Contacts of the helix formed by residues 395 - 403 (chain C) in PDB entry 5E9W
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 395 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C PHE* 4.4 2.6 - + + -
176C ASN* 4.0 13.5 - - - -
179C MET* 3.4 39.1 - - + +
285C PHE* 4.0 15.7 - + - -
317C THR* 3.7 17.0 - - + -
394C THR* 1.3 72.4 - - - +
396C LEU* 1.3 57.5 + - - +
398C PHE* 4.4 0.4 - - - -
399C TYR* 2.8 31.2 + - - +
461C TRP* 5.4 2.0 - - - -
464C THR* 3.3 44.2 - - + +
465C SER* 4.5 2.4 + - - -
467C TYR* 2.9 41.8 + + + +
468C LEU 3.6 12.3 - - - -
469C VAL* 3.4 26.2 - - + -
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Residues in contact with LEU 396 (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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394C THR* 3.0 10.4 + - - +
395C PHE* 1.3 75.6 - - - +
397C GLU* 1.3 60.8 + - + +
399C TYR* 3.1 5.7 + - - +
400C GLU* 2.9 40.4 + - + +
451C LEU* 4.7 7.9 - - + +
452C PRO* 3.6 35.7 - - + -
461C TRP* 4.1 14.1 - - + -
465C SER* 3.7 29.5 - - - +
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Residues in contact with GLU 397 (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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392C LYS* 4.3 2.9 - - - +
393C LYS* 3.3 22.2 - - + +
394C THR* 2.9 45.5 + - - +
396C LEU* 1.3 75.8 - - + +
398C PHE* 1.3 62.4 + - - +
400C GLU* 3.3 8.7 + - - +
401C GLU* 3.2 27.0 + - - +
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Residues in contact with PHE 398 (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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178C TRP* 5.6 0.7 - + - -
179C MET* 3.5 45.3 - - + -
182C VAL* 4.4 3.8 - - + -
183C LEU* 4.0 28.5 - - + -
186C GLU* 4.5 0.4 - - - -
391C TYR* 3.4 22.4 - - - -
393C LYS* 4.1 21.3 - - + +
394C THR 3.0 16.1 + - - +
395C PHE 3.8 2.7 - - - +
397C GLU* 1.3 78.2 - - - +
399C TYR* 1.3 62.7 + - - +
401C GLU* 4.4 2.0 - - - -
402C LYS* 3.1 68.3 + - + +
469C VAL* 3.5 26.2 - - + -
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Residues in contact with TYR 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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175C PHE* 3.6 34.3 - + + -
178C TRP* 4.0 12.1 - + - -
179C MET* 4.5 5.6 - - - -
395C PHE 2.8 19.3 + - - +
396C LEU 3.4 4.3 - - - +
398C PHE* 1.3 77.5 - - - +
400C GLU* 1.3 78.5 + - + +
402C LYS* 3.9 0.5 - - - +
403C ILE* 3.1 59.5 + - + +
412C LEU* 4.6 3.8 - - + -
452C PRO* 3.8 20.6 - - + +
454C GLY* 4.3 7.4 + - - -
455C THR* 2.9 25.7 + - - -
461C TRP* 3.5 24.2 - + + -
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Residues in contact with GLU 400 (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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396C LEU* 2.9 29.6 + - + +
397C GLU* 3.3 7.1 + - - +
399C TYR* 1.3 87.8 - - + +
401C GLU* 1.3 62.5 + - - +
403C ILE* 3.8 9.4 - - - +
404C LYS* 3.3 26.2 - - - +
451C LEU 6.0 0.2 - - - -
452C PRO* 4.8 15.9 - - + +
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Residues in contact with GLU 401 (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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393C LYS* 3.0 35.9 + - - +
397C GLU* 3.2 14.3 + - - +
398C PHE 3.8 4.9 - - - +
400C GLU* 1.3 76.7 - - - +
402C LYS* 1.3 103.4 + - + +
404C LYS* 3.3 32.4 + - + +
405C ASN* 4.4 0.9 + - - +
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Residues in contact with LYS 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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178C TRP* 4.0 17.5 - - + -
182C VAL* 3.4 26.5 - - + -
186C GLU* 3.7 23.5 + - - -
391C TYR* 5.0 2.0 + - - -
393C LYS* 5.4 1.4 - - - +
398C PHE* 3.1 55.5 + - + +
399C TYR 4.0 0.2 - - - +
401C GLU* 1.3 109.5 + - + +
403C ILE* 1.3 56.8 + - - +
404C LYS 3.2 0.4 - - - -
405C ASN* 3.2 12.7 + - - +
408C ASN* 3.1 29.6 + - - +
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Residues in contact with ILE 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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178C TRP* 4.4 7.2 - - + -
399C TYR* 3.1 59.3 + - + +
400C GLU* 3.8 11.0 - - - +
402C LYS* 1.3 74.7 - - - +
404C LYS* 1.3 59.3 + - + +
405C ASN 3.1 13.5 + - - +
409C LYS* 4.0 45.7 + - + +
412C LEU* 3.8 21.1 - - + -
413C LYS* 4.9 2.2 - - - +
455C THR* 4.3 2.2 - - - +
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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