Contacts of the helix formed by residues 387 - 401 (chain C) in PDB entry 3UO8
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 THR 387 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354C ARG* 3.7 27.4 - - - +
385C ASP 5.3 0.7 - - - +
386C LEU* 1.3 76.4 - - - +
388C GLU* 1.3 66.5 + - - +
389C TYR* 3.6 7.8 + - - +
390C GLU* 3.0 38.9 + - - +
391C MET* 2.9 20.6 + - - +
427C PRO* 3.4 2.2 - - - -
428C VAL* 4.2 6.7 - - + -
429C ASP* 3.3 26.2 - - + +
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Residues in contact with GLU 388 (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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387C THR* 1.3 72.4 - - - +
389C TYR* 1.3 64.7 + - - +
391C MET* 3.2 4.0 + - - +
392C ARG* 2.7 59.2 + - - +
427C PRO* 3.2 16.7 - - + +
429C ASP* 3.0 17.3 + - - +
437C GLU 3.3 22.3 - - - +
438C ASN* 3.4 24.2 - - - +
440C LEU* 3.9 9.6 - - + -
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Residues in contact with TYR 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C THR* 3.6 6.2 + - - +
388C GLU* 1.3 81.4 - - - +
390C GLU* 1.3 71.8 + - + +
392C ARG* 3.4 9.1 + - + +
393C ASN* 3.1 52.3 + - - -
429C ASP* 5.1 1.0 + - - +
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Residues in contact with GLU 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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385C ASP 4.0 3.6 - - - +
386C LEU* 3.4 28.1 - - + +
387C THR* 3.0 41.6 + - - +
389C TYR* 1.3 86.8 - - + +
391C MET* 1.3 65.5 + - - +
393C ASN* 3.3 7.1 + - - +
394C ALA* 2.9 25.8 + - - +
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Residues in contact with MET 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C ILE* 4.3 13.0 - - + +
350C ASN* 3.6 19.5 - - - -
386C LEU* 3.5 24.7 - - + -
387C THR 2.9 17.0 + - - +
388C GLU 3.2 5.1 + - - +
390C GLU* 1.3 77.5 - - - +
392C ARG* 1.3 56.3 + - - +
394C ALA* 3.3 2.1 + - - +
395C VAL* 2.9 31.7 + - - +
412C TYR* 3.9 16.8 - - + -
425C MET* 3.8 40.6 - - + -
427C PRO* 3.8 27.1 - - - -
440C LEU* 3.6 18.8 - - + -
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Residues in contact with ARG 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C GLU* 2.7 47.9 + - - +
389C TYR* 3.8 8.7 - - + +
391C MET* 1.3 77.1 - - - +
393C ASN* 1.3 58.3 + - - +
395C VAL* 3.4 4.2 + - - +
396C ASP* 3.0 39.2 + - - +
436C SER 4.8 0.8 + - - -
437C GLU* 4.3 4.9 + - - +
439C CYS 3.0 25.4 + - - -
440C LEU* 3.9 25.6 - - + +
441C CYS 5.4 1.4 - - - +
444C ASN* 6.0 2.0 - - - +
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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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389C TYR* 3.1 62.2 + - - +
390C GLU* 3.3 7.3 + - - +
392C ARG* 1.3 75.0 - - - +
394C ALA* 1.3 66.8 + - - +
396C ASP* 3.1 11.9 + - - +
397C GLU* 3.0 31.0 + - + +
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Residues in contact with ALA 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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346C LEU* 3.9 16.8 - - + +
348C ILE* 4.7 0.9 - - + -
383C LEU* 3.6 31.4 - - + -
386C LEU* 4.4 5.6 - - + -
390C GLU 2.9 17.7 + - - +
391C MET* 3.6 4.7 - - - +
393C ASN* 1.3 77.2 - - - +
395C VAL* 1.3 56.3 + - - +
397C GLU* 3.1 9.7 + - - +
398C PHE* 2.9 28.4 + - - +
580C TRP* 5.2 0.5 - - - -
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Residues in contact with VAL 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C LEU* 3.9 19.1 - - + -
348C ILE* 5.1 4.3 - - + -
391C MET 2.9 20.9 + - - +
392C ARG* 3.7 6.7 - - - +
394C ALA* 1.3 75.9 - - - +
396C ASP* 1.3 59.4 + - - +
398C PHE* 3.3 5.0 - - + +
399C LEU* 2.9 45.0 + - + +
410C LEU* 5.4 2.5 - - + -
425C MET* 5.7 0.7 - - + -
440C LEU* 3.9 19.3 - - + -
445C ILE* 3.9 37.7 - - + -
448C LEU* 5.4 2.7 - - + -
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Residues in contact with ASP 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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392C ARG* 3.0 25.0 + - - +
393C ASN* 3.1 15.2 + - - +
395C VAL* 1.3 80.9 - - - +
397C GLU* 1.3 62.8 + - + +
399C LEU* 3.4 17.6 + - - +
400C LEU* 3.2 27.9 + - - +
448C LEU* 5.3 3.5 - - - +
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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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393C ASN* 3.0 21.7 + - + +
394C ALA* 3.1 10.3 + - - +
396C ASP* 1.3 73.7 - - + +
398C PHE* 1.3 67.5 + - - +
400C LEU* 3.2 34.7 + - - +
401C LEU* 3.5 4.2 + - - +
580C TRP* 3.5 25.4 - - + -
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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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344C VAL* 3.7 36.3 - - + -
346C LEU* 3.8 31.6 - - + -
394C ALA 2.9 13.1 + - - +
395C VAL* 3.3 16.4 - - + +
397C GLU* 1.3 76.9 - - - +
399C LEU* 1.3 70.4 + - + +
401C LEU* 3.2 14.4 + - - +
402C LEU* 3.5 21.6 + - + +
408C GLY* 4.0 7.2 - - - -
409C LEU 3.5 32.5 - - - -
410C LEU* 4.6 10.8 - - + -
445C ILE* 5.1 3.6 - - + -
449C MET* 4.0 26.9 - - + -
580C TRP* 3.6 11.8 - + + -
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Residues in contact with LEU 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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395C VAL* 2.9 34.9 + - + +
396C ASP* 3.4 15.9 + - - +
397C GLU 3.2 0.2 - - - -
398C PHE* 1.3 81.3 - - + +
400C LEU* 1.3 63.0 + - + +
402C LEU* 3.0 19.7 + - + +
445C ILE* 4.5 1.6 - - + +
448C LEU* 3.7 35.4 - - + +
449C MET* 3.6 44.6 - - + +
452C LYS* 3.3 29.0 + - + +
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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
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396C ASP* 3.2 19.2 + - + +
397C GLU* 3.2 29.6 + - - +
398C PHE 3.2 0.4 - - - -
399C LEU* 1.3 79.1 - - + +
401C LEU* 1.3 63.1 + - + +
402C LEU 3.5 4.2 + - - +
403C ASP* 6.0 0.3 - - - +
452C LYS* 4.8 10.0 + - - +
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Residues in contact with LEU 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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342C ASP* 5.3 4.5 - - - +
344C VAL* 3.9 30.6 - - + +
379C LYS* 4.4 10.5 - - + -
397C GLU 3.5 5.1 + - - +
398C PHE 3.2 10.7 + - - +
400C LEU* 1.3 82.9 - - + +
402C LEU* 1.3 63.3 + - - +
403C ASP* 3.8 3.3 + - - +
406C VAL* 4.1 7.1 - - - +
577C ASN* 4.3 20.9 - - - +
580C TRP* 3.0 71.1 - - + +
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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