Contacts of the helix formed by residues 219 - 223 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181D ASP* 3.4 11.9 + - - -
182D ILE 5.2 0.2 - - - -
183D LYS* 3.4 28.3 + - - +
216D PTR 5.7 0.2 - - - -
218D CYS* 1.3 77.5 - - - +
220D ARG* 1.3 67.2 + - - +
221D TYR 4.5 0.9 - - - -
222D TYR* 2.8 41.7 + - - -
223D ARG* 2.9 10.6 + - - +
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Residues in contact with ARG 220 (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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183C LYS* 6.0 2.4 - - - +
216D PTR 3.0 47.3 + - - +
219D SER* 1.3 70.4 - - - +
221D TYR* 1.3 75.0 + - + +
222D TYR 3.0 1.0 + - - -
223D ARG* 3.2 29.9 + - - +
259D GLY* 2.9 33.4 + - - -
260D ASP* 3.3 23.3 + - - +
261D SER* 3.5 23.4 - - - +
262D GLY 4.6 0.2 - - - +
265D GLN* 3.1 30.9 + - + +
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Residues in contact with TYR 221 (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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219D SER* 3.2 1.8 - - - -
220D ARG* 1.3 90.2 + - + +
222D TYR* 1.3 84.8 + + + +
223D ARG 3.5 0.2 - - - -
241D TRP* 5.0 0.2 + - - -
245D CYS* 3.7 15.2 - - - +
255D PRO* 3.8 33.9 - - + -
257D PHE* 3.4 26.1 + - - +
258D PRO* 3.6 11.1 - - + +
259D GLY 3.4 35.5 + - - -
265D GLN* 3.2 12.4 + - - +
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Residues in contact with TYR 222 (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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140D TYR* 5.7 0.2 - - - -
182D ILE 3.5 18.2 - - - +
183D LYS* 3.8 15.5 - - + -
184D PRO* 3.4 23.9 - - + +
185D GLN* 4.6 10.8 + - - -
218D CYS* 3.6 4.6 - - - -
219D SER* 2.8 28.0 + - - +
221D TYR* 1.3 102.8 - + + +
223D ARG* 1.3 63.0 + - - +
224D ALA 3.6 0.3 + - - -
241D TRP* 3.5 8.1 - - - -
242D SER* 2.6 39.7 + - - +
245D CYS* 3.5 30.5 - - + -
246D VAL* 4.3 6.3 - - + -
249D GLU* 2.8 34.3 + - - -
255D PRO* 5.0 1.0 - - + +
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Residues in contact with ARG 223 (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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215D SER 4.6 4.0 - - - -
216D PTR 2.9 69.1 + - - -
217D ILE 2.9 21.4 + - - +
218D CYS* 2.9 27.3 + - - -
219D SER 2.9 6.1 + - - +
220D ARG* 3.2 33.9 + - - +
221D TYR 3.5 0.4 - - - -
222D TYR* 1.3 77.4 - - - +
224D ALA* 1.3 76.6 + - - +
225D PRO 3.7 0.7 - - - -
227D LEU* 3.6 19.5 - - + -
228D ILE* 4.1 24.8 - - + +
241D TRP* 3.3 11.3 + - - -
262D GLY* 4.0 13.3 + - - -
265D GLN* 4.5 2.4 + - + +
269D ILE* 4.2 4.5 - - - +
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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