Contacts of the strand formed by residues 281 - 287 (chain B) in PDB entry 4FDI
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 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B ASN* 2.9 34.1 + - + +
34B LEU* 4.5 5.8 - - + -
226B PHE* 4.1 5.2 - - + -
272B LEU* 3.8 33.0 - - + +
277B VAL* 2.8 27.0 + - - +
278B ALA 3.0 13.0 + - - +
279B ASP 3.4 1.2 - - - -
280B ASN* 1.3 77.3 - - - +
282B PHE* 1.3 66.0 + - - +
283B VAL* 3.7 11.1 + - + +
325B TRP* 3.6 8.3 - - - +
326B TRP* 3.2 15.6 - - - +
327B PRO* 4.3 1.0 - - - +
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Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PRO* 4.9 1.7 - - + +
32B ASN 2.8 13.3 + - - +
33B ILE* 3.5 9.0 - - + -
34B LEU* 2.9 25.5 + - - +
35B LEU* 4.9 5.6 - - + -
280B ASN 4.2 0.2 - - - -
281B THR* 1.3 70.7 - - - +
283B VAL* 1.3 63.1 + - - +
284B PHE* 3.8 39.7 - + + -
324B ALA* 4.5 7.2 - - + -
325B TRP 3.8 2.5 - - - -
326B TRP* 3.7 40.3 - + + +
330B VAL* 4.8 4.3 - - + -
345B LEU* 5.3 3.1 - - + -
348B THR* 4.5 9.0 - - + -
349B SER* 5.5 2.5 - - - -
352B LEU* 3.5 33.0 - - + -
369B LEU* 4.9 1.8 - - + -
372B LEU* 3.8 34.8 - - + -
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.2 18.8 - - + +
36B LEU* 4.0 17.7 - - + -
62B MET* 3.6 21.2 - - + +
269B LEU* 4.0 17.3 - - + -
272B LEU* 4.1 10.8 - - + -
281B THR* 3.9 7.0 - - + +
282B PHE* 1.3 78.6 - - - +
284B PHE* 1.3 63.0 + - - +
324B ALA* 3.5 3.5 - - - +
325B TRP* 2.8 71.2 + - + +
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Residues in contact with PHE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU 2.9 7.1 + - - +
35B LEU* 3.6 20.9 - - + +
36B LEU* 2.7 35.4 + - - +
62B MET* 4.4 1.6 - - - -
69B PHE* 3.9 22.2 - + - -
72B PHE* 3.7 33.4 - + - -
282B PHE* 3.8 17.9 - + + -
283B VAL* 1.3 73.4 - - - +
285B PHE* 1.3 79.7 + - - +
286B THR* 4.1 4.9 - - + -
322B ALA* 4.0 7.6 - - + -
323B LEU 3.2 7.6 - - - -
324B ALA* 3.7 26.5 - - + -
345B LEU* 3.5 30.7 - - + +
368B LEU* 5.0 4.7 - - + -
372B LEU* 4.5 5.6 - - + -
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Residues in contact with PHE 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 3.4 15.5 - - + -
38B MET* 3.3 40.4 - - + -
41B MET* 4.6 4.0 - - - -
46B LEU* 3.8 29.4 - - + -
59B LEU* 3.7 31.9 - - + -
62B MET* 3.8 22.6 - - + +
265B ILE* 3.8 18.2 - - + -
284B PHE* 1.3 73.9 - - - +
286B THR* 1.3 64.5 + - - +
321B PRO* 4.2 18.2 - - + -
322B ALA* 3.2 7.3 - - - -
323B LEU* 2.8 45.5 + - + +
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Residues in contact with THR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU 3.0 12.6 + - - +
37B LEU* 3.8 18.2 - - + -
38B MET* 2.8 29.5 + - - +
72B PHE* 3.7 20.1 - - + -
86B LEU* 5.4 0.2 - - + -
284B PHE* 4.1 9.6 - - + +
285B PHE* 1.3 81.0 - - - +
287B SER* 1.3 66.5 + - - +
320B GLU* 3.9 5.2 - - - +
321B PRO 2.8 19.8 + - - -
342B ILE* 4.3 9.4 - - + +
345B LEU* 4.0 25.8 - - + -
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.6 7.1 - - - +
38B MET* 3.6 18.3 + - - -
40B ASP 3.9 0.5 + - - -
41B MET* 2.7 47.6 + - - +
74B SER* 4.1 3.8 + - - -
286B THR* 1.3 84.0 + - - +
288B ASP* 1.3 63.1 + - - +
289B ASN 3.3 5.1 + - - -
320B GLU* 3.3 26.1 - - - +
321B PRO* 4.0 9.6 + - - -
342B ILE* 4.3 2.8 - - - +
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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