Contacts of the helix formed by residues 223 - 229 (chain A) in PDB entry 6DWN
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 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ASN 4.2 7.0 - - - +
222A ASN* 1.3 72.1 - - - +
224A PHE* 1.3 66.8 + - - +
225A GLY 3.3 2.2 - - - -
226A GLU* 2.8 39.2 + - + +
227A VAL* 3.0 19.4 + - - +
247A SER* 2.9 40.6 + - - +
250A ALA* 4.1 12.0 - - - +
251A PHE* 3.9 11.6 + - - +
254A LEU* 5.0 0.7 - - - +
602A AQ4 3.8 14.2 - - - +
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Residues in contact with PHE 224 (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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115A ILE* 3.8 31.6 - - + -
123A PHE* 3.9 8.3 - + - -
222A ASN* 3.4 22.2 + - - +
223A ASN* 1.3 77.4 + - - +
225A GLY* 1.3 60.9 + - - +
227A VAL* 3.9 0.3 - - - -
228A VAL* 2.9 51.3 + - + +
251A PHE* 3.6 21.8 - + - -
255A ASN* 4.2 1.8 - - - -
320A ASP* 5.0 2.0 - - - -
496A LEU* 3.9 20.9 - - + -
602A AQ4 3.5 79.1 - + - +
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Residues in contact with GLY 225 (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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222A ASN 5.1 0.2 + - - -
223A ASN 3.3 0.6 - - - -
224A PHE* 1.3 82.1 - - - +
226A GLU* 1.3 61.9 + - - +
228A VAL 4.1 0.2 - - - -
229A GLY 3.5 6.2 + - - -
320A ASP* 5.2 1.6 - - - -
495A GLY* 3.1 7.8 - - - -
496A LEU* 2.8 44.3 + - - -
497A THR* 4.6 11.0 - - - -
499A LYS* 6.0 0.7 - - - -
602A AQ4 4.5 8.6 - - - -
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Residues in contact with GLU 226 (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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223A ASN* 2.8 36.9 + - + +
225A GLY* 1.3 80.2 - - - +
227A VAL* 1.3 57.4 + - + +
229A GLY* 4.5 2.8 + - - -
232A ASN* 5.0 2.1 + - - +
247A SER* 3.8 22.2 + - - +
494A TYR* 5.0 6.6 - - - +
495A GLY* 4.8 6.1 - - - -
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Residues in contact with VAL 227 (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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111A THR* 3.8 21.8 + - + +
223A ASN* 3.0 27.2 + - + +
226A GLU* 1.3 79.3 - - + +
228A VAL* 1.3 63.6 + - - +
229A GLY 3.4 0.7 - - - -
232A ASN* 2.7 44.8 + - - +
235A ASP* 4.8 0.3 - - - +
247A SER* 3.6 29.2 - - - +
248A LEU* 4.5 7.4 - - + +
251A PHE* 3.9 32.1 - - + -
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Residues in contact with VAL 228 (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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111A THR* 5.1 3.1 - - - -
112A PHE* 3.9 23.5 - - + -
115A ILE* 3.9 7.6 - - + -
123A PHE* 3.8 26.9 - - + -
224A PHE* 2.9 39.2 + - + +
227A VAL* 1.3 76.2 - - + +
229A GLY* 1.3 67.1 + - - +
230A SER* 3.4 2.3 + - - -
235A ASP* 5.6 1.2 - - - +
251A PHE* 3.8 25.4 - - + -
386A ILE* 5.8 0.9 - - + -
387A PRO* 5.1 4.7 - - + +
496A LEU* 3.9 21.3 - - + +
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Residues in contact with GLY 229 (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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225A GLY 3.5 9.7 + - - -
226A GLU 4.5 3.0 + - - +
227A VAL 3.4 2.7 - - - -
228A VAL* 1.3 79.4 - - - +
230A SER* 1.3 68.8 + - - +
231A GLY 3.3 2.4 + - - -
232A ASN* 3.4 16.8 + - - +
235A ASP* 5.6 0.2 - - - +
494A TYR* 3.9 9.5 - - - -
495A GLY* 4.3 4.0 - - - -
496A LEU* 3.8 25.2 - - - +
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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