Contacts of the helix formed by residues 184 - 190 (chain P) 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 ASN 184 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157P GLY 5.2 3.1 - - - +
159P TYR 3.9 9.4 - - - +
160P PRO* 3.4 32.6 + - + +
162P ILE* 5.3 3.6 - - + +
182P ILE 3.2 5.0 + - - -
183P PHE* 1.3 73.0 - - - +
185P ALA* 1.3 68.9 + - - +
186P LYS* 2.8 9.1 + - + +
187P THR* 2.9 23.9 + - - +
188P ILE* 3.3 5.5 - - - +
210P PHE* 3.5 11.0 - - - -
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Residues in contact with ALA 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184P ASN* 1.3 70.7 - - - +
186P LYS* 1.3 61.2 + - - +
188P ILE* 3.3 29.1 + - + +
189P GLU* 3.6 13.1 + - - +
206P PRO 4.7 3.1 - - - +
207P ARG* 4.1 22.9 - - + +
210P PHE* 3.4 25.6 - - + -
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Residues in contact with LYS 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184P ASN* 2.8 10.3 + - + +
185P ALA* 1.3 70.2 - - - +
187P THR* 1.3 58.5 + - - +
188P ILE 2.8 11.1 + - - -
189P GLU* 3.3 19.3 - - - +
190P GLN* 3.2 39.7 + - - +
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Residues in contact with THR 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56P GLU 5.0 2.5 - - - +
160P PRO 4.5 5.4 + - - -
183P PHE* 4.4 27.4 - - + -
184P ASN* 2.9 24.9 + - - +
186P LYS* 1.3 73.1 - - - +
188P ILE* 1.3 57.0 + - - +
190P GLN* 3.8 10.9 - - - +
191P SER* 2.9 20.6 + - - -
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Residues in contact with ILE 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P PHE* 4.3 26.9 - - + -
52P TYR* 3.6 24.5 - - + +
55P ALA* 4.9 0.9 - - - +
183P PHE* 3.5 28.5 - - + +
184P ASN 3.3 10.5 - - - +
185P ALA* 3.3 20.0 - - - +
186P LYS 2.8 2.2 + - - -
187P THR* 1.3 77.5 - - - +
189P GLU* 1.3 60.7 + - - +
190P GLN 3.1 1.3 - - - -
191P SER* 2.8 30.6 + - - +
194P PHE* 4.0 6.0 - - + -
206P PRO 4.8 4.5 - - - +
209P LEU* 3.8 18.6 - - + -
210P PHE* 4.3 8.1 - - + +
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Residues in contact with GLU 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185P ALA* 3.6 8.9 + - - +
186P LYS* 3.3 28.3 + - - +
188P ILE* 1.3 76.7 - - - +
190P GLN* 1.3 66.6 + - + +
191P SER 3.1 4.1 + - - +
194P PHE* 3.4 35.7 - - + -
206P PRO* 5.2 10.7 - - + +
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Residues in contact with GLN 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186P LYS* 3.2 35.8 + - - +
187P THR* 3.8 10.3 - - - +
188P ILE 3.1 0.8 - - - -
189P GLU* 1.3 86.1 + - + +
191P SER* 1.3 61.1 + - - +
192P PRO* 3.8 5.5 - - - +
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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