Contacts of the helix formed by residues 219 - 223 (chain C) in PDB entry 4J1R
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 SER 219 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C ASP* 3.5 8.8 + - - -
182C ILE 5.3 0.4 + - - -
183C LYS* 3.3 31.5 + - - +
216C PTR 5.3 0.2 - - - -
218C CYS* 1.3 77.4 - - - +
220C ARG* 1.3 68.0 + - - +
221C TYR 4.5 0.9 - - - -
222C TYR* 2.8 40.2 + - - -
223C ARG* 2.9 11.4 + - - +
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Residues in contact with ARG 220 (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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216C PTR 2.8 49.9 + - - +
219C SER* 1.3 71.9 - - - +
221C TYR* 1.3 72.8 + - + +
222C TYR 3.1 1.2 + - - -
223C ARG* 3.2 26.8 + - - +
259C GLY* 2.7 45.2 + - - -
260C ASP* 3.0 23.5 + - - +
261C SER* 3.6 13.3 - - - +
262C GLY 4.7 0.2 - - - +
265C GLN* 3.1 36.9 + - + +
183D LYS* 5.9 3.4 - - - +
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Residues in contact with TYR 221 (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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219C SER* 3.1 1.6 + - - -
220C ARG* 1.3 88.5 + - + +
222C TYR* 1.3 86.5 + + + +
223C ARG 3.5 0.2 - - - -
245C CYS* 3.7 15.4 - - - +
255C PRO* 3.9 33.0 - - + -
256C ILE* 5.7 0.2 - - - +
257C PHE* 3.4 26.2 + - - +
258C PRO* 3.6 10.9 + - + +
259C GLY 3.4 35.3 + - - -
265C GLN* 3.3 12.7 + - - -
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Residues in contact with TYR 222 (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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182C ILE 3.5 18.4 - - - +
183C LYS* 3.8 16.2 - - + -
184C PRO* 3.4 24.2 - - + +
185C GLN* 4.6 10.5 + - - -
218C CYS* 3.5 4.6 - - - -
219C SER* 2.8 28.6 + - - +
221C TYR* 1.3 101.7 - + + +
223C ARG* 1.3 62.7 + - - +
224C ALA 3.6 0.2 + - - -
241C TRP* 3.6 5.1 - - - -
242C SER* 2.5 43.2 + - - +
245C CYS* 3.5 32.5 - - + -
246C VAL* 4.3 4.3 - - + -
249C GLU* 2.7 34.0 + - - -
255C PRO* 5.4 0.8 - - + +
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Residues in contact with ARG 223 (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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215C SER 4.5 4.3 - - - -
216C PTR 2.4 71.8 + - - -
217C ILE 2.9 17.5 + - - +
218C CYS* 2.8 26.5 + - - -
219C SER 2.9 5.6 + - - +
220C ARG* 3.2 32.6 + - - +
221C TYR 3.5 0.4 - - - -
222C TYR* 1.3 76.3 - - - +
224C ALA* 1.3 76.8 + - - +
225C PRO 3.7 0.5 - - - -
227C LEU* 3.7 23.8 - - + -
228C ILE* 4.1 25.2 - - + +
241C TRP* 3.3 12.1 + - - -
262C GLY* 4.0 12.9 + - - -
265C GLN* 4.6 2.4 + - + +
269C ILE* 4.2 3.5 - - - +
64D ASN* 6.2 0.2 - - - +
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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