Contacts of the helix formed by residues 222 - 229 (chain D) in PDB entry 7A62
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 222 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A GLN* 5.9 2.5 - - - +
215A HIS* 6.5 1.3 - - + -
157D GLY 5.1 1.0 + - - -
159D CYS* 3.5 15.8 - - - -
221D VAL* 1.3 76.5 - - - +
223D PRO* 1.3 72.3 - - + +
224D LYS* 3.5 11.8 + - - +
225D ALA* 2.9 40.1 + - - +
226D PHE* 3.0 12.1 + - - +
353D TYR* 3.7 1.3 - - - -
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Residues in contact with PRO 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLN* 5.5 6.5 - - - +
221D VAL 4.2 1.1 - - - +
222D ASN* 1.3 84.8 - - + +
224D LYS* 1.3 67.2 + - - +
225D ALA 3.1 0.2 + - - -
226D PHE 3.2 0.2 + - - -
227D PHE* 2.8 30.1 + - - +
352D LYS* 3.6 50.0 - - + +
353D TYR* 3.5 19.5 - - + -
357D PRO* 4.1 11.0 - - + -
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Residues in contact with LYS 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D ASN* 3.4 8.6 + - - +
223D PRO* 1.3 79.1 - - - +
225D ALA* 1.3 56.2 + - + +
227D PHE* 5.0 2.5 - - - -
228D SER* 2.3 58.3 + - - +
357D PRO* 5.1 5.5 - - - +
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Residues in contact with ALA 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D GLY 3.5 23.3 - - - +
158D ASP 4.3 3.2 - - - +
159D CYS* 3.7 10.1 - - + -
222D ASN* 2.9 34.7 + - - +
224D LYS* 1.3 76.7 - - - +
226D PHE* 1.3 66.1 + - - +
228D SER* 4.2 1.8 - - - -
229D VAL* 3.0 26.6 + - - +
230D LEU 3.3 7.1 + - - -
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Residues in contact with PHE 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D ASP 4.7 2.2 + - - -
163D PHE* 3.9 34.5 - + - -
221D VAL* 3.8 23.9 - - + +
222D ASN 3.0 8.1 + - - +
223D PRO 3.9 3.8 - - - +
225D ALA* 1.3 78.3 - - - +
227D PHE* 1.3 69.8 + - - +
228D SER 3.4 0.2 + - - -
230D LEU* 3.9 30.3 - - + -
231D ARG* 2.9 50.0 + - + +
234D LEU* 4.9 4.0 - - + -
353D TYR* 4.0 19.3 - + + -
354D ILE* 3.7 15.3 - - + -
504D HEM 3.5 33.0 - + + -
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Residues in contact with PHE 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D PRO 2.8 20.5 + - - +
224D LYS* 4.4 1.6 - - - +
226D PHE* 1.3 81.5 - - - +
228D SER* 1.3 67.3 + - - +
231D ARG* 3.0 68.8 + - - +
232D ILE* 4.6 0.7 - - - +
353D TYR 3.5 14.4 - - - +
354D ILE* 3.7 30.1 - - + -
357D PRO* 3.7 24.9 - - + -
358D ALA* 3.6 22.2 - - + -
362D PRO* 3.7 33.4 - - + -
379D THR* 4.6 3.6 - - - -
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Residues in contact with SER 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D GLY 5.0 3.6 - - - +
96D HIS* 5.7 4.3 - - - -
224D LYS* 2.3 51.5 + - - +
225D ALA* 4.2 0.2 - - - -
227D PHE* 1.3 87.7 - - - +
229D VAL* 1.3 71.1 + - - +
231D ARG* 5.2 0.4 - - - +
232D ILE* 3.7 16.6 - - - +
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Residues in contact with VAL 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D HIS* 6.5 0.9 - - + -
155D ARG* 4.1 24.7 - - + +
156D ASP 5.8 0.7 - - - +
157D GLY 5.4 2.7 - - - +
158D ASP* 3.9 25.1 - - + -
224D LYS* 6.3 0.4 - - - -
225D ALA* 3.0 16.0 + - - +
227D PHE 3.6 0.4 - - - -
228D SER* 1.3 93.4 - - - +
230D LEU* 1.3 68.3 + - - +
231D ARG 3.3 0.9 - - - -
232D ILE* 3.0 19.1 + - - +
233D TYR* 3.3 17.1 - - + -
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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