B ALA* 3.0 27.6 + - + +
328B GLU* 3.0 31.5 + - - +
172D PRO* 3.6 18.0 + - - +
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Residues in contact with TYR 325 (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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76B ALA 5.3 0.5 + - - -
77B LYS* 6.0 0.2 - - - -
78B GLY* 2.6 36.0 + - - -
79B ALA* 4.4 5.8 - - - -
80B GLY 4.8 1.1 - - - -
112B ARG* 4.7 1.9 + - - -
262B ILE* 4.8 5.4 - - + -
322B PRO* 4.4 4.7 - - + +
324B ASN* 1.3 70.3 - - - +
326B PHE* 1.3 63.4 + - - +
329B VAL* 2.7 63.5 + - + +
330B GLU* 3.0 35.5 + - + -
172D PRO 3.0 16.7 + - - +
173D GLN 3.9 15.2 + - - +
174D THR 4.6 3.1 - - - -
175D HIS* 3.3 62.3 + + + +
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Residues in contact with PHE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ASP* 3.4 47.8 - - + +
390A GLY 3.4 32.3 - - - -
393A CYS* 3.8 5.8 - - + -
397A ASN* 4.1 3.6 - - - -
67B GLU 4.1 6.5 - - - -
68B ARG* 5.7 0.4 - - - -
69B ILE* 4.1 29.8 - - + -
324B ASN* 3.4 6.9 + - - +
325B TYR* 1.3 80.0 - - + +
327B ALA* 1.3 59.5 + - - +
330B GLU* 3.5 30.7 - - + +
331B GLN* 3.0 49.1 + - + +
172D PRO 4.7 1.0 + - - -
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Residues in contact with ALA 327 (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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393A CYS* 5.0 3.6 - - - +
395A GLN 4.5 8.3 - - - +
396A ASP* 4.3 8.1 - - - +
397A ASN* 3.9 17.7 - - + -
324B ASN* 3.0 24.2 + - + +
326B PHE* 1.3 81.1 - - - +
328B GLU* 1.3 65.5 + - + +
331B GLN* 3.9 22.1 + - - +
373B ILE* 4.5 2.3 - - - +
375B VAL* 3.6 18.0 + - - +
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Residues in contact with GLU 328 (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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396A ASP 5.6 0.2 - - - +
82B PHE* 3.6 39.8 - - + -
320B ARG* 4.9 7.4 + - - -
321B ASN 4.7 1.0 - - - +
322B PRO* 3.7 5.8 - - + +
323B VAL* 2.9 39.8 + - - +
324B ASN* 3.0 21.2 + - - +
327B ALA* 1.3 82.8 - - + +
329B VAL* 1.3 62.5 + - - +
332B ILE* 3.7 11.2 - - - +
375B VAL* 3.6 25.3 - - + +
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Residues in contact with VAL 329 (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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72B ARG* 3.0 16.5 + - - -
79B ALA 4.1 1.1 - - - -
80B GLY* 3.8 27.1 - - - +
82B PHE* 5.1 2.0 - - + -
112B ARG* 3.9 20.2 - - + +
322B PRO* 3.7 31.0 - - + -
325B TYR* 2.7 51.8 + - + +
328B GLU* 1.3 78.8 - - - +
330B GLU* 1.3 66.6 + - - +
331B GLN 3.2 1.1 - - - -
332B ILE* 3.2 13.0 + - - +
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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