Contacts of the helix formed by residues 208 - 214 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C PHE* 3.6 44.9 + - + -
150C LEU 6.0 0.2 + - - -
152C SER* 4.4 10.8 + - - -
153C SER 4.4 8.8 + - - -
154C ASN* 4.4 12.0 + - - +
156C THR* 3.6 43.5 - - + +
157C ASP 3.3 18.4 + - - +
158C TYR* 4.1 2.1 - - - +
159C ILE* 5.2 0.2 - - + -
206C LEU 3.8 1.0 + - - -
207C SER* 1.3 71.4 - - - +
209C GLN* 1.3 57.6 + - - +
211C TYR 3.3 0.5 + - - -
212C ARG* 2.9 43.8 + - + +
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Residues in contact with GLN 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C SER* 3.1 9.2 + - - +
208C LYS* 1.3 79.7 - - - +
210C HIS* 1.3 80.2 + - + +
212C ARG* 3.3 7.2 + - - +
213C LEU* 2.9 30.4 + - + +
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Residues in contact with HIS 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C PRO 4.3 3.0 + - - -
179C GLU 3.4 25.1 + - - -
180C ALA 4.2 3.1 - - - -
181C GLY* 3.6 27.0 - - - -
182C PRO* 3.8 4.9 - - + +
206C LEU* 4.2 11.7 - - + -
207C SER* 3.0 25.1 + - - +
209C GLN* 1.3 98.4 + - + +
211C TYR* 1.3 65.8 + - - +
213C LEU* 3.4 12.2 + - + +
214C CYS* 3.2 27.0 + - - -
240C LEU* 3.7 34.1 - - + +
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Residues in contact with TYR 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ILE* 3.5 21.4 - - + +
146C ASN* 2.7 25.8 + - - -
149C PHE* 3.3 50.3 - + + -
159C ILE* 4.1 15.5 - - + -
161C MET* 4.0 21.3 - - + -
206C LEU* 4.1 13.1 - - + +
207C SER 3.0 13.8 + - - +
210C HIS* 1.3 76.9 - - - +
212C ARG* 1.3 60.2 + - - +
214C CYS* 3.4 3.6 + - - +
215C ASN 3.4 1.7 + - - -
216C GLY* 2.9 49.8 + - - -
217C MET* 3.5 12.2 - - + +
231C PHE* 4.1 17.0 - + - -
287C LEU* 4.1 7.2 - - + -
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Residues in contact with ARG 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C PHE* 3.6 25.0 + - + -
150C LEU* 3.9 22.0 - - - +
208C LYS* 2.9 30.7 + - + +
209C GLN* 3.5 6.7 - - - +
211C TYR* 1.3 74.5 - - - +
213C LEU* 1.3 60.1 - - - +
215C ASN* 2.8 21.3 + - - -
287C LEU* 3.7 25.7 - - - +
288C ASN* 6.3 1.6 - - - +
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C GLN* 2.9 17.9 + - + +
210C HIS* 3.4 16.4 - - + +
211C TYR 3.3 0.2 - - - -
212C ARG* 1.3 76.9 - - - +
214C CYS* 1.3 59.6 + - - +
215C ASN* 3.4 1.2 + - - +
238C ALA* 4.1 22.1 - - + +
240C LEU* 3.8 35.7 - - + -
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Residues in contact with CYS 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LEU* 4.8 1.6 - - - -
210C HIS 3.2 18.3 + - - +
211C TYR 3.9 4.7 - - - +
212C ARG 3.2 0.6 - - - -
213C LEU* 1.3 76.7 - - - +
215C ASN* 1.3 69.1 + - - +
216C GLY 3.2 14.9 + - - +
231C PHE* 4.2 14.4 - - + -
234C ARG* 3.3 25.6 + - + +
235C ILE* 4.1 28.9 - - - -
238C ALA* 4.4 6.7 - - - -
240C LEU* 4.0 19.1 - - - -
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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