Contacts of the helix formed by residues 188 - 193 (chain U) in PDB entry 3FKS
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 GLN 188 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148U VAL* 3.7 13.1 - - - +
149U GLN 3.3 27.7 + - - +
163U ARG* 3.9 5.7 + - - +
184U THR* 3.3 19.9 + - + +
185U ILE* 3.4 13.7 - - - +
186U LEU 3.1 1.4 - - - -
187U ASN* 1.3 74.4 - - - +
189U LYS* 1.3 55.9 + - - +
190U ARG 3.2 2.4 + - - -
191U TRP* 3.5 21.5 + - - +
192U ASN* 2.8 48.7 + - - +
199U LYS 4.7 0.3 - - - +
201U LEU* 3.2 49.2 + - + +
203U CYS* 4.6 3.4 - - - -
230U TYR* 4.0 1.1 - - + -
267U LEU* 5.8 0.7 - - + -
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Residues in contact with LYS 189 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186U LEU 3.1 16.4 + - - +
187U ASN* 3.0 1.7 - - - -
188U GLN* 1.3 77.6 - - - +
190U ARG* 1.3 64.5 + - + +
191U TRP 3.1 1.7 + - - -
192U ASN* 3.9 2.5 - - - -
193U ASN* 3.3 44.4 + - - +
225U HIS* 2.8 29.2 + - + +
226U ASP* 3.8 22.7 + - - +
227U ALA* 6.1 0.2 - - + -
230U TYR* 3.5 16.3 + - + +
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Residues in contact with ARG 190 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149U GLN* 5.2 0.2 - - - -
187U ASN* 3.3 26.0 + - - +
188U GLN 3.2 0.4 - - - -
189U LYS* 1.3 79.1 - - + +
191U TRP* 1.3 94.3 + - + +
193U ASN* 5.5 0.7 - - - +
194U GLY* 4.7 5.7 + - - -
437U PRO 4.6 3.4 + - - -
438U LEU* 3.5 6.9 + - - +
439U ALA* 3.2 48.1 - - - +
441U GLU* 4.8 3.4 + - - -
442U GLU* 3.6 9.3 + - - -
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Residues in contact with TRP 191 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149U GLN* 3.1 54.6 - - + +
163U ARG* 5.3 3.4 - - - -
187U ASN* 3.1 30.5 - - - -
188U GLN* 3.5 29.8 - - - +
190U ARG* 1.3 102.8 - - + +
192U ASN* 1.3 67.0 + - - +
193U ASN 3.2 2.7 - - - -
194U GLY* 3.1 16.3 + - - +
196U ASP* 4.4 2.1 - - - +
199U LYS* 3.2 59.5 - - + +
200U LYS* 3.7 13.5 - - - +
201U LEU 5.5 0.2 - - - +
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Residues in contact with ASN 192 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188U GLN* 2.8 34.6 + - - +
189U LYS* 3.5 2.0 + - - -
191U TRP* 1.3 77.4 - - - +
193U ASN* 1.3 61.3 + - - +
194U GLY 3.4 0.8 + - - +
200U LYS* 3.6 25.6 + - - +
201U LEU 3.0 33.0 + - - -
202U TYR* 4.2 1.9 + - - -
229U LYS* 4.6 7.4 + - - -
230U TYR* 3.0 62.3 - - + +
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Residues in contact with ASN 193 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189U LYS* 3.3 49.1 + - - +
190U ARG 5.5 1.1 - - - +
191U TRP 3.2 0.4 - - - -
192U ASN* 1.3 75.8 - - - +
194U GLY* 1.3 66.6 + - - +
226U ASP* 4.3 5.6 + - - +
229U LYS* 3.0 34.2 + - - +
230U TYR* 5.2 1.3 - - - -
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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