Contacts of the helix formed by residues 191 - 202 (chain B) in PDB entry 4KZX
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 ASP 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B GLU* 5.0 7.1 - - - +
81B PHE* 5.7 0.7 - - - -
82B ARG* 2.5 47.8 + - - -
187B LYS 3.3 7.1 + - - -
188B LEU* 2.7 17.3 - - - +
189B ILE 3.1 2.4 - - - +
190B PRO* 1.3 81.8 - - - +
192B SER* 1.3 62.9 + - - +
193B ILE* 3.2 4.5 - - - +
194B GLY* 3.3 15.2 + - - +
195B LYS* 3.5 11.4 + - - +
212B VAL* 5.9 2.8 - - - +
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Residues in contact with SER 192 (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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187B LYS* 3.4 22.2 + - - +
190B PRO* 3.8 20.6 + - - +
191B ASP* 1.3 73.9 - - - +
193B ILE* 1.3 67.3 + - - +
195B LYS* 3.6 8.7 + - - +
196B ASP* 3.0 23.0 + - - +
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Residues in contact with ILE 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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171B ILE* 4.4 11.7 - - + -
172B MET* 4.9 8.1 - - + -
175B GLU* 2.8 44.4 - - + +
187B LYS* 4.0 18.2 - - + +
188B LEU* 4.6 19.1 - - + -
191B ASP 3.2 0.8 - - - -
192B SER* 1.3 77.1 - - - +
194B GLY* 1.3 67.8 + - - +
196B ASP* 2.7 17.9 + - + +
197B ILE* 2.8 26.9 + - + +
212B VAL* 3.6 29.6 - - + -
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Residues in contact with GLY 194 (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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191B ASP* 3.3 12.3 + - - +
193B ILE* 1.3 80.0 - - - +
195B LYS* 1.3 65.2 + - - +
197B ILE* 3.1 7.4 + - - +
198B GLU* 3.0 19.4 + - - +
210B VAL* 3.7 28.6 - - - +
211B PHE* 5.2 4.7 - - - -
212B VAL* 5.4 2.8 - - - +
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Residues in contact with LYS 195 (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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191B ASP 3.5 11.1 + - - +
192B SER* 3.9 9.6 - - - +
193B ILE 3.2 0.8 - - - -
194B GLY* 1.3 74.4 - - - +
196B ASP* 1.3 63.7 + - - +
198B GLU* 2.9 39.6 + - + +
199B LYS* 3.0 42.3 + - + +
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Residues in contact with ASP 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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171B ILE* 3.8 15.6 - - + +
174B ARG* 2.7 32.0 + - - -
175B GLU* 3.7 8.1 - - - +
192B SER 3.0 14.0 + - - +
193B ILE* 2.7 19.0 + - + +
195B LYS* 1.3 73.7 - - - +
197B ILE* 1.3 62.0 + - - +
199B LYS* 3.1 10.5 + - - +
200B ALA* 3.0 21.5 + - - +
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Residues in contact with ILE 197 (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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139B CYS* 4.0 22.2 - - + -
168B MET* 4.2 29.4 - - + +
171B ILE* 4.0 22.2 - - + -
193B ILE* 2.8 35.4 + - + +
194B GLY* 3.4 6.5 - - - +
196B ASP* 1.3 73.2 - - - +
198B GLU* 1.3 65.9 + - - +
200B ALA* 3.0 2.4 + - - -
201B CYS* 2.9 46.0 + - + -
207B LEU* 5.4 2.7 - - + -
210B VAL* 3.8 28.0 - - + -
211B PHE 5.4 1.6 - - - -
212B VAL* 4.9 1.6 - - + -
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Residues in contact with GLU 198 (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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194B GLY 3.0 12.7 + - - +
195B LYS* 2.9 42.4 + - + +
197B ILE* 1.3 77.7 - - - +
199B LYS* 1.3 65.2 + - + +
201B CYS* 4.9 2.9 - - - -
202B GLN* 3.3 35.2 + - + +
207B LEU* 4.2 20.0 - - + +
209B ASP 4.3 12.5 - - - +
210B VAL* 4.7 9.2 - - + +
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Residues in contact with LYS 199 (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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195B LYS* 3.0 36.8 + - + +
196B ASP* 3.1 12.1 + - - +
198B GLU* 1.3 83.6 - - + +
200B ALA* 1.3 61.3 + - - +
201B CYS 3.4 0.5 + - - -
202B GLN* 4.1 6.2 + - - +
203B SER* 4.8 5.2 + - - -
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Residues in contact with ALA 200 (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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167B LYS* 4.0 30.3 + - + +
171B ILE* 3.9 20.4 - - + -
196B ASP* 3.0 17.7 + - - +
197B ILE 3.8 3.4 - - - +
199B LYS* 1.3 75.7 - - - +
201B CYS* 1.3 61.1 + - - +
203B SER* 3.6 14.8 + - - -
204B ILE* 4.0 4.2 - - - +
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Residues in contact with CYS 201 (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 ILE* 4.1 27.1 - - + -
167B LYS* 4.4 16.8 - - - -
168B MET 5.1 1.1 - - - -
197B ILE* 2.9 38.1 + - - +
198B GLU* 4.4 1.8 - - - +
199B LYS 3.2 0.2 - - - -
200B ALA* 1.3 81.1 - - - +
202B GLN* 1.3 60.4 + - - +
203B SER 3.1 3.4 - - - -
204B ILE* 2.8 25.6 + - - +
205B TYR 3.2 12.8 + - - +
207B LEU* 3.4 22.8 - - + +
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Residues in contact with GLN 202 (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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144B LYS* 5.5 7.0 + - - +
198B GLU* 3.3 26.2 + - + +
199B LYS* 4.1 4.4 + - - +
201B CYS* 1.3 76.9 - - - +
203B SER* 1.3 60.0 + - - +
204B ILE 3.0 1.6 + - - -
205B TYR* 3.8 8.6 + - - -
206B PRO* 3.2 40.3 + - - +
207B LEU 5.0 1.7 - - - +
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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