Contacts of the strand formed by residues 207 - 215 (chain E) in PDB entry 1YFL
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 PHE 207 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167E PHE* 3.2 9.7 - - - -
168E VAL* 3.4 19.1 - - + +
197E LEU* 3.0 63.3 - - + -
200E LEU* 4.6 9.0 - - + -
205E ILE* 5.0 0.9 - - + +
206E LYS* 1.3 74.4 - - - +
208E GLY* 1.3 68.6 + - - +
209E LEU* 4.9 2.2 - - + -
226E TRP* 3.6 27.1 - + - -
230E TYR* 3.6 21.5 - + - -
257E ILE* 3.9 6.5 - - + -
258E PHE* 3.4 24.9 - - - +
259E ASN* 2.8 41.5 + - - +
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Residues in contact with GLY 208 (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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167E PHE* 3.2 4.8 - - - -
168E VAL 3.0 6.7 + - - +
169E TYR* 3.4 1.9 - - - -
170E VAL* 2.5 34.8 + - - +
207E PHE* 1.3 77.6 - - - +
209E LEU* 1.3 56.5 + - - +
256E TYR* 3.4 30.1 - - - -
257E ILE 3.7 4.7 - - - -
258E PHE* 4.0 0.4 - - - -
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Residues in contact with LEU 209 (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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169E TYR* 4.8 0.2 - - - -
170E VAL* 3.0 35.7 - - + -
172E PRO* 3.7 11.2 - - + -
190E GLU* 5.8 0.9 - - - +
193E LEU* 4.5 3.4 - - + -
194E LEU* 4.7 2.5 - - + -
197E LEU* 4.1 18.4 - - + -
207E PHE* 4.9 2.7 - - + -
208E GLY* 1.3 77.2 - - - +
210E SER* 1.3 75.6 + - - +
211E ASN* 4.3 5.6 + - - +
223E LEU* 4.6 9.2 - - + -
226E TRP* 4.3 15.7 - - + -
256E TYR* 3.4 9.4 - - - -
257E ILE* 2.7 71.9 + - + +
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Residues in contact with SER 210 (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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11E LYS* 4.1 4.4 - - - -
14E LEU* 5.5 1.7 - - - +
18E LEU* 4.0 8.3 - - - +
169E TYR* 2.9 31.6 + - - -
170E VAL 2.8 6.3 + - - -
171E ASP* 3.8 4.3 - - - -
172E PRO* 3.6 20.6 - - - +
174E TYR* 3.7 20.2 - - - -
209E LEU* 1.3 76.3 - - - +
211E ASN* 1.3 67.4 + - - +
254E GLU* 5.6 2.0 - - - -
255E VAL 3.5 8.9 + - - -
256E TYR* 4.0 8.0 - - - +
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Residues in contact with ASN 211 (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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172E PRO* 3.9 19.6 - - - +
174E TYR* 3.7 32.7 + - - +
175E LEU 4.5 2.8 + - - -
176E ILE* 5.4 0.3 - - - +
190E GLU* 3.9 23.0 + - - -
209E LEU* 4.4 6.5 - - + +
210E SER* 1.3 80.1 + - - +
212E VAL* 1.3 87.3 + - - +
220E ASN* 5.2 4.5 + - - -
223E LEU* 3.7 26.7 - - + +
254E GLU* 3.8 1.9 - - - +
255E VAL* 2.9 35.7 + - + +
257E ILE* 5.2 0.4 - - + -
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Residues in contact with VAL 212 (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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174E TYR* 3.3 38.8 - - + -
176E ILE* 3.0 38.5 - - + +
177E THR* 4.3 4.3 - - + -
211E ASN* 1.3 91.8 + - - +
213E LEU* 1.3 63.0 + - - +
214E GLU 4.6 0.9 - - - +
215E HIS* 4.0 10.3 - - + -
220E ASN* 4.2 6.8 - - - +
252E THR* 4.6 13.5 - - + -
253E ASP 3.4 10.3 - - - +
254E GLU* 3.8 18.8 - - + -
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Residues in contact with LEU 213 (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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176E ILE* 3.7 1.3 - - - -
212E VAL* 1.3 79.2 - - - +
214E GLU* 1.3 69.5 + - + +
219E GLU* 3.1 26.0 - - - +
220E ASN* 3.2 8.0 + - + +
223E LEU* 3.9 33.4 - - + -
224E LYS* 4.4 24.1 - - + +
227E SER* 4.9 5.6 - - - +
232E VAL* 4.6 6.3 - - + -
234E HIS* 4.0 9.0 - - + -
253E ASP* 3.1 17.7 + - - +
255E VAL* 3.4 41.1 - - + -
257E ILE* 4.4 2.2 - - + -
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Residues in contact with GLU 214 (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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176E ILE* 3.9 0.2 - - - -
212E VAL* 3.4 1.1 - - - -
213E LEU* 1.3 91.1 - - - +
215E HIS* 1.3 59.8 + - - +
217E GLY 5.4 1.1 - - - +
218E LYS 3.2 13.5 - - - +
219E GLU* 4.0 11.2 - - + +
251E GLY 3.1 6.4 - - - +
252E THR* 2.8 9.0 - - - +
253E ASP* 2.8 44.4 + - + +
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Residues in contact with HIS 215 (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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176E ILE* 3.4 28.1 - - + +
177E THR* 3.3 23.9 - - + +
212E VAL* 4.0 10.5 - - + -
214E GLU* 1.3 74.1 - - - +
216E HIS* 1.3 115.9 + + + +
217E GLY 3.1 2.7 + - - +
218E LYS* 3.2 22.3 + - - +
251E GLY 3.8 0.7 - - - -
252E THR* 3.0 28.4 + - + +
608I A 5.5 0.9 - - - -
609I T 2.8 28.7 + - - -
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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