Contacts of the strand formed by residues 215 - 221 (chain E) in PDB entry 5TWV
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 ILE 215 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183E PHE* 6.3 0.4 - - + -
202E VAL* 6.2 3.1 - - + -
213E ALA 4.1 9.9 - - - +
214E THR* 1.3 76.0 - - - +
216E HIS* 1.3 75.8 + - - +
217E MET* 4.6 15.9 - - + -
240E MET* 3.2 38.7 - - + +
247E ASN* 3.2 15.9 + - - +
248E SER* 4.5 7.4 - - - -
249E ILE* 4.6 12.8 - - + +
257E ILE* 5.3 11.2 - - + -
285E VAL* 4.7 7.9 - - + -
286E ILE 3.3 15.7 - - - +
287E LEU* 3.7 26.5 - - + -
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Residues in contact with HIS 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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214E THR* 4.2 12.5 + - - +
215E ILE* 1.3 85.5 - - - +
217E MET* 1.3 62.4 + - - +
218E GLN* 5.3 4.9 - - - +
237E ASP* 5.3 11.0 - - - +
240E MET* 4.9 3.1 - - + -
247E ASN* 5.3 8.3 + - - +
286E ILE* 2.8 55.4 + - + +
288E GLU* 3.5 24.1 + - - -
212G SER* 5.7 3.1 - - - -
247G ASN* 5.9 5.9 + - + -
248G SER* 4.2 25.4 + - - -
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Residues in contact with MET 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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198E PHE* 4.9 6.3 - - - -
200E LEU* 4.0 30.1 - - + -
215E ILE* 4.3 12.1 - - + -
216E HIS* 1.3 77.0 - - - +
218E GLN* 1.3 63.6 + - - +
237E ASP* 3.0 24.9 + - - +
238E ILE* 3.4 37.9 + - + +
240E MET* 4.7 11.4 - - + +
257E ILE* 3.6 43.3 - - + -
283E ILE* 5.2 4.7 - - + -
284E ILE 3.5 11.0 - - - +
285E VAL* 4.3 19.1 - - + -
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Residues in contact with GLN 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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216E HIS* 4.1 6.0 + - - +
217E MET* 1.3 80.8 + - - +
219E VAL* 1.3 66.1 + - - +
220E VAL 3.8 0.2 - - - -
235E GLN* 3.3 50.2 + - + +
236E VAL 3.6 4.9 - - - +
237E ASP* 3.6 26.9 - - - +
283E ILE* 3.5 4.1 - - - +
284E ILE* 2.9 54.8 + - + +
286E ILE* 4.5 5.9 - - + +
242G ASN* 5.3 2.0 + - - -
249G ILE* 4.1 23.6 - - - +
250G PHE* 6.0 2.0 - - + -
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Residues in contact with VAL 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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218E GLN* 1.3 72.2 - - - +
220E VAL* 1.3 60.9 + - - +
221E ARG* 3.6 15.9 + - + -
234E HIS 3.1 14.6 - - - +
235E GLN* 3.8 1.5 - - - -
236E VAL* 3.0 37.3 + - + +
238E ILE* 3.8 29.2 - - + -
266E PRO* 5.2 13.9 - - + -
267E LEU* 5.5 10.5 - - + -
281E LEU* 5.1 8.5 - - + -
282E GLU 4.1 4.7 - - - +
283E ILE* 4.1 31.4 - - + -
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Residues in contact with VAL 220 (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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35E PHE* 4.9 22.0 - - + -
218E GLN 3.7 2.0 + - - -
219E VAL* 1.3 71.2 - - - +
221E ARG* 1.3 58.3 + - - +
233E LEU* 3.4 43.9 - - + +
234E HIS 3.5 7.0 - - - +
235E GLN* 4.4 17.7 - - + +
281E LEU* 4.2 1.7 - - - +
282E GLU* 3.0 55.2 + - + +
283E ILE* 5.0 0.2 - - - -
284E ILE* 5.0 14.1 - - + -
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Residues in contact with ARG 221 (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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219E VAL* 3.6 12.6 + - + +
220E VAL* 1.3 75.2 - - - +
222E LYS* 1.3 71.3 + - - +
223E THR* 3.4 21.2 + - + +
233E LEU* 4.5 4.9 - - - -
234E HIS* 2.9 31.3 + - - +
266E PRO* 4.9 16.6 + - - +
270E LEU* 5.4 2.0 - - - +
279E GLN* 3.8 27.3 - - - +
281E LEU* 3.8 34.0 - - + +
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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