Contacts of the strand formed by residues 319 - 326 (chain E) in PDB entry 1E81
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 PRO 319 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125E PHE* 4.1 23.3 - + + -
183E ALA* 4.7 0.3 - - - -
184E VAL* 3.6 25.7 + - + +
185E THR* 3.7 27.6 - - + -
190E TRP* 4.2 6.1 - - + -
315E ASN 3.1 18.4 - - - +
316E GLY* 4.9 1.1 - - - -
317E ALA 3.2 10.9 + - - +
318E THR 3.1 12.1 - - - -
319E THR* 1.3 90.4 - - + +
320E THR* 1.3 63.7 + - - +
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Residues in contact with THR 320 (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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181E TYR* 3.6 23.5 - - + -
182E THR 3.4 17.5 - - - +
183E ALA* 4.7 4.0 - - - -
184E VAL* 3.8 7.2 - - - -
190E TRP* 3.9 4.5 - - - -
313E VAL 3.8 0.2 - - - +
315E ASN* 3.0 47.7 + - - +
319E PRO* 1.3 98.7 + - + +
321E LEU* 1.3 60.8 + - - +
322E GLY 4.2 0.2 - - - -
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Residues in contact with LEU 321 (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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180E THR 3.6 1.6 - - - +
181E TYR* 3.2 3.9 - - - -
182E THR* 2.7 50.2 + - + +
184E VAL* 3.6 13.6 - - + +
190E TRP* 3.7 17.7 - - + +
192E TRP* 3.3 39.7 - - + +
214E ALA* 3.8 9.2 - - + -
312E VAL* 3.7 22.9 - - + -
313E VAL 3.5 13.2 - - - +
314E PHE* 3.8 24.0 - - + -
320E THR* 1.3 72.0 - - - +
322E GLY* 1.3 59.5 + - - +
323E PHE* 4.0 9.1 - - + -
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Residues in contact with GLY 322 (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 ILE* 3.7 18.8 - - - -
180E THR 3.5 5.8 - - - -
181E TYR* 3.8 11.9 - - - -
311E PHE 3.5 0.6 - - - +
312E VAL* 3.3 12.3 - - - +
313E VAL* 2.8 39.4 + - - -
321E LEU* 1.3 74.8 - - - +
323E PHE* 1.3 60.9 + - - -
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Residues in contact with PHE 323 (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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178E SER 4.0 1.0 - - - +
179E ILE* 3.7 1.7 - - - +
180E THR* 2.9 36.4 + - - +
182E THR* 4.7 1.8 - - + -
192E TRP* 3.7 40.6 - + - -
214E ALA* 5.2 0.7 - - + -
259E PHE* 4.2 20.0 - + - -
261E VAL* 3.9 34.5 - - + +
266E ILE* 4.1 8.9 - - + +
302E PHE* 5.9 0.4 - + + -
307E LEU* 4.1 18.4 - - + -
310E ALA* 4.1 11.9 - - + -
311E PHE 3.6 1.1 - - - -
312E VAL* 3.9 29.8 - - + -
321E LEU* 4.0 29.4 - - + -
322E GLY* 1.3 75.1 - - - -
324E ALA* 1.3 61.1 + - - +
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Residues in contact with ALA 324 (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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175E TYR* 3.8 26.9 - - + -
176E THR 4.3 0.4 - - - +
178E SER 3.6 18.4 - - - +
179E ILE* 3.9 16.8 - - + -
266E ILE* 4.1 5.2 - - - -
310E ALA* 3.3 5.9 - - - +
311E PHE* 2.8 41.0 + - + +
323E PHE* 1.3 76.5 - - - +
325E SER* 1.3 61.8 + - - +
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Residues in contact with SER 325 (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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175E TYR* 3.3 5.7 - - - +
176E THR* 2.9 36.7 + - - +
178E SER 4.9 1.0 + - - -
265E ARG 4.2 15.2 + - - -
266E ILE* 4.2 9.7 - - - +
267E VAL 5.8 0.2 + - - -
309E ALA 4.8 5.8 - - - -
324E ALA* 1.3 77.7 - - - +
326E LYS* 1.3 61.4 + - - +
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Residues in contact with LYS 326 (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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154E ASP* 2.7 32.1 + - - +
155E LEU 2.7 28.7 + - - +
156E GLY* 5.7 0.2 - - - -
174E ALA 3.5 18.6 - - - +
175E TYR* 4.2 1.6 - - - +
176E THR* 4.0 17.7 + - - +
308E LYS 3.0 22.9 + - - -
309E ALA 4.1 8.9 + - - +
310E ALA 3.1 32.5 + - - +
311E PHE* 3.8 5.6 - - + +
325E SER* 1.3 77.5 - - - +
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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