Contacts of the strand formed by residues 281 - 287 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASN* 2.8 36.4 + - + +
34A LEU* 4.5 4.5 - - + -
226A PHE* 4.2 4.7 - - + -
272A LEU* 3.8 22.1 - - + +
277A VAL* 2.8 27.5 + - - +
278A ALA* 3.1 15.9 + - - +
279A ASP 3.5 1.0 - - - -
280A ASN* 1.3 78.0 - - - +
282A PHE* 1.3 63.9 + - - +
283A VAL* 3.8 20.3 + - + -
325A TRP* 3.7 10.9 - - - +
326A TRP* 3.2 11.9 - - - +
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PRO* 4.7 2.2 - - + +
32A ASN 2.8 13.8 + - - +
33A ILE* 3.5 10.5 - - + -
34A LEU 2.8 26.3 + - - -
35A LEU* 5.1 4.0 - - + -
280A ASN 4.3 0.4 - - - -
281A THR* 1.3 70.5 - - - +
283A VAL* 1.3 63.9 + - - +
284A PHE* 3.9 37.0 - + + -
324A ALA* 4.4 7.9 - - + -
325A TRP 3.8 2.0 - - - -
326A TRP* 3.8 39.4 - + + +
330A VAL* 4.6 5.6 - - + -
345A LEU* 5.6 2.9 - - + -
348A THR* 4.7 5.2 - - + -
349A SER* 5.7 1.8 - - - -
352A LEU* 3.5 34.8 - - + -
369A LEU* 5.3 0.4 - - + -
372A LEU* 3.8 37.2 - - + -
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.3 26.9 - - + +
36A LEU* 5.2 5.2 - - + -
62A MET* 3.5 13.8 - - + +
269A LEU* 3.8 10.5 - - + -
272A LEU* 3.9 16.4 - - + -
281A THR* 3.8 14.8 - - + -
282A PHE* 1.3 80.1 - - - +
284A PHE* 1.3 60.7 + - - +
324A ALA* 3.5 3.3 - - - +
325A TRP* 2.9 76.9 + - + -
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Residues in contact with PHE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU 2.9 7.4 + - - +
35A LEU* 3.7 21.0 - - + +
36A LEU* 2.8 35.0 + - - +
62A MET* 4.3 1.3 - - - -
69A PHE* 3.9 16.4 - + - -
72A PHE* 3.6 30.3 - + - -
282A PHE* 3.9 18.3 - + + -
283A VAL* 1.3 74.5 - - - +
285A PHE* 1.3 74.3 + - - +
286A THR* 4.0 5.5 + - - +
322A ALA* 3.9 17.5 - - + -
323A LEU 3.3 7.6 - - - -
324A ALA* 3.7 24.7 - - + -
345A LEU* 3.6 32.3 - - + -
368A LEU* 4.9 4.9 - - + -
372A LEU* 4.8 2.2 - - + -
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Residues in contact with PHE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.5 15.0 - - + -
38A MET* 3.4 38.4 - - + -
41A MET* 4.6 4.0 - - + -
46A LEU* 3.9 24.0 - - + -
59A LEU* 3.5 37.5 - - + -
62A MET* 3.8 22.6 - - + +
265A ILE* 3.7 15.7 - - + -
284A PHE* 1.3 75.0 - - - +
286A THR* 1.3 64.9 + - - +
321A PRO* 4.0 22.7 - - + -
322A ALA* 3.1 6.2 - - - -
323A LEU* 2.9 45.1 + - + +
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Residues in contact with THR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU 3.0 11.9 + - - +
37A LEU* 3.8 18.2 - - + -
38A MET* 2.9 28.8 + - - +
72A PHE* 3.9 13.5 - - + -
86A LEU* 5.2 0.2 - - + -
284A PHE* 4.0 11.0 - - + +
285A PHE* 1.3 80.8 - - - +
287A SER* 1.3 71.1 + - - +
320A GLU* 3.8 9.9 - - - +
321A PRO 2.9 19.6 + - - -
342A ILE* 4.5 7.3 - - + +
345A LEU* 3.9 27.4 - - + -
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Residues in contact with SER 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.7 6.8 - - - +
38A MET* 3.6 18.5 + - - -
40A ASP 3.9 0.7 + - - -
41A MET* 2.7 41.3 + - - -
74A SER* 4.1 4.0 + - - -
286A THR* 1.3 81.1 + - - +
288A ASP* 1.3 64.9 + - - +
289A ASN 3.1 8.6 + - - -
320A GLU* 3.3 22.8 - - - +
321A PRO* 4.0 11.0 + - - -
342A ILE* 4.1 3.1 - - - +
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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