Contacts of the strand formed by residues 254 - 260 (chain C) in PDB entry 5TF6
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 CYS 254 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C ILE 3.9 0.3 - - - +
215C ARG 3.9 0.7 - - - -
216C ASN 3.3 7.4 + - - -
217C LEU* 2.8 38.6 + - + +
218C SER 4.0 0.9 - - - +
219C THR* 3.9 36.3 - - - -
222C LEU* 3.8 35.9 - - + -
246C GLN* 3.3 16.4 - - - +
251C PHE* 4.3 5.6 - - - -
253C ASN* 1.3 79.6 - - - +
255C CYS* 1.3 59.3 + - - +
41D A 4.0 3.6 - - - -
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Residues in contact with CYS 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C MET* 3.9 25.4 - - + -
214C ILE 3.1 11.9 - - - +
215C ARG* 4.3 3.4 - - + -
217C LEU* 4.4 0.4 - - - -
222C LEU* 3.5 7.8 - - - +
242C ILE* 4.1 0.5 - - - +
243C PRO* 3.6 24.2 - - - +
246C GLN* 2.6 41.3 + - - -
254C CYS* 1.3 74.6 - - - +
256C ALA* 1.3 64.9 + - - +
257C PHE* 4.6 2.5 - - - -
41D A 3.8 29.8 - - + +
42D A 4.5 2.7 - - - -
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Residues in contact with ALA 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C MET* 3.5 5.0 - - - +
214C ILE* 2.8 38.0 + - + +
217C LEU* 4.2 9.4 - - + +
222C LEU* 4.3 0.2 - - + -
227C LEU* 3.9 17.3 - - + -
240C ILE* 5.4 0.9 - - + -
241C ASN 3.7 6.5 - - - +
242C ILE* 3.9 24.9 - - + -
243C PRO* 4.3 2.7 - - - -
255C CYS* 1.3 76.2 - - - +
257C PHE* 1.3 69.1 + - - +
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Residues in contact with PHE 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C GLU* 3.5 25.4 - - - +
212C ILE 3.3 7.6 - - - +
213C MET* 3.6 38.4 - - + -
214C ILE* 5.2 1.1 - - - -
240C ILE* 3.6 6.4 - - - +
241C ASN* 2.9 36.9 + - - +
243C PRO* 4.0 12.6 - - + -
255C CYS* 4.6 1.3 - - - -
256C ALA* 1.3 79.7 - - - +
258C MET* 1.3 62.3 + - - +
287C ALA* 4.1 2.9 - - + -
42D A 3.2 50.3 - + - -
43D C 3.4 50.7 - + - +
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Residues in contact with MET 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ARG 3.8 0.9 - - - +
211C GLU* 3.4 2.6 - - - -
212C ILE* 2.9 44.7 + - + +
214C ILE* 4.0 12.8 - - + -
227C LEU* 3.9 18.2 - - + +
231C PHE* 3.5 49.1 - - + -
237C ILE* 3.6 12.3 - - + -
239C LYS 3.4 10.3 - - - +
240C ILE* 4.1 20.4 - - + -
257C PHE* 1.3 75.8 - - - +
259C VAL* 1.3 70.9 + - - +
260C PHE* 3.6 24.9 + - + -
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Residues in contact with VAL 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C ALA* 3.7 34.5 - - + -
210C ARG* 3.4 13.0 - - - +
211C GLU* 4.1 17.5 - - + +
237C ILE* 3.7 6.2 - - - +
238C GLU* 2.8 35.6 + - + +
239C LYS* 2.6 33.3 + - + +
241C ASN* 4.7 9.2 - - - +
258C MET* 1.3 78.7 - - - +
260C PHE* 1.3 76.6 + - - +
44D A 5.9 2.9 - - - +
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Residues in contact with PHE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ARG* 2.9 27.2 + - - +
212C ILE* 3.8 25.8 - - + -
231C PHE* 4.0 14.4 - - + -
234C PHE* 4.2 8.1 - - + -
235C GLY 3.8 7.9 - - - -
236C SER 3.4 18.4 - - - +
237C ILE* 3.8 17.3 - - + -
238C GLU* 4.0 4.6 - - - +
258C MET* 3.6 25.1 - - + -
259C VAL* 1.3 88.4 - - - +
261C GLU* 1.3 63.8 + - - +
262C ASN 3.7 16.8 - - - +
265C SER* 3.7 17.5 - - - -
266C ALA* 3.8 15.3 - - + +
269C ALA* 3.7 23.3 - - + -
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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