Contacts of the strand formed by residues 211 - 217 (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 GLU 211 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205C ALA* 3.9 1.0 + - + -
206C THR* 2.5 42.9 + - - +
209C GLY* 3.5 2.3 - - - -
210C ARG* 1.3 79.8 - - - +
212C ILE* 1.3 71.5 + - - +
241C ASN* 4.3 4.2 + - - -
257C PHE* 3.5 13.6 - - + +
258C MET 3.4 11.2 - - - +
259C VAL* 4.1 16.3 - - + +
286C LEU* 3.6 10.5 - - - +
287C ALA* 3.0 29.1 + - + +
43D C 2.6 42.9 + - - +
44D A 4.1 5.9 - - - +
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Residues in contact with ILE 212 (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* 1.3 82.7 - - - +
213C MET* 1.3 60.1 + - - +
214C ILE* 4.1 9.1 + - + -
231C PHE* 4.1 19.3 - - + -
257C PHE* 3.3 4.4 - - - -
258C MET* 2.9 49.2 + - + +
260C PHE* 3.8 18.2 - - + -
266C ALA* 3.8 32.8 - - + +
269C ALA* 4.3 2.2 - - + -
270C LEU* 4.1 15.9 - - + -
284C VAL* 3.9 22.7 - - + -
285C SER 3.3 7.9 - - - +
286C LEU* 4.6 2.5 - - + -
287C ALA 4.4 0.9 - - - -
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Residues in contact with MET 213 (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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212C ILE* 1.3 71.5 - - - +
214C ILE* 1.3 64.6 + - - +
215C ARG* 3.8 40.4 + - + +
255C CYS* 3.9 18.4 - - + -
256C ALA 3.5 8.3 - - - +
257C PHE* 3.6 29.2 - - + -
283C SER 3.5 4.9 - - - +
284C VAL* 3.5 1.7 - - - -
285C SER* 2.8 36.7 + - - +
286C LEU 5.3 0.4 - - - +
287C ALA* 4.2 7.5 - - - +
41D A 3.9 8.1 - - - +
42D A 3.7 51.8 - - + +
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Residues in contact with ILE 214 (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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212C ILE* 4.1 16.2 - - + -
213C MET* 1.3 73.9 - - - +
215C ARG* 1.3 62.1 + - - +
217C LEU* 3.6 33.4 - - + -
227C LEU* 4.5 9.0 - - + -
231C PHE* 3.7 32.1 - - + -
254C CYS 3.9 0.7 - - - +
255C CYS* 3.1 8.3 - - - +
256C ALA* 2.8 45.1 + - + +
258C MET* 4.0 22.9 - - + -
282C ILE* 4.5 17.3 - - + -
283C SER 3.2 8.1 - - - +
284C VAL* 4.5 4.3 - - + -
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Residues in contact with ARG 215 (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* 3.8 33.1 + - + +
214C ILE* 1.3 76.5 - - - +
216C ASN* 1.3 69.7 + - - +
217C LEU 3.3 4.2 + - - -
254C CYS 3.9 2.9 - - - -
255C CYS* 4.3 2.2 - - + -
282C ILE* 3.5 6.8 - - - +
283C SER* 2.8 36.1 + - - -
285C SER* 2.6 30.9 + - - -
41D A 3.3 29.6 + - - +
42D A 4.6 12.9 - - - +
91D A 3.0 73.8 + - + +
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Residues in contact with ASN 216 (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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215C ARG* 1.3 74.7 - - - +
217C LEU* 1.3 61.8 + - - +
253C ASN* 3.1 36.7 + - - +
254C CYS 3.3 7.1 + - - +
280C ARG* 2.9 31.9 + - - +
281C GLU 3.9 15.5 + - - +
282C ILE* 4.8 2.2 - - - -
283C SER* 4.7 2.2 + - - +
39D G 4.3 1.5 - - - +
40D A 3.6 12.8 + - - +
41D A 5.3 1.6 + - - -
91D A 3.5 17.2 - - - -
92D C 2.7 35.8 + - - +
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Residues in contact with LEU 217 (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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214C ILE* 3.6 32.5 - - + +
215C ARG 3.3 0.8 + - - -
216C ASN* 1.3 80.3 - - - +
218C SER* 1.3 68.2 + - - +
221C LEU* 3.9 25.8 - - + +
222C LEU* 3.9 21.5 - - + -
227C LEU* 3.9 26.2 - - + -
253C ASN* 3.5 1.2 - - - -
254C CYS* 2.8 40.3 + - + +
256C ALA* 4.2 6.3 - - + +
277C LEU* 4.3 4.7 - - + -
280C ARG* 3.3 6.6 + - - -
282C ILE* 3.8 22.0 - - + +
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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