Contacts of the helix formed by residues 394 - 405 (chain C) in PDB entry 2UZ1
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 ALA 394 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393C GLY* 1.3 74.0 - - - +
395C LEU* 1.3 69.8 + - - +
396C THR 3.1 1.3 + - - +
397C TYR* 3.1 14.8 + - + -
398C LEU* 3.0 27.1 + - + +
421C MET* 4.2 4.3 - - + -
480C ALA* 3.4 20.4 - - + -
1557C TPP 3.1 38.2 + - - +
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Residues in contact with LEU 395 (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 ALA* 1.3 72.7 - - - +
396C THR* 1.3 55.6 + - - +
398C LEU* 3.2 9.7 + - + +
399C TRP* 2.9 46.7 + - + +
475C ASN* 4.4 6.3 - - - +
479C GLY* 3.5 25.8 - - - -
480C ALA* 3.6 15.5 - - + +
483C HIS* 3.4 26.0 - - + +
546C LEU* 4.2 9.2 - - + +
548C PRO 4.9 1.3 - - - +
550C PRO* 3.7 16.6 - - + -
553C GLU* 3.5 34.8 - - - +
1557C TPP 2.9 14.3 + - - +
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Residues in contact with THR 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C PRO* 6.2 0.7 - - - -
376C SER* 4.8 1.0 + - - -
391C ALA* 6.3 0.2 - - + -
392C ASP 3.8 17.0 - - - +
393C GLY* 4.3 2.2 - - - -
394C ALA 4.3 2.2 - - - -
395C LEU* 1.3 76.2 - - - +
397C TYR* 1.3 58.4 + - - +
399C TRP* 3.6 5.6 + - - +
400C LEU* 3.0 26.4 + - + +
445C VAL* 3.8 16.8 - - + +
446C THR 3.8 10.8 - - - +
447C GLY* 3.9 6.6 - - - -
473C MET* 3.4 41.1 + - + +
475C ASN* 5.2 0.7 + - - -
1557C TPP 2.8 21.1 + - - -
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Residues in contact with TYR 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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239C TYR* 3.4 33.1 - + - -
282C LEU* 5.9 3.3 - - - +
391C ALA* 3.8 22.2 - - + -
392C ASP 3.8 8.5 + - - +
393C GLY 3.2 26.5 - - - -
394C ALA* 3.1 23.3 + - + -
396C THR* 1.3 77.6 - - - +
398C LEU* 1.3 77.8 + - + +
400C LEU* 3.7 6.9 - - - +
401C SER* 2.8 31.9 + - - -
412C PHE* 5.8 1.4 - - + -
414C CYS* 3.4 20.2 - - - -
415C HIS* 3.6 25.4 - - + +
419C GLY* 6.1 0.7 - - - -
421C MET* 4.8 3.4 - - + -
112D LEU* 5.6 5.9 - - - +
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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
----------------------------------------------------------
239C TYR* 4.4 7.9 - - - +
394C ALA* 3.0 20.5 + - + +
395C LEU* 3.5 13.9 - - + +
397C TYR* 1.3 103.9 - - + +
399C TRP* 1.3 60.1 + - - +
401C SER* 2.6 24.2 + - - +
402C GLU* 3.8 9.2 - - - +
480C ALA* 5.8 3.1 - - + -
550C PRO* 3.9 28.6 - - + +
552C GLU* 3.9 22.8 - - + +
553C GLU* 4.4 19.3 - - + +
556C ILE* 5.8 5.8 - - + -
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Residues in contact with TRP 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C ILE* 4.0 13.0 - - + -
364C SER* 5.0 0.4 - - - -
371C HIS* 3.5 19.5 - + - -
372C PRO* 3.3 37.0 - - + +
373C PHE* 3.9 26.1 - + + -
376C SER* 3.7 16.5 + - - +
395C LEU* 2.9 34.8 + - + +
396C THR* 3.9 4.0 - - - +
398C LEU* 1.3 73.7 - - - +
400C LEU* 1.3 66.1 + - - +
402C GLU* 3.0 22.8 + - + +
403C VAL* 4.2 1.6 + - - +
548C PRO* 3.5 24.0 + - + -
549C ILE 3.4 10.8 - - - -
550C PRO* 3.3 44.2 - - + +
