Contacts of the helix formed by residues 201 - 205 (chain D) in PDB entry 4JZJ
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 PHE 201 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ILE* 4.0 20.1 - - + +
120D LEU* 4.3 18.2 - - + -
140D LEU* 5.1 2.5 - - + -
142D VAL* 4.9 2.9 - - + -
169D ILE* 4.6 11.4 - - + -
173D SER* 3.5 26.9 - - - -
176D SER 3.4 20.2 - - - -
177D GLN* 2.9 17.7 + - - +
178D SER* 4.0 11.2 - - - -
179D SER* 3.6 22.2 - - - -
199D VAL* 3.9 23.3 - - + -
200D VAL* 1.3 69.8 - - - +
202D SER* 1.3 62.0 + - - +
204D ILE* 3.3 14.5 + - + +
205D GLU* 3.3 15.9 + - - +
231D PHE* 3.5 37.5 - + + -
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Residues in contact with SER 202 (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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177D GLN 4.6 0.8 + - - -
200D VAL* 3.8 12.9 - - - +
201D PHE* 1.3 77.2 - - - +
203D GLN* 1.3 63.5 + - - +
204D ILE 3.5 0.2 + - - -
205D GLU* 3.7 8.0 + - - +
231D PHE* 3.4 22.1 - - - +
232D ASN* 3.3 39.4 + - - +
278D TYR* 3.6 24.9 + - - -
280D PHE* 3.6 15.3 - - - +
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Residues in contact with GLN 203 (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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200D VAL* 3.1 34.2 + - + +
202D SER* 1.3 80.8 + - - +
204D ILE* 1.3 64.2 + - + +
205D GLU 3.5 1.8 + - - +
278D TYR* 6.1 0.3 - - - -
280D PHE* 3.6 29.8 - - + -
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Residues in contact with ILE 204 (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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112D CYS 3.7 22.0 - - - +
113D TRP* 3.5 13.3 - - - +
114D ILE* 3.2 42.6 + - + +
120D LEU* 3.9 10.5 - - + -
199D VAL* 3.9 38.4 - - + -
200D VAL 3.2 19.0 + - - +
201D PHE* 3.3 8.0 + - + +
203D GLN* 1.3 84.1 - - + +
205D GLU* 1.3 63.2 + - - +
206D ILE* 3.5 3.3 + - - +
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Residues in contact with GLU 205 (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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114D ILE* 3.3 26.8 - - + +
116D ASP 3.7 17.0 - - - +
117D VAL* 4.7 3.5 - - - +
201D PHE 3.3 14.1 + - - +
202D SER 3.7 9.1 + - - +
203D GLN 3.5 3.5 - - - +
204D ILE* 1.3 77.2 - - - +
206D ILE* 1.3 71.3 + - - +
207D LEU* 3.2 26.8 + - + +
208D THR 5.7 0.2 + - - -
228D ARG 4.5 2.8 - - - +
229D SER* 2.5 36.6 + - - -
230D HIS 5.0 0.2 + - - -
231D PHE* 4.3 7.9 - - + +
232D ASN* 3.0 14.8 + - - +
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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