Contacts of the helix formed by residues 392 - 402 (chain C) in PDB entry 5H2U
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 SER 392 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339B GLU* 3.4 20.4 + - - +
340B ASP* 3.3 19.1 + - - -
352C LYS* 4.1 0.2 - - - -
390C GLY 4.3 0.4 + - - -
391C MET* 1.3 75.6 - - - +
393C ASN* 1.3 62.0 + - - +
395C GLU* 3.3 26.3 + - - +
396C ALA* 2.9 27.4 + - - +
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Residues in contact with ASN 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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340B ASP* 2.7 21.3 + - - +
346C ASP 3.6 6.1 + - - -
347C HIS* 2.8 24.4 + - - +
348C ASN* 3.4 20.6 - - + +
349C ILE* 3.2 30.4 - - - +
351C TYR* 3.7 18.2 - - + +
352C LYS* 3.3 31.1 + - + +
392C SER* 1.3 73.5 - - - +
394C HIS* 1.3 60.7 + - - +
396C ALA* 3.6 2.6 + - - +
397C PHE* 3.2 16.8 + - - +
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Residues in contact with HIS 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLU* 3.6 29.2 - - - +
340B ASP* 3.2 15.7 + - - +
343B LEU* 3.8 25.6 - - + +
351B TYR* 5.3 3.4 + - - -
358B ALA 4.3 4.2 + - - -
359B LEU* 3.5 33.4 - - + -
362B GLY* 4.3 10.3 - - - -
364B TYR* 5.5 3.0 - + - -
348C ASN* 5.7 2.2 - - + +
351C TYR* 4.6 18.1 - - + -
393C ASN* 1.3 72.1 - - - +
395C GLU* 1.3 59.5 + - - +
397C PHE* 3.3 6.9 + + - +
398C LEU* 2.9 62.9 + - + +
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Residues in contact with GLU 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLU* 3.9 7.7 + - - +
390C GLY 4.0 6.1 - - - +
391C MET* 3.4 26.6 - - + +
392C SER* 3.3 32.4 + - - +
394C HIS* 1.3 78.4 - - - +
396C ALA* 1.3 56.1 + - - +
398C LEU* 3.1 11.0 + - - +
399C ARG* 2.9 48.7 + - + +
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Residues in contact with ALA 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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351C TYR 5.4 0.4 - - - -
352C LYS* 3.7 33.7 - - + -
388C TYR* 3.8 19.9 - - + -
391C MET* 3.9 12.5 - - + +
392C SER 2.9 22.1 + - - +
393C ASN 3.7 1.6 - - - +
394C HIS 3.3 0.2 - - - -
395C GLU* 1.3 72.2 - - - +
397C PHE* 1.3 58.3 + - - +
399C ARG* 3.5 1.2 + - - +
400C VAL* 2.9 36.1 + - - +
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Residues in contact with PHE 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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359B LEU 5.4 4.5 - - - -
360B SER* 5.1 5.4 - - - -
351C TYR* 4.1 30.2 + + + +
354C THR 4.8 3.6 - - - -
356C PRO* 3.6 30.3 - - + -
359C LEU* 3.6 32.5 - - + -
360C SER* 3.3 26.0 - - - -
393C ASN 3.2 14.6 + - - +
394C HIS* 3.3 6.9 + + - +
396C ALA* 1.3 78.2 - - - +
398C LEU* 1.3 72.6 + - + +
400C VAL* 3.4 8.8 + - + +
401C ASP* 2.9 41.4 + - + +
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Residues in contact with LEU 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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339B GLU* 5.6 0.4 - - - +
359B LEU 3.9 4.5 - - - +
360B SER 3.3 26.5 - - - +
361B ARG* 4.1 12.3 - - - +
362B GLY* 4.1 13.2 - - - -
394C HIS* 2.9 56.6 + - + +
395C GLU* 3.1 11.4 + - - +
397C PHE* 1.3 86.8 - - + +
399C ARG* 1.3 63.0 + - + +
401C ASP* 3.4 5.0 + - - +
402C ALA* 3.2 21.5 + - - +
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Residues in contact with ARG 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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391C MET* 3.8 24.0 - - - +
395C GLU* 2.9 38.7 + - + +
396C ALA 4.0 3.1 - - - +
398C LEU* 1.3 72.5 - - + +
400C VAL* 1.3 60.7 + - - +
402C ALA* 3.1 15.0 + - - +
403C GLY 3.3 0.5 + - - -
404C TYR* 2.9 76.5 + - + +
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Residues in contact with VAL 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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351C TYR 6.0 0.9 - - - +
354C THR 5.6 1.8 - - - +
356C PRO* 4.6 9.7 - - + +
371C TRP* 3.5 33.0 - - + -
388C TYR* 3.4 40.6 - - + +
396C ALA 2.9 26.5 + - - +
397C PHE* 3.7 10.1 - - + +
398C LEU 3.3 0.2 - - - -
399C ARG* 1.3 77.2 - - - +
401C ASP* 1.3 59.2 + - - +
403C GLY* 2.9 9.9 + - - -
404C TYR* 3.6 11.9 - - + +
405C ARG* 2.9 29.6 + - - +
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Residues in contact with ASP 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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360B SER 4.7 10.9 - - - +
356C PRO* 3.5 26.1 - - + +
360C SER* 4.4 8.7 + - - -
397C PHE* 2.9 32.8 + - + +
398C LEU* 3.8 6.3 - - - +
400C VAL* 1.3 77.9 - - - +
402C ALA* 1.3 57.6 - - - +
403C GLY 3.3 1.0 + - - -
426C ARG* 3.1 39.1 + - - +
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Residues in contact with ALA 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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398C LEU 3.2 11.3 + - - +
399C ARG* 3.1 12.9 + - - +
400C VAL 3.1 1.0 - - - -
401C ASP* 1.3 76.5 - - - +
403C GLY* 1.3 57.0 + - - +
404C TYR 3.5 0.8 + - - -
426C ARG* 5.3 1.1 - - - +
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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