Contacts of the helix formed by residues 208 - 214 (chain D) in PDB entry 4IRQ
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 LYS 208 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D PHE* 3.9 41.0 + - + -
152D SER* 3.0 28.0 + - - -
153D SER 3.6 3.0 + - - -
154D ASN* 4.9 2.8 - - - +
156D THR* 3.1 37.5 + - - +
157D ASP* 3.2 25.9 + - - +
158D TYR* 4.1 3.1 - - - +
159D ILE* 4.6 10.1 - - - -
206D LEU 3.9 0.4 + - - -
207D SER* 1.3 71.5 - - - +
209D GLN* 1.3 63.9 + - - +
211D TYR* 3.2 2.6 + - - +
212D ARG* 2.9 32.7 + - + +
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Residues in contact with GLN 209 (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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179D GLU* 5.1 11.0 + - - -
207D SER* 4.0 8.1 + - - +
208D LYS* 1.3 78.4 - - - +
210D HIS* 1.3 81.4 + - + +
212D ARG* 3.3 7.1 + - - +
213D LEU* 2.9 28.0 + - + +
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Residues in contact with HIS 210 (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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178D PRO 4.3 1.8 + - - -
179D GLU 3.3 25.7 + - - -
180D ALA 4.0 3.1 - - - -
181D GLY* 3.5 28.7 - - - -
182D PRO* 3.8 5.6 - - + +
206D LEU* 4.2 9.2 - - + -
207D SER* 3.2 23.9 + - - +
209D GLN* 1.3 101.3 + - + +
211D TYR* 1.3 62.0 + - - +
213D LEU* 3.3 10.6 + - + +
214D CYS* 3.2 27.2 + - - -
240D LEU* 3.5 35.9 - - + +
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Residues in contact with TYR 211 (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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145D ILE* 3.4 27.6 - - + +
146D ASN* 2.5 26.1 + - - -
149D PHE* 3.4 48.7 - + + -
159D ILE* 3.4 22.9 - - + -
161D MET* 4.2 9.9 - - + -
206D LEU* 3.9 24.3 - - + +
207D SER 3.0 16.7 + - - +
208D LYS 3.7 3.6 - - - +
210D HIS* 1.3 79.2 - - - +
212D ARG* 1.3 59.8 + - - +
214D CYS* 3.4 4.5 + - - +
216D GLY* 2.9 48.6 + - - -
217D MET* 3.5 10.1 - - + +
231D PHE* 4.3 4.3 - + - -
287D LEU* 4.1 6.3 - - + -
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Residues in contact with ARG 212 (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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149D PHE* 3.7 28.7 - - + -
150D LEU* 4.2 17.6 - - - +
208D LYS* 2.9 24.4 + - - +
209D GLN* 3.6 7.0 - - - +
211D TYR* 1.3 77.0 - - - +
213D LEU* 1.3 57.9 + - - +
215D ASN* 2.8 21.3 + - - +
287D LEU* 3.6 25.9 - - - +
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Residues in contact with LEU 213 (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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209D GLN* 2.9 15.7 + - + +
210D HIS* 3.3 15.0 + - + +
212D ARG* 1.3 76.6 - - - +
214D CYS* 1.3 57.2 + - - +
215D ASN* 3.4 1.2 + - - +
238D ALA* 4.0 27.2 - - + +
240D LEU* 3.8 29.4 - - + -
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Residues in contact with CYS 214 (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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206D LEU* 4.6 2.2 - - - -
210D HIS 3.2 16.3 + - - -
211D TYR 3.9 6.1 - - - +
212D ARG 3.2 0.2 - - - -
213D LEU* 1.3 72.8 - - - +
215D ASN* 1.3 69.2 + - - +
216D GLY 3.2 14.5 - - - +
231D PHE* 4.0 13.9 - - + -
234D ARG* 3.2 26.8 + - + +
235D ILE* 4.0 29.2 - - - -
238D ALA* 4.7 3.4 - - - -
240D LEU* 3.9 21.1 - - - -
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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