Contacts of the helix formed by residues 223 - 230 (chain D) in PDB entry 2GRA
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 HIS 223 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217D LEU* 3.6 12.6 - - - +
221D GLU 3.5 3.7 - - - +
222D GLN* 1.3 82.1 - - - +
224D PRO* 1.3 102.3 - - + +
225D GLY* 3.0 24.3 + - - -
226D GLN* 3.1 18.6 + - + +
227D LEU* 3.4 6.1 + - - +
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Residues in contact with PRO 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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217D LEU* 3.6 30.3 - - + -
223D HIS* 1.3 100.8 - - + +
225D GLY* 1.3 67.2 + - - +
226D GLN 2.6 2.9 + - - -
227D LEU* 2.9 4.9 + - + +
228D LYS* 2.9 23.0 + - - +
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Residues in contact with GLY 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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186B ASP* 5.3 8.1 - - - -
223D HIS* 3.0 17.4 + - - -
224D PRO* 1.3 75.9 - - - +
226D GLN* 1.3 59.8 + - - +
228D LYS* 3.3 12.7 - - - +
229D ASP* 2.5 35.7 + - - +
251D ARG* 6.1 2.9 - - - -
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Residues in contact with GLN 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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199B ARG* 6.0 1.2 - - - +
222D GLN* 3.5 35.2 - - + +
223D HIS* 3.1 15.9 + - + +
224D PRO 2.6 4.6 + - - -
225D GLY* 1.3 67.3 - - - +
227D LEU* 1.3 56.5 + - + +
228D LYS 2.6 3.9 + - - -
229D ASP* 2.6 41.1 + - - +
230D ASN* 3.1 35.4 + - - +
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Residues in contact with LEU 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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213D ALA 5.6 0.7 - - - +
216D MET* 4.2 29.1 - - + +
217D LEU* 3.6 48.0 - - + +
220D SER* 4.0 7.6 - - - +
222D GLN* 3.6 32.8 - - + +
223D HIS 3.8 2.0 - - - +
224D PRO* 2.9 7.5 + - + +
226D GLN* 1.3 77.7 - - + +
228D LYS* 1.3 64.0 + - - +
230D ASN* 3.5 21.5 + - + +
231D VAL* 3.3 21.3 - - - +
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Residues in contact with LYS 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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186B ASP* 3.9 12.7 + - - -
190B ASP* 2.9 39.3 + - - -
224D PRO 2.9 13.0 + - - +
225D GLY* 3.3 14.8 - - - +
226D GLN 2.6 4.2 + - - -
227D LEU* 1.3 72.6 - - - +
229D ASP* 1.3 86.4 + - - +
231D VAL* 2.8 18.5 + - - +
232D SER* 2.9 11.5 + - - -
238D THR* 5.8 0.2 - - - +
239D ILE* 5.9 0.2 - - - -
242D LEU* 4.0 33.2 - - + +
246D GLU* 6.3 1.6 - - - -
251D ARG* 4.9 15.9 - - - +
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Residues in contact with ASP 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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190B ASP* 4.3 0.4 - - - +
199B ARG* 2.7 56.7 + - + +
225D GLY 2.5 26.5 - - - +
226D GLN* 2.6 19.9 + - - +
228D LYS* 1.3 88.1 - - - +
230D ASN* 1.3 57.4 + - - +
231D VAL 2.6 13.2 + - - -
232D SER* 2.7 28.9 + - - +
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Residues in contact with ASN 230 (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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216D MET* 6.2 1.8 - - + -
222D GLN* 5.8 1.0 + - - -
226D GLN* 3.1 33.5 + - - +
227D LEU* 3.6 24.0 - - + +
228D LYS 3.2 0.2 - - - -
229D ASP* 1.3 73.3 - - - +
231D VAL* 1.3 62.0 + - + +
232D SER 3.5 1.2 + - - -
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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