Contacts of the helix formed by residues 183 - 188 (chain B) in PDB entry 3NJ4
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 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A ARG* 5.4 0.2 - - - +
179B ASN 4.2 3.7 + - - -
180B VAL* 2.9 22.8 + - - -
181B ASN 3.0 0.8 - - - -
182B ASP* 1.3 77.8 - - - +
184B VAL* 1.3 65.6 + - - +
186B LYS* 3.0 15.7 + - - +
187B SER* 3.1 14.3 + - - -
364B ASN* 3.1 26.6 + - - -
385B PHE* 5.9 1.3 - - - -
386B LEU* 4.7 13.6 - - - +
391B ASP* 3.1 22.4 + - - -
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 3.8 25.6 - - + -
251A GLN* 5.8 0.2 - - - +
431A ARG* 3.4 33.0 - - - +
182B ASP 3.7 1.4 + - - -
183B SER* 1.3 66.1 - - - +
185B THR* 1.3 56.0 + - - +
186B LYS 2.6 16.7 + - - -
187B SER* 4.2 2.2 - - - -
188B LYS* 3.2 36.5 + - + +
189B PHE* 3.3 5.9 - - - -
388B LYS* 4.2 6.5 - - - +
391B ASP* 3.0 20.1 + - - +
432B TYR* 3.6 38.8 - - + -
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Residues in contact with THR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 4.4 7.6 - - + -
183B SER* 3.8 0.5 + - - -
184B VAL* 1.3 70.8 - - - +
186B LYS* 1.3 56.2 + - - +
189B PHE* 3.6 19.1 - - + +
360B ASN* 2.9 31.0 + - - +
364B ASN* 2.8 27.1 + - - -
391B ASP* 2.7 44.5 + - - +
394B VAL* 3.5 12.9 - - - +
395B ALA* 3.6 28.0 - - + +
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Residues in contact with LYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLU* 3.4 23.5 + - - -
180B VAL* 3.5 22.7 - - + +
181B ASN* 2.9 26.0 - - - +
183B SER* 3.2 12.6 - - - +
184B VAL 2.6 7.7 + - - -
185B THR* 1.3 75.6 + - - +
187B SER* 1.3 61.9 + - - +
188B LYS 3.2 0.7 - - - -
189B PHE 2.9 3.8 + - - -
190B ASP* 2.6 54.0 + - - +
191B ASN* 2.7 22.7 - - - +
361B SER* 4.2 17.3 - - - +
364B ASN* 4.5 4.3 - - - +
602B AFX 2.6 28.4 + - - -
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ARG* 4.2 6.2 + - - +
181B ASN* 3.2 23.3 + - - -
182B ASP* 4.2 9.4 + - - -
183B SER 3.1 14.2 + - - -
184B VAL* 4.0 1.7 + - - -
186B LYS* 1.3 79.1 - - - +
188B LYS* 1.3 68.1 + - - +
189B PHE 3.2 0.4 + - - -
191B ASN* 3.2 34.8 - - - +
192B LEU* 3.8 1.7 + - - +
223B ASP* 3.5 25.8 - - - +
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Residues in contact with LYS 188 (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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188A LYS* 3.2 19.0 - - - +
251A GLN* 4.3 8.9 - - - +
431A ARG* 4.5 12.6 - - + -
432A TYR* 2.9 29.1 + - - +
184B VAL* 3.2 31.4 + - + +
187B SER* 1.3 83.7 + - - +
189B PHE* 1.3 69.7 + - + +
192B LEU* 3.8 24.1 - - - +
193B TYR* 3.4 18.7 + - - -
223B ASP* 4.2 11.9 + - - +
226B LYS* 5.8 3.2 - - - +
431B ARG 3.9 14.3 + - - +
432B TYR* 4.0 12.3 + - + -
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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