Contacts of the strand formed by residues 197 - 201 (chain E) in PDB entry 5FHK
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 TRP 197 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164E LEU* 3.6 22.7 - - + -
183E LEU* 4.1 16.8 - - + -
188E LEU* 3.9 30.5 - - + -
189E LEU 3.6 16.2 - - - -
190E LYS* 3.7 18.6 - - + +
194E LEU 3.1 26.8 + - - -
195E LEU 4.2 3.4 - - - -
196E LYS* 1.3 74.1 - - - +
198E THR* 1.3 62.2 + - - +
199E LEU* 3.4 11.5 + - + +
207E VAL 3.3 3.6 - - - +
208E VAL* 3.2 5.4 - - - -
209E ASN* 2.9 51.6 + - + +
233E ILE* 3.4 24.2 - - + -
234E THR* 3.9 5.2 - - - -
235E LEU* 3.5 47.6 + - + +
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Residues in contact with THR 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E LYS* 3.8 25.0 + - - +
197E TRP* 1.3 71.6 + - - +
199E LEU* 1.3 60.2 + - - +
200E ILE* 3.9 3.0 + - + +
206E THR* 4.2 20.9 - - + +
207E VAL 3.9 2.0 - - - -
208E VAL* 4.1 10.9 - - + +
235E LEU* 5.2 0.2 - - - +
259E ALA* 3.2 25.9 - - - +
260E ASN* 4.4 14.6 + - - +
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Residues in contact with LEU 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E LEU* 3.8 26.7 - - + -
180E ALA* 4.1 14.6 - - + -
183E LEU* 3.6 31.2 - - + -
197E TRP* 4.2 18.6 - - + +
198E THR* 1.3 72.8 - - - +
200E ILE* 1.3 60.0 + - - +
206E THR* 3.2 5.7 - - - +
207E VAL* 2.8 47.7 + - + +
209E ASN* 5.2 3.4 - - + -
235E LEU* 4.0 22.7 - - + -
257E TRP* 3.6 18.9 - - + -
258E SER* 3.5 12.3 - - - +
259E ALA* 4.3 4.3 - - + -
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Residues in contact with ILE 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E THR* 5.1 2.7 - - + +
199E LEU* 1.3 74.3 - - - +
201E ASN* 1.3 68.4 + - - +
204E GLY* 3.2 32.5 - - - +
205E GLU 3.0 18.6 - - - +
206E THR* 3.7 11.2 - - - +
256E ASP 3.9 0.3 - - - +
257E TRP* 3.5 3.1 - - - -
258E SER* 2.8 47.8 + - - +
259E ALA* 4.7 4.7 - - - +
260E ASN 5.4 0.2 - - - +
261E PRO* 5.1 12.8 - - + -
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Residues in contact with ASN 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E ILE* 1.3 85.2 - - - +
202E SER* 1.3 59.8 + - - +
203E LYS* 3.0 13.6 + - - +
204E GLY* 3.1 11.3 + - - -
205E GLU* 2.9 65.2 + - - -
256E ASP* 3.2 24.6 + - - +
257E TRP* 3.4 33.3 - - + -
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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