Contacts of the helix formed by residues 184 - 198 (chain B) in PDB entry 4Z2C
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 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B ARG* 3.2 21.6 - - - +
98B TYR* 3.3 5.3 + - - -
183B HIS* 1.3 71.3 - - - +
185B LEU* 1.3 60.8 + - - +
186B GLY* 3.3 19.9 + - - -
187B GLU* 3.3 37.7 + - + +
188B THR* 2.7 31.5 + - - -
210B LEU* 5.5 0.2 - - - +
214B ASP* 3.4 23.4 + - + +
477B SER* 3.5 4.9 + - - -
478B ASP 2.7 27.0 + - - +
479B LYS 3.8 5.9 + - - -
480B ARG* 4.1 4.0 - - - +
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Residues in contact with LEU 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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98B TYR* 3.1 34.5 + - + +
128B ILE* 3.9 17.7 - - + -
161B PHE* 4.2 17.5 - - + -
162B PRO* 4.7 0.7 - - + -
166B VAL* 4.2 21.3 - - + -
184B ASN* 1.3 70.9 - - - +
186B GLY* 1.3 64.7 + - - +
188B THR* 3.2 3.8 + - - -
189B ILE* 2.9 43.4 + - + +
472B VAL* 4.0 12.3 - - + +
473B LYS* 5.0 0.2 - - - -
476B PHE* 3.7 30.5 - - + -
477B SER* 3.8 13.7 - - - +
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Residues in contact with GLY 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASN* 3.3 3.7 + - - -
185B LEU* 1.3 78.7 - - - +
187B GLU* 1.3 57.7 + - - +
189B ILE* 3.4 3.0 + - - +
190B ASP* 2.9 39.0 + - - +
473B LYS* 3.8 26.2 - - - -
477B SER* 3.1 17.6 + - - -
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Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASN* 3.3 26.9 + - + +
185B LEU 3.2 0.4 - - - -
186B GLY* 1.3 72.6 - - - +
188B THR* 1.3 61.6 + - - +
190B ASP* 3.2 12.3 + - - +
191B ALA* 2.9 27.7 + - - +
209B VAL 3.3 16.6 - - - +
210B LEU* 3.6 18.5 - - + +
211B PRO* 3.3 22.2 - - - +
212B GLY 4.2 0.3 - - - +
480B ARG* 2.6 44.5 + - - +
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PRO* 3.6 24.0 - - + -
165B LEU* 3.9 33.9 - - + -
166B VAL* 3.5 17.2 - - + +
183B HIS* 3.5 12.8 - - - +
184B ASN 2.7 21.9 + - - -
185B LEU 3.6 5.2 - - - -
187B GLU* 1.3 76.2 - - - +
189B ILE* 1.3 58.5 + - - +
191B ALA* 3.1 8.6 + - - +
192B VAL* 2.9 27.2 + - - +
210B LEU* 4.3 9.4 - - + +
348B LEU* 4.6 4.4 - - + +
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PRO* 4.5 7.0 - - + -
185B LEU* 2.9 39.0 + - + +
186B GLY* 3.6 5.6 - - - +
188B THR* 1.3 75.2 - - - +
190B ASP* 1.3 60.3 + - - +
192B VAL* 3.2 7.6 + - - +
193B LYS* 2.9 48.1 + - + +
469B LEU* 3.2 50.7 - - + +
470B ASP* 4.5 0.4 - - - +
472B VAL* 3.9 6.3 - - + -
473B LYS* 3.6 31.2 - - + +
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Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLY 2.9 27.1 + - - +
187B GLU* 3.2 13.1 + - - +
189B ILE* 1.3 75.4 - - - +
191B ALA* 1.3 57.6 + - - +
193B LYS* 3.5 16.8 + - - +
194B LEU* 2.9 29.7 + - - +
209B VAL* 4.1 27.4 - - + +
473B LYS* 2.9 31.6 + - - +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU 2.9 12.8 + - - +
188B THR* 3.1 9.4 + - - +
190B ASP* 1.3 75.8 - - - +
