Contacts of the strand formed by residues 398 - 404 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C TYR* 5.7 2.7 - - + +
37C THR* 3.9 15.9 - - - +
38C HIS 3.9 4.9 - - - +
39C ALA* 4.3 15.0 - - + +
40C LEU* 5.6 0.2 - - - -
372C GLY 4.5 1.6 - - - +
373C HIS* 3.8 22.5 - - + +
374C THR* 4.5 4.3 - - + +
393C VAL* 3.9 1.8 - - - +
394C SER* 3.2 33.7 + - - +
396C ASP* 2.9 36.3 + - - +
397C ASN* 1.3 71.5 - - - +
399C MET* 1.3 58.0 + - - +
400C GLN* 3.8 22.2 - - - +
468D ARG* 4.0 32.1 - - + +
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Residues in contact with MET 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C MET 3.6 2.2 - - - +
37C THR* 3.3 1.7 - - - -
38C HIS* 2.9 39.1 + - + +
40C LEU* 3.8 16.6 - - + -
66C LEU* 3.3 29.2 - - + -
68C LEU* 3.6 28.5 - - - -
82C ALA* 5.3 2.5 - - + -
84C VAL* 4.1 1.3 - - + -
115C ILE* 3.6 37.5 - - + -
391C CYS* 4.4 7.9 - - - -
392C SER 3.7 4.5 - - - -
393C VAL* 4.0 17.0 - - + -
397C ASN 3.5 0.4 + - - -
398C ILE* 1.3 72.4 - - - +
400C GLN* 1.3 63.4 + - - +
401C VAL* 3.7 15.9 - - + -
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Residues in contact with GLN 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TYR* 4.8 3.8 + - - -
24C TRP* 4.2 13.6 - - - -
35C VAL* 5.6 3.1 - - + -
36C MET 4.0 4.0 - - - -
37C THR* 3.6 26.1 + - - +
370C HIS* 2.8 27.3 + - + -
372C GLY* 3.1 34.0 + - - -
373C HIS* 3.5 21.2 + - + +
391C CYS* 3.5 0.3 - - - -
392C SER 3.0 32.5 + - - -
398C ILE* 3.8 15.1 - - + +
399C MET* 1.3 72.8 - - - +
401C VAL* 1.3 61.4 + - - +
402C TRP* 3.3 17.9 - - + -
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Residues in contact with VAL 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 4.5 2.2 - - + +
35C VAL* 3.5 1.7 + - - -
36C MET* 2.8 65.5 + - + +
49C TRP* 3.7 25.8 - - + -
66C LEU* 4.3 2.7 - - + -
84C VAL* 4.2 11.4 - - + -
86C LEU* 4.0 3.1 - - + -
115C ILE* 4.7 0.9 - - + -
389C VAL* 3.9 12.6 - - + -
390C ILE 3.5 3.8 - - - +
391C CYS* 4.2 15.7 - - + -
399C MET* 3.7 28.9 - - + -
400C GLN* 1.3 71.2 - - - +
402C TRP* 1.3 59.1 + - - +
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Residues in contact with TRP 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C TYR* 3.6 20.9 - + + -
34C LEU* 3.2 13.7 - - - +
35C VAL* 4.2 9.4 - - + -
342C LEU* 3.8 24.7 - - + -
344C VAL* 4.3 8.1 - - + -
368C PHE* 4.0 19.3 - + - -
370C HIS* 3.1 49.6 + + + -
388C TRP 5.1 1.1 - - - -
389C VAL* 3.4 5.0 - - - -
390C ILE* 2.7 77.2 + - + +
392C SER* 3.2 15.3 + - - -
400C GLN* 3.3 20.8 + - + -
401C VAL* 1.3 74.9 - - - +
403C GLN* 1.3 62.0 + - - +
404C MET* 3.9 17.3 - - + -
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Residues in contact with GLN 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C TYR* 3.3 7.0 - - - +
33C ASP* 3.1 33.0 + - - +
34C LEU* 2.8 34.6 + - + +
386C GLU* 5.1 7.6 + - - +
387C PRO* 3.2 20.3 + - - +
388C TRP* 3.6 22.3 - - + +
389C VAL* 4.0 14.8 - - + +
402C TRP* 1.3 74.5 - - - +
404C MET* 1.3 71.2 + - - +
409C TYR* 3.7 19.8 + - - -
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Residues in contact with MET 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU 3.7 4.7 - - - -
32C TYR* 4.0 5.2 - - - -
33C ASP* 3.9 4.6 + - - -
344C VAL* 3.7 27.8 - - + -
367C LEU* 4.4 4.9 - - - -
368C PHE* 3.4 59.7 - - + -
382C TRP* 5.6 0.9 - - + -
388C TRP* 4.1 26.9 + - + +
390C ILE* 5.6 1.1 - - + -
402C TRP* 3.9 12.9 - - + -
403C GLN* 1.3 89.9 - - - +
405C ALA* 1.3 66.0 + - - +
406C GLU 3.7 0.9 + - - -
408C ILE* 3.9 16.2 - - - -
409C TYR* 3.8 23.0 - - + -
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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