Contacts of the helix formed by residues 223 - 229 (chain B) in PDB entry 6DWM
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B ASN 4.1 4.3 - - - +
222B ASN* 1.3 72.6 - - - +
224B PHE* 1.3 65.2 + - - +
225B GLY 3.3 2.9 - - - -
226B GLU* 3.1 36.9 + - + +
227B VAL* 3.1 23.5 + - - +
247B SER* 2.9 37.8 + - - +
250B ALA* 3.9 13.3 - - - +
251B PHE* 4.0 16.0 + - - +
254B LEU* 4.1 7.2 - - - +
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Residues in contact with PHE 224 (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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115B ILE* 3.8 30.3 - - + -
123B PHE* 4.0 11.7 - + - -
222B ASN 3.4 3.4 + - - -
223B ASN* 1.3 77.5 + - - +
225B GLY* 1.3 67.4 + - - +
227B VAL* 3.4 0.7 + - - -
228B VAL* 3.1 35.1 + - + +
251B PHE* 3.6 22.6 - + - -
254B LEU* 3.9 6.1 - - + +
255B ASN* 4.0 8.3 - - - -
320B ASP* 5.6 2.9 - - - -
496B LEU* 4.3 8.3 - - + -
602B HJJ 3.5 91.8 - + + +
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Residues in contact with GLY 225 (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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222B ASN 5.2 0.8 + - - -
223B ASN 3.3 0.4 - - - -
224B PHE* 1.3 83.8 - - - +
226B GLU* 1.3 62.6 + - - +
229B GLY 3.0 10.9 + - - -
320B ASP* 5.4 3.0 + - - -
495B GLY* 3.4 3.0 - - - -
496B LEU* 2.8 41.2 + - - -
497B THR* 4.4 15.7 - - - -
499B LYS* 6.3 1.5 - - - +
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Residues in contact with GLU 226 (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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222B ASN 5.4 1.8 - - - +
223B ASN* 3.1 29.2 + - + +
225B GLY* 1.3 77.6 - - - +
227B VAL* 1.3 61.8 + - + +
229B GLY* 4.1 6.4 + - - +
232B ASN* 4.8 3.5 + - - +
493B ILE* 4.3 17.6 - - + +
494B TYR* 4.2 17.4 - - - +
495B GLY* 4.2 8.3 - - - -
497B THR 6.1 0.7 - - - +
499B LYS* 5.2 12.1 - - - -
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Residues in contact with VAL 227 (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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111B THR* 3.8 22.0 + - + +
223B ASN* 3.1 34.3 + - + +
224B PHE 4.1 0.2 - - - +
226B GLU* 1.3 81.5 - - + +
228B VAL* 1.3 60.6 + - - +
229B GLY 3.4 0.2 - - - -
232B ASN* 2.7 44.1 + - - +
235B ASP* 4.7 0.2 - - - +
247B SER* 4.0 18.4 - - - +
248B LEU* 4.0 8.1 - - + -
251B PHE* 3.7 35.0 - - + -
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Residues in contact with VAL 228 (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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111B THR* 5.0 3.6 - - - +
112B PHE* 3.9 20.2 - - + -
115B ILE* 3.9 10.1 - - + -
123B PHE* 3.6 27.4 - - + -
224B PHE* 3.1 31.3 + - + +
225B GLY 4.5 0.2 - - - +
227B VAL* 1.3 76.2 - - + +
229B GLY* 1.3 66.2 + - - +
230B SER* 3.4 2.8 + - - -
232B ASN* 5.6 0.2 - - - -
235B ASP* 5.8 0.8 - - - +
251B PHE* 3.7 26.2 - - + -
386B ILE* 5.5 0.7 - - + -
387B PRO* 4.8 5.5 - - - +
496B LEU* 3.7 24.7 - - + +
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Residues in contact with GLY 229 (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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225B GLY 3.0 11.2 + - - -
226B GLU 4.1 3.7 + - - +
227B VAL 3.4 2.2 - - - -
228B VAL* 1.3 77.2 - - - +
230B SER* 1.3 69.0 + - - +
231B GLY 3.2 2.3 + - - -
232B ASN* 3.3 17.0 + - - +
494B TYR* 3.9 10.4 - - - -
495B GLY* 4.1 4.7 - - - -
496B LEU* 3.5 25.7 - - - +
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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