Contacts of the strand formed by residues 278 - 283 (chain E) in PDB entry 1F9E
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 LYS 278 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230E PHE* 3.5 10.5 - - + -
265E PHE* 3.0 36.6 - - + +
266E THR 5.1 3.8 - - - -
267E GLY* 5.5 0.6 - - - +
273E LEU* 3.2 40.7 + - + -
274E ALA* 4.4 2.2 - - - +
275E GLY 4.1 4.4 - - - +
276E LYS 2.7 30.3 + - - +
277E PRO* 1.3 73.6 - - - +
279E VAL* 1.3 60.4 + - - +
280E PHE* 4.0 8.9 - - + -
323F ASP 5.6 0.9 - - - -
325F ALA 3.7 10.0 + - - -
326F ASP* 3.0 17.2 + - - +
327F PHE* 3.5 35.8 - - + -
328F LEU* 3.1 22.6 + - - +
394F LEU* 5.2 0.4 - - - +
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Residues in contact with VAL 279 (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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229E CYS* 4.4 8.1 - - - -
230E PHE 2.9 15.5 + - - +
231E ILE* 3.3 14.3 - - + +
232E CYS 2.9 25.5 + - - -
277E PRO* 4.7 0.4 - - + -
278E LYS* 1.3 75.1 - - - +
280E PHE* 1.3 69.2 + - - +
281E PHE* 3.5 40.8 - - + -
328F LEU* 3.4 22.2 - - + +
398F LEU* 3.7 29.8 - - + -
400F PHE* 4.6 3.6 - - + -
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Residues in contact with PHE 280 (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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215E LEU* 5.2 1.1 - - + -
230E PHE* 4.4 8.5 - + - -
232E CYS* 3.2 32.1 - - + +
234E ILE* 5.4 4.5 - - + -
261E LEU* 4.2 11.0 - - + -
262E THR* 3.7 37.2 - - + -
265E PHE* 3.6 31.2 - + - -
278E LYS* 4.0 15.7 - - + -
279E VAL* 1.3 80.6 - - - +
281E PHE* 1.3 58.3 + - - +
282E ILE* 4.0 7.9 - - + -
327F PHE* 3.9 24.5 - + - -
328F LEU 2.7 12.5 + - - +
329F LEU* 3.3 15.7 - - + +
330F GLY* 2.7 32.7 + - - -
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Residues in contact with PHE 281 (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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193E PHE* 3.7 25.4 - + - -
231E ILE* 4.2 5.4 - - + -
232E CYS 3.0 6.7 + - - +
233E CYS* 3.3 27.1 - - + +
234E ILE 2.9 26.3 + - - +
235E LEU* 5.4 0.9 - - - +
279E VAL* 3.5 28.9 - - + -
280E PHE* 1.3 76.7 - - - +
282E ILE* 1.3 62.2 + - - +
283E GLN* 4.0 0.6 + - - -
328F LEU* 5.4 0.7 - - + -
330F GLY* 3.5 6.5 - - - +
349F TYR* 3.8 19.5 - - + -
350F ILE* 4.9 6.7 - - + -
353F LEU* 3.4 44.6 - - + -
357F LEU* 5.2 1.1 - - + -
366F ILE* 4.4 16.4 - - + -
370F LEU* 4.4 13.0 - - + -
400F PHE* 5.8 2.0 - + - -
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Residues in contact with ILE 282 (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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234E ILE* 3.6 23.3 - - + +
243E ILE* 3.4 29.4 - - + -
258E ILE* 3.3 49.6 - - + -
261E LEU* 5.2 2.5 - - + -
262E THR* 5.7 0.9 - - + -
280E PHE* 3.9 8.0 + - + -
281E PHE* 1.3 78.8 - - - +
283E GLN* 1.3 65.2 + - - +
284E ALA* 3.9 3.8 + - + +
286E GLN* 5.4 0.7 - - - +
329F LEU* 4.2 13.0 - - + -
330F GLY 3.0 8.6 + - - +
331F MET* 3.8 14.2 - - + +
332F ALA* 3.2 25.8 + - - +
349F TYR* 4.3 2.2 - - - -
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Residues in contact with GLN 283 (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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179E ARG* 4.0 7.1 + - - +
185E ASP* 4.3 1.8 - - - +
234E ILE 2.8 13.1 + - - +
235E LEU* 4.0 4.9 - - + -
236E SER 3.0 24.9 + - - +
281E PHE 4.0 1.0 + - - -
282E ILE* 1.3 70.9 - - - +
284E ALA* 1.3 62.1 + - - +
332F ALA* 3.3 7.9 - - + +
339F SER* 3.2 22.9 + - - -
340F TYR 4.5 1.6 + - - +
347F THR* 3.3 35.5 - - + +
349F TYR* 3.2 28.5 + - + +
350F ILE* 3.7 24.0 - - + -
385F GLN* 4.7 0.5 + - - -
4304S ASA 2.9 26.7 + - - -
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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