551C PRO* 3.8 16.8 - - + -
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Residues in contact with LEU 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C SER* 3.6 16.5 + - - +
379C ILE* 4.4 30.3 - - + -
389C VAL* 3.9 20.6 - - + -
391C ALA* 3.9 27.6 - - + -
396C THR 3.0 18.9 + - - +
397C TYR* 3.7 5.4 - - - +
399C TRP* 1.3 74.6 - - - +
401C SER* 1.3 62.8 + - - +
402C GLU 3.0 1.0 + - - -
403C VAL* 3.0 37.3 + - + +
404C MET* 3.4 15.3 - - + +
412C PHE* 4.2 6.1 - - + -
445C VAL* 4.0 17.0 - - + -
473C MET* 6.0 0.2 - - + -
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Residues in contact with SER 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C TYR* 4.4 11.8 + - - -
256C LEU* 3.6 28.8 - - - +
258C GLN* 3.1 29.0 + - - +
397C TYR 2.8 19.3 + - - -
398C LEU* 2.6 22.4 + - - -
400C LEU* 1.3 72.6 - - - +
402C GLU* 1.3 63.2 + - - +
404C MET* 3.2 16.3 + - - -
405C SER* 4.2 3.8 + - - -
412C PHE* 5.3 3.6 - - - -
552C GLU* 4.6 3.5 - - - +
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Residues in contact with GLU 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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258C GLN* 3.9 9.7 - - - +
259C ASN* 4.9 0.9 - - - +
356C ARG* 2.8 48.8 + - - -
357C TYR* 3.7 19.2 - - - +
360C ILE* 3.3 26.1 - - + +
373C PHE* 4.1 11.9 - - + -
398C LEU 3.8 8.1 - - - +
399C TRP* 3.0 19.9 + - + +
401C SER* 1.3 77.1 + - - +
403C VAL* 1.3 58.4 + - - +
404C MET 3.5 0.2 - - - -
405C SER* 4.9 4.3 + - - -
406C ARG* 5.2 1.0 - - - -
551C PRO* 3.5 22.6 - - + +
552C GLU* 4.1 8.0 - - - +
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Residues in contact with VAL 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C TYR* 4.3 12.3 - - + +
373C PHE* 3.7 26.5 - - + -
376C SER* 3.6 38.4 - - - +
377C GLN* 4.1 16.8 - - + +
380C ALA* 3.8 18.0 - - + +
399C TRP 4.8 0.2 - - - +
400C LEU* 3.0 24.8 + - + +
402C GLU* 1.3 76.1 - - - +
404C MET* 1.3 67.1 + - + +
405C SER 3.4 2.1 + - - -
406C ARG* 3.9 13.5 + - + +
407C VAL* 3.6 15.9 + - - +
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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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242C LEU* 3.7 24.3 - - + +
256C LEU* 4.4 5.2 - - + -
379C ILE* 6.2 0.4 - - - -
380C ALA* 6.1 0.7 - - - -
383C VAL* 4.3 8.7 - - + -
389C VAL* 4.4 11.9 - - + -
400C LEU* 3.4 33.9 - - + +
401C SER* 3.2 11.4 + - - +
403C VAL* 1.3 81.5 - - - +
405C SER* 1.3 63.3 + - - +
406C ARG 3.4 0.2 - - - -
407C VAL* 3.3 33.2 - - + +
409C PRO* 3.7 31.9 - - + -
412C PHE* 3.6 42.4 - - + -
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Residues in contact with SER 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU* 4.8 3.4 - - - -
253C ARG* 2.9 28.2 + - - +
254C GLY 4.8 0.4 - - - -
255C GLY* 3.9 14.4 - - - -
256C LEU* 2.9 34.7 + - - +
259C ASN* 3.6 21.0 + - - -
353C ALA* 6.0 1.8 - - - -
401C SER 4.2 4.0 + - - -
402C GLU 4.9 3.7 + - - -
403C VAL 3.4 0.6 - - - -
404C MET* 1.3 78.4 - - - +
406C ARG* 1.3 59.5 + - - +
407C VAL 4.0 0.2 - - - -
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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