Contacts of the helix formed by residues 182 - 187 (chain B) in PDB entry 4J15
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 182 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B PRO* 3.4 43.7 + - + +
154B LEU* 4.4 6.3 - - + +
178B THR* 2.8 33.2 + - - +
179B ARG 3.8 3.5 - - - +
181B ASP* 1.3 87.0 - - - +
183B ARG* 1.3 63.9 + - - +
184B VAL 3.3 2.9 - - - -
185B ILE* 3.3 11.9 + - + +
186B ASP* 3.1 20.4 + - - +
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Residues in contact with ARG 183 (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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256A MET* 3.8 16.2 - - + -
179B ARG* 3.1 23.7 + - - +
180B LEU* 4.1 21.5 - - - +
181B ASP 3.5 3.0 + - - +
182B ASN* 1.3 76.0 - - - +
184B VAL* 1.3 57.7 + - - +
186B ASP* 2.7 38.5 + - - +
187B LEU* 2.9 61.7 + - + +
192B SER* 5.1 1.0 + - - -
196B PHE* 4.5 6.1 - - - -
487B ARG 5.0 4.0 + - - -
488B GLN 5.8 0.6 + - - -
490B SER 3.9 12.1 + - - -
491B MET 3.1 27.5 + - - +
492B PHE* 4.1 12.8 - - + +
493B PRO* 3.7 18.3 - - - +
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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
----------------------------------------------------------
256A MET* 3.7 40.6 - - + +
259A CYS* 3.5 33.0 - - + +
260A ALA* 3.4 13.7 - - - +
458A SER* 3.8 31.4 - - - +
182B ASN 3.3 0.6 - - - -
183B ARG* 1.3 76.9 - - - +
185B ILE* 1.3 61.9 + - + +
187B LEU* 4.9 0.9 - - - -
188B ARG* 3.2 34.1 + - - +
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Residues in contact with ILE 185 (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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461A PHE* 4.0 24.5 - - + -
111B GLU* 5.7 1.1 - - + -
152B LEU* 4.4 8.3 - - + -
153B PRO* 4.3 20.9 - - + -
154B LEU* 3.8 32.8 - - + +
156B LEU* 3.3 21.5 - - + +
182B ASN* 3.3 14.3 + - + +
183B ARG 3.2 0.2 - - - -
184B VAL* 1.3 79.4 - - + +
186B ASP* 1.3 64.7 + - - +
188B ARG* 3.1 53.8 - - - +
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Residues in contact with ASP 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 4.2 6.9 - - + +
156B LEU* 5.1 0.2 - - - -
159B ALA* 4.0 11.8 - - - +
179B ARG* 3.6 46.3 + - + +
182B ASN 3.1 12.4 + - - +
183B ARG* 2.7 33.1 + - - +
185B ILE* 1.3 79.6 - - - +
187B LEU* 1.3 54.1 + - - +
188B ARG 3.1 0.4 - - - -
189B THR* 3.1 19.0 + - - +
192B SER* 2.7 28.3 + - - -
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Residues in contact with LEU 187 (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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256A MET* 5.5 1.6 - - + +
257A CYS* 5.4 2.0 - - - -
260A ALA* 3.5 22.4 - - + -
262A PHE* 4.1 10.0 - - + -
183B ARG* 2.9 55.1 + - + +
184B VAL* 4.9 0.9 - - - +
185B ILE 3.3 0.2 - - - -
186B ASP* 1.3 73.0 - - - +
188B ARG* 1.3 57.5 + - - +
189B THR 3.4 0.4 - - - -
192B SER* 3.3 17.3 - - - -
193B GLN* 3.0 22.5 + - - +
196B PHE* 3.6 36.1 - - + -
491B MET* 3.9 23.6 - - + +
492B PHE* 4.2 11.4 - - + -
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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