Contacts of the strand formed by residues 389 - 394 (chain C) in PDB entry 3IXK
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 PHE 389 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C LEU 3.9 6.2 - - - +
201C GLN* 4.3 5.2 - - - -
202C LEU 4.5 0.7 + - - -
346C ILE* 3.6 30.3 - - + -
347C THR 3.8 18.6 - - - -
348C ILE* 3.7 17.9 - - + -
385C ILE* 3.0 32.1 - - + -
386C MET 2.9 17.0 + - - +
387C GLU 3.4 1.0 + - - -
388C GLY* 1.3 85.0 - - - +
390C TYR* 1.3 67.9 + - - +
391C VAL* 3.7 13.9 + - + +
402C PHE* 4.2 16.8 - + + -
403C ALA 3.2 10.3 - - - +
404C VAL* 4.1 2.0 - - - -
405C SER* 3.6 9.5 - - - -
416C ALA* 4.3 8.7 - - + -
417C ALA 3.6 22.0 - - - -
418C VAL* 3.6 22.9 - - + -
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Residues in contact with TYR 390 (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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199C SER* 2.7 38.9 + - - -
200C LEU 3.7 14.8 - - - -
201C GLN* 4.1 10.1 - - + +
223C ILE* 3.7 6.0 - - + +
227C ILE* 3.5 15.2 - - + -
228C ASP* 2.9 31.7 + - - -
231C LEU* 3.9 24.2 - - + +
232C TYR* 3.0 52.9 - + + -
236C LEU* 4.6 4.2 - - + +
389C PHE* 1.3 73.5 - - - +
391C VAL* 1.3 62.4 + - - +
392C VAL* 4.1 8.9 + - + -
401C GLY 3.6 0.9 - - - +
402C PHE* 3.4 5.5 - - - -
403C ALA* 2.8 31.3 + - + +
405C SER* 3.8 3.9 - - - +
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Residues in contact with VAL 391 (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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199C SER* 3.1 3.1 - - - -
200C LEU 2.8 40.2 + - - +
275C VAL* 4.5 6.1 - - + -
386C MET* 4.2 25.6 - - + -
389C PHE* 3.9 22.7 - - + +
390C TYR* 1.3 76.5 - - - +
392C VAL* 1.3 63.5 + - - +
393C PHE* 3.6 27.8 + - + -
400C ILE* 3.8 17.7 - - + -
401C GLY 3.2 8.5 - - - +
402C PHE* 4.1 17.3 - - + -
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Residues in contact with VAL 392 (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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197C LEU* 4.1 12.6 - - + -
198C PHE 4.3 3.4 - - - +
199C SER* 4.0 14.6 - - - -
227C ILE* 3.8 34.5 - - + -
236C LEU* 3.6 28.3 - - + -
238C TYR* 4.3 6.7 - - + +
390C TYR* 4.3 10.1 - - + -
391C VAL* 1.3 74.4 - - - +
393C PHE* 1.3 60.8 + - - +
394C ASP* 3.2 15.2 + - + +
400C ILE* 3.2 8.4 - - - +
401C GLY* 2.7 43.5 + - - +
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Residues in contact with PHE 393 (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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81C THR* 3.8 20.2 - - + -
197C LEU* 3.3 17.1 - - - +
198C PHE* 2.8 54.4 + + + +
199C SER* 4.7 0.2 - - - -
200C LEU* 4.0 12.6 - - + -
241C ILE* 5.7 0.7 - - - -
247C TYR* 3.6 57.4 - + + +
275C VAL* 4.1 13.9 - - + -
386C MET* 4.3 4.5 - - + -
391C VAL* 3.6 33.2 - - + -
392C VAL* 1.3 70.4 - - - +
394C ASP* 1.3 59.7 + - - +
395C ARG* 3.0 10.5 + - + +
399C ARG 3.9 2.5 - - - -
400C ILE* 4.3 13.0 - - + -
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Residues in contact with ASP 394 (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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197C LEU* 3.9 20.6 - - - +
227C ILE* 6.1 0.4 - - - +
238C TYR* 4.4 4.1 + - + -
241C ILE* 4.9 1.1 - - - -
392C VAL* 3.2 13.2 + - + -
393C PHE* 1.3 70.4 - - - +
395C ARG* 1.3 56.6 + - - +
396C ALA* 3.5 10.0 + - - +
397C ARG* 3.2 24.4 + - - +
398C LYS 2.8 23.7 + - - -
399C ARG* 2.8 66.5 + - + +
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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