Contacts of the strand formed by residues 398 - 404 (chain E) in PDB entry 5FXY
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 398 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E TYR* 5.3 6.5 - - + -
37E THR* 3.9 15.0 - - - +
38E HIS 3.6 4.7 - - - -
39E ALA* 4.2 16.4 - - + +
372E GLY 4.5 2.0 - - - +
373E HIS* 3.8 22.2 - - + +
374E THR* 4.4 4.3 - - - +
393E VAL* 3.8 2.8 - - - +
394E SER* 3.3 32.9 + - - +
396E ASP* 2.9 37.1 + - - +
397E ASN* 1.3 74.9 - - + +
399E MET* 1.3 58.8 + - - +
400E GLN* 3.9 21.1 - - - +
469F GLN 6.3 0.9 - - - +
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Residues in contact with MET 399 (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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36E MET 3.6 4.2 - - - +
37E THR* 3.5 1.0 - - - -
38E HIS* 2.9 39.9 + - + +
40E LEU* 4.0 25.8 - - + -
66E LEU* 3.7 27.1 - - + -
68E LEU* 3.9 24.7 - - - -
82E ALA* 4.8 9.0 - - + -
84E VAL* 5.6 0.4 - - + -
115E ILE* 3.4 35.9 - - + -
391E CYS* 4.0 11.2 - - - -
392E SER 3.7 3.8 - - - -
393E VAL* 3.9 17.5 - - + -
397E ASN 3.5 0.4 + - - -
398E ILE* 1.3 72.5 - - - +
400E GLN* 1.3 61.2 + - - +
401E VAL* 4.9 3.8 - - + +
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Residues in contact with GLN 400 (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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21E TYR* 4.5 4.0 - - - -
24E TRP* 4.2 12.5 - - - -
35E VAL* 5.6 3.3 - - + +
36E MET 4.0 3.6 - - - -
37E THR* 3.5 31.1 + - - +
370E HIS* 2.8 31.9 + - - -
372E GLY* 3.2 31.9 + - - -
373E HIS* 3.6 20.4 + - + +
391E CYS* 3.4 1.6 - - - -
392E SER 3.0 33.2 + - - -
398E ILE* 3.9 11.8 - - + +
399E MET* 1.3 72.8 - - - +
401E VAL* 1.3 60.5 - - - +
402E TRP* 3.5 12.5 - - + -
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Residues in contact with VAL 401 (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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34E LEU* 4.5 2.7 - - + +
35E VAL* 3.6 1.4 - - - +
36E MET* 2.8 69.6 + - + +
49E TRP* 3.7 30.5 - - + -
66E LEU* 4.6 2.2 - - + -
84E VAL* 4.2 18.4 - - + -
86E LEU* 4.3 1.8 - - + -
115E ILE* 4.5 7.4 - - + -
389E VAL* 3.9 12.1 - - + -
390E ILE 3.5 3.6 - - - +
391E CYS* 4.3 18.4 - - + +
399E MET* 4.9 5.4 - - + -
400E GLN* 1.3 73.0 - - - +
402E TRP* 1.3 61.7 + - - +
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Residues in contact with TRP 402 (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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32E TYR* 3.6 24.5 - + + -
34E LEU* 3.2 13.7 - - - +
35E VAL* 4.5 7.6 - - + -
342E LEU* 3.6 25.8 - - + -
344E VAL* 4.2 6.5 - - + -
368E PHE* 4.0 19.5 - + - -
370E HIS* 3.4 43.2 + + + -
388E TRP 3.8 0.8 - - - +
389E VAL* 3.4 5.4 - - - -
390E ILE* 2.8 82.0 + - + +
392E SER* 3.1 19.7 + - - -
400E GLN* 3.5 17.0 - - + -
401E VAL* 1.3 74.9 - - - +
403E GLN* 1.3 62.5 + - - +
404E MET* 4.0 15.0 - - + -
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Residues in contact with GLN 403 (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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32E TYR* 3.3 11.9 - - - +
33E ASP* 3.0 42.0 + - - +
34E LEU* 2.9 23.6 + - + +
386E GLU* 4.4 10.7 + - - -
387E PRO 3.1 22.6 + - - -
388E TRP* 3.5 25.4 - - + +
389E VAL* 4.0 14.3 - - + +
402E TRP* 1.3 75.3 - - - +
404E MET* 1.3 68.5 + - - +
409E TYR* 4.2 11.3 + - - -
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Residues in contact with MET 404 (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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31E LEU 3.6 9.2 - - - +
32E TYR* 3.9 4.5 - - - +
33E ASP* 3.8 4.9 - - - +
344E VAL* 3.7 32.1 - - + -
367E LEU* 4.1 11.2 - - - -
368E PHE* 3.5 50.0 - - + -
388E TRP* 4.0 21.2 + - + +
390E ILE* 5.4 2.9 - - + -
402E TRP* 4.0 11.2 - - + -
403E GLN* 1.3 88.9 - - - +
405E ALA* 1.3 65.6 + - - +
406E GLU 3.6 0.7 + - - -
408E ILE* 4.0 17.3 - - + -
409E TYR* 3.8 22.5 - - + -
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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