Contacts of the helix formed by residues 164 - 168 (chain B) in PDB entry 1JRX
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 ASN 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLY* 1.3 70.6 - - - -
165B ALA* 1.3 64.3 + - - +
166B LYS 3.2 0.9 - - - -
167B LEU* 2.9 26.0 + - - +
168B ALA 3.7 2.6 + - - -
315B GLY 5.1 2.4 - - - +
337B ASN* 3.2 28.0 + - - +
338B GLN* 2.9 30.5 + - - +
341B ALA* 3.6 14.3 - - - +
504B HIS 5.2 0.2 + - - -
534B GLU* 4.5 9.9 + - - -
2805B FAD 3.0 60.6 + - + +
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLY* 3.3 24.0 - - - +
162B GLY 2.9 5.6 + - - +
164B ASN* 1.3 76.3 - - - +
166B LYS* 1.3 54.7 + - - +
168B ALA* 3.1 10.9 + - - +
254B GLY* 3.0 23.9 - - - +
257B VAL* 6.4 0.7 - - + -
258B VAL* 3.8 10.7 - - + +
550B ILE* 4.2 4.6 - - + +
553B ILE* 3.8 14.4 - - + -
2805B FAD 2.8 29.9 + - - +
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B HIS* 4.9 6.3 + - - +
62B PHE* 3.5 42.0 - - + -
63B PRO* 3.5 37.0 - - + -
81B TYR* 5.3 2.3 + - - -
160B VAL* 4.0 8.8 - - - +
161B ILE 2.9 27.8 + - - +
162B GLY* 3.1 9.8 + - - +
163B GLY* 2.7 35.2 + - - +
165B ALA* 1.3 75.5 - - - +
167B LEU* 1.3 68.3 + - + +
168B ALA 3.3 0.2 - - - -
254B GLY 3.7 9.6 - - - -
255B ALA* 3.1 22.7 + - - +
258B VAL* 3.7 2.6 - - + +
338B GLN* 4.8 7.9 - - - +
804B HEM 5.9 0.7 - - - -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B HIS* 4.2 15.5 - - + -
163B GLY 4.2 4.3 - - - +
164B ASN* 2.9 36.8 + - - +
166B LYS* 1.3 95.0 - - + +
168B ALA* 1.3 67.1 + - - +
169B ALA* 3.6 5.9 + - - +
336B THR 4.0 2.9 - - - +
338B GLN* 4.1 0.7 - - + +
375B MET* 4.4 1.6 - - - +
431B LYS* 5.6 0.8 + - - -
804B HEM 3.3 65.4 - - + +
2805B FAD 3.2 35.0 - - + +
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ASN 3.7 1.2 + - - -
165B ALA 3.1 17.0 + - - +
166B LYS 3.3 0.2 - - - -
167B LEU* 1.3 81.1 - - - +
169B ALA* 1.3 59.7 + - - +
252B GLY* 3.9 3.8 - - - -
253B VAL* 3.6 4.2 + - + -
254B GLY* 2.8 24.8 + - - -
255B ALA 4.3 1.0 + - - -
431B LYS* 5.0 1.6 + - - -
550B ILE* 3.5 21.1 - - + -
2805B FAD 3.1 37.7 - - + +
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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