Contacts of the strand formed by residues 211 - 219 (chain E) in PDB entry 5FJV
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 THR 211 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209E ASN* 3.3 19.6 + - - +
210E ALA* 1.3 73.0 - - - +
212E GLY* 1.3 69.5 + - - +
213E THR* 4.1 13.4 + - + +
230E THR 4.0 1.2 - - - +
231E TYR* 3.6 2.5 - - - -
232E ALA* 2.5 44.2 + - - +
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Residues in contact with GLY 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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189E GLN* 3.5 19.9 + - - +
192E GLN* 5.1 4.9 + - - +
196E LEU* 5.5 2.0 - - - +
210E ALA 4.2 1.4 + - - -
211E THR* 1.3 74.5 - - - +
213E THR* 1.3 72.0 + - - +
230E THR 3.7 8.5 - - - -
231E TYR* 3.9 21.2 - - - -
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Residues in contact with THR 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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189E GLN* 3.3 8.2 - - - +
211E THR* 4.1 16.4 + - + +
212E GLY* 1.3 80.0 - - - +
214E TYR* 1.3 66.2 + - - +
215E ASN* 3.6 17.3 + - - -
229E VAL* 4.8 2.4 - - - +
230E THR* 3.4 28.2 + - - +
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Residues in contact with TYR 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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182E LYS* 3.4 25.3 + - - +
186E ASP* 3.0 26.1 + - - -
187E LEU* 3.1 31.0 - - + -
188E GLU* 5.2 1.3 - - - -
189E GLN* 2.9 22.5 + - + +
213E THR* 1.3 74.4 + - - +
215E ASN* 1.3 89.8 + - - +
216E SER* 3.9 8.5 - - - -
227E PRO* 3.2 16.1 - - + +
228E ASP 3.7 8.7 - - - -
229E VAL* 4.1 9.0 - - + -
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Residues in contact with ASN 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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213E THR* 3.6 22.0 + - - -
214E TYR* 1.3 94.6 - - - +
216E SER* 1.3 63.1 + - - +
227E PRO* 3.3 1.0 - - - +
228E ASP* 2.8 52.9 + - - +
230E THR* 4.4 9.7 + - - +
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Residues in contact with SER 216 (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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182E LYS* 4.5 8.6 + - - +
214E TYR* 3.9 18.4 + - - -
215E ASN* 1.3 81.4 + - - +
217E LYS* 1.3 65.2 + - - +
225E ILE* 3.3 22.9 - - - +
226E TYR 3.8 7.6 + - - -
227E PRO* 4.2 3.1 - - - +
228E ASP* 4.9 0.9 - - - -
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Residues in contact with LYS 217 (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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199A TYR* 5.0 12.8 - - + +
174E LYS* 4.5 6.4 - - - +
216E SER* 1.3 80.4 + - - +
218E LYS* 1.3 85.8 + - - +
219E TYR* 3.6 45.5 + - + +
225E ILE* 2.9 11.3 - - - +
226E TYR 2.8 34.0 + - - +
228E ASP* 5.4 4.9 - - - +
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Residues in contact with LYS 218 (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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199A TYR* 4.8 1.4 - - - -
217E LYS* 1.3 91.8 - - - +
219E TYR* 1.3 78.9 + - - +
220E ASP* 4.4 10.8 + - - +
222E CYS 3.5 16.8 - - - +
223E ALA* 4.1 20.5 + - - +
224E GLU 4.1 4.5 - - - +
225E ILE* 3.1 20.4 - - + +
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Residues in contact with TYR 219 (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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84A TRP* 3.7 24.5 - + - -
199A TYR* 2.8 37.2 - + + +
122E TYR* 3.9 5.5 + - - -
174E LYS* 2.9 31.1 + - - -
217E LYS* 3.6 41.2 - - + +
218E LYS* 1.3 86.9 - - - +
220E ASP* 1.3 58.3 + - - +
221E CYS* 3.0 22.6 + - - -
222E CYS* 3.1 20.7 + - + +
224E GLU 4.7 0.6 + - - -
226E TYR* 4.2 24.3 + + + -
228E ASP* 4.4 6.8 + - - +
300E EPJ 3.5 24.9 - - + -
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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