Contacts of the helix formed by residues 324 - 329 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PRO* 3.5 16.1 + - - +
322C PRO* 4.5 2.0 - - - -
323C VAL* 1.3 78.6 - - + +
325C TYR* 1.3 64.8 + - - +
326C PHE* 3.4 4.2 + - - +
327C ALA* 3.1 23.7 + - + +
328C GLU* 3.0 31.0 + - - +
388D ARG* 4.7 2.8 - - - +
396D ASP 3.4 15.7 - - - +
397D ASN* 2.9 46.3 + - - +
399D GLY* 2.8 23.1 + - - +
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Residues in contact with TYR 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PRO 3.0 15.0 + - - +
173A GLN 3.8 18.4 + - - +
174A THR 4.8 1.1 - - - -
175A HIS* 3.3 62.0 + + + +
76C ALA 5.4 0.3 + - - -
78C GLY* 2.6 34.1 + - - -
79C ALA* 4.5 5.4 - - - -
80C GLY 4.8 1.1 - - - -
112C ARG* 4.7 2.1 + - - -
262C ILE* 4.8 6.1 - - + -
322C PRO* 4.6 4.7 - - + -
324C ASN* 1.3 71.3 - - - +
326C PHE* 1.3 60.9 + - + +
329C VAL* 2.7 66.7 + - + +
330C GLU* 3.1 29.7 + - + -
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Residues in contact with PHE 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PRO 4.7 0.8 + - - -
67C GLU 4.1 5.8 - - - -
68C ARG* 5.6 0.2 - - - -
69C ILE* 4.0 37.0 - - + -
324C ASN* 3.4 6.0 + - - +
325C TYR* 1.3 81.1 - - + +
327C ALA* 1.3 60.4 + - - +
330C GLU* 3.8 22.9 - - + -
331C GLN* 3.0 52.1 + - + +
389D ASP* 3.3 47.1 - - + +
390D GLY 3.3 33.0 - - - -
393D CYS* 3.8 5.2 - - + -
397D ASN* 4.0 3.8 - - - -
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Residues in contact with ALA 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C ASN* 3.1 22.7 + - + +
326C PHE* 1.3 81.8 - - - +
328C GLU* 1.3 63.2 + - + +
331C GLN* 3.7 24.8 + - - +
373C ILE* 4.4 2.3 - - - +
375C VAL* 3.6 18.5 + - - +
393D CYS* 5.0 4.3 - - - +
395D GLN 4.7 7.6 - - - +
396D ASP* 4.2 7.6 - - - +
397D ASN* 3.9 17.7 - - + -
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Residues in contact with GLU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PHE* 3.5 40.5 - - + -
320C ARG* 4.7 7.1 + - - -
321C ASN 4.8 0.7 - - - +
322C PRO* 3.7 8.8 - - + +
323C VAL* 2.8 35.5 + - - +
324C ASN* 3.0 20.7 + - - +
327C ALA* 1.3 84.7 - - + +
329C VAL* 1.3 58.9 + - - +
332C ILE* 3.6 11.7 - - - +
375C VAL* 3.6 26.2 - - + +
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Residues in contact with VAL 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ARG* 2.9 17.3 + - - -
79C ALA 4.1 0.9 - - - -
80C GLY* 3.8 24.9 - - - +
82C PHE* 5.1 1.6 - - + -
112C ARG* 3.8 21.5 - - + +
322C PRO* 3.6 33.0 - - + -
325C TYR* 2.7 53.2 + - + +
328C GLU* 1.3 78.5 - - - +
330C GLU* 1.3 65.6 + - - +
331C GLN 3.2 1.1 - - - -
332C ILE* 3.0 13.3 - - - +
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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