192B VAL* 1.3 59.2 + - - +
194B LEU* 3.3 6.7 + - - +
195B VAL* 2.9 29.8 + - - +
206B LEU* 4.1 13.6 - - + +
209B VAL* 4.5 5.1 - - + +
210B LEU* 4.1 24.9 - - + -
348B LEU* 4.2 19.6 - - + +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PRO* 5.7 2.7 - - + -
188B THR 2.9 12.9 + - - +
189B ILE* 3.2 8.5 + - - +
191B ALA* 1.3 76.1 - - - +
193B LYS* 1.3 58.8 + - - +
195B VAL* 3.2 6.6 + - - +
196B MET* 2.9 34.9 + - - +
348B LEU* 4.2 14.3 - - + +
351B TYR* 4.9 11.4 - - + -
352B ILE* 3.8 13.4 - - + +
469B LEU* 4.1 20.6 - - + -
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Residues in contact with LYS 193 (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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189B ILE* 2.9 32.3 + - + +
190B ASP* 3.8 20.8 + - - +
192B VAL* 1.3 76.8 - - - +
194B LEU* 1.3 57.1 + - - +
196B MET* 3.3 8.8 + - - +
197B ASP* 2.9 40.6 + - - +
466B LYS* 4.2 33.9 - - + +
469B LEU* 4.7 6.5 - - + -
470B ASP* 2.6 40.0 + - - +
473B LYS* 4.6 5.1 - - - +
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Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ASP 2.9 17.3 + - - +
191B ALA* 3.6 6.7 - - - +
192B VAL 3.2 0.2 - - - -
193B LYS* 1.3 74.2 - - - +
195B VAL* 1.3 60.0 + - - +
197B ASP* 3.9 5.8 - - + +
198B ASN* 3.1 31.8 + - + +
201B VAL* 3.8 25.8 - - + -
205B ASP* 4.2 17.3 - - + +
206B LEU* 3.8 15.0 - - + -
209B VAL* 3.7 30.7 - - + -
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ALA 2.9 16.3 + - - +
192B VAL* 3.2 5.6 + - - +
194B LEU* 1.3 80.0 - - - +
196B MET* 1.3 62.9 + - - +
198B ASN 3.8 17.2 - - - +
199B PRO* 3.8 10.4 - - - +
201B VAL* 5.5 1.8 - - - -
206B LEU* 5.1 4.9 - - + -
348B LEU* 4.7 14.4 - - + -
349B ASP* 4.7 7.8 - - - +
352B ILE* 3.8 17.7 - - + -
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Residues in contact with MET 196 (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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192B VAL 2.9 25.5 + - - +
193B LYS* 3.6 6.1 - - - +
195B VAL* 1.3 79.1 - - - +
197B ASP* 1.3 67.4 + - - +
199B PRO* 4.5 6.4 - - - +
352B ILE* 3.6 33.7 - - + -
356B LYS* 5.1 3.1 - - - -
462B SER* 3.2 50.5 + - - +
465B ILE* 3.7 31.6 - - + -
466B LYS* 3.8 15.7 - - + -
469B LEU* 5.0 5.2 - - - -
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Residues in contact with ASP 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LYS* 2.9 25.1 + - - +
194B LEU* 3.9 5.6 - - - +
195B VAL 3.4 0.2 - - - -
196B MET* 1.3 79.1 - - - +
198B ASN* 1.3 60.8 + - + +
199B PRO* 3.3 9.7 - - - +
466B LYS* 3.2 34.3 + - - +
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Residues in contact with ASN 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 3.1 15.8 + - + +
195B VAL* 3.8 5.1 - - - +
197B ASP* 1.3 80.9 - - + +
199B PRO* 1.3 63.2 - - - +
200B GLU* 3.1 9.6 + - + +
201B VAL* 3.3 24.9 + - + +
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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