Contacts of the helix formed by residues 423 - 437 (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 VAL 423 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C HIS* 3.3 47.0 - - + +
62C ARG* 6.0 2.5 - - - +
83C THR* 4.3 3.6 - - + -
87C ASN* 4.2 18.6 - - - +
392C ASP* 3.3 0.2 + - - -
414C CYS 6.4 0.2 - - - -
415C HIS* 3.8 20.6 - - + +
420C SER* 3.2 38.6 - - - +
421C MET 4.8 0.7 - - - +
422C GLY* 1.3 76.7 - - - +
424C GLY* 1.3 60.7 + - - +
425C PHE 3.3 0.8 + - - -
426C GLY 3.7 1.0 + - - -
427C THR* 2.7 33.2 + - - +
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Residues in contact with GLY 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C VAL* 3.8 5.7 - - - +
391C ALA 5.2 1.6 - - - -
392C ASP* 2.7 23.5 + - - -
423C VAL* 1.3 83.3 - - - +
425C PHE* 1.3 57.8 + - - +
427C THR* 3.6 6.4 - - - -
428C ALA* 2.8 32.7 + - - +
444C LEU* 3.6 17.2 - - - +
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Residues in contact with PHE 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C ASP* 4.3 1.6 + - - -
422C GLY 3.8 3.8 + - - +
423C VAL 3.3 0.8 - - - -
424C GLY* 1.3 74.4 - - - +
426C GLY* 1.3 68.7 + - - +
428C ALA* 3.3 1.2 + - - +
429C LEU* 3.0 21.3 + - + +
444C LEU* 3.7 14.8 - - + +
450C SER 6.2 0.2 - - - +
451C VAL* 4.0 26.0 - - + +
454C SER* 3.5 38.1 - - - +
455C ILE* 4.2 2.2 - - - -
457C GLU* 3.7 18.6 - - + -
458C PHE* 3.7 55.4 - + - -
461C LEU* 3.9 20.2 - - + -
468C LEU* 4.1 7.6 - - + -
470C VAL* 3.9 10.5 - - + -
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Residues in contact with GLY 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA* 3.6 33.0 - - - +
55C HIS* 3.9 6.4 - - - -
56C ALA* 3.0 15.7 - - - +
423C VAL 3.7 3.4 + - - -
425C PHE* 1.3 77.3 - - - +
427C THR* 1.3 63.2 + - - +
429C LEU* 3.2 8.6 + - - +
430C GLY 3.0 18.7 + - - -
454C SER* 4.9 3.2 + - - -
457C GLU* 5.3 0.4 - - - +
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Residues in contact with THR 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C HIS* 3.2 21.8 + - - +
58C GLU* 4.9 3.8 + - - +
59C GLY* 3.3 21.5 - - - +
62C ARG* 3.8 20.1 + - - +
87C ASN* 5.2 0.5 + - - -
390C VAL* 4.0 10.3 - - + -
413C LEU* 3.7 18.8 - - + -
423C VAL* 2.7 30.3 + - - +
424C GLY* 3.6 8.5 - - - -
426C GLY* 1.3 75.3 - - - +
428C ALA* 1.3 58.1 + - - +
431C ALA* 2.9 25.3 + - - +
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Residues in contact with ALA 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C VAL* 3.8 25.8 - - + +
424C GLY 2.8 21.7 + - - +
425C PHE 3.8 2.9 - - - +
427C THR* 1.3 71.1 - - - +
429C LEU* 1.3 59.8 + - - +
431C ALA* 3.5 2.0 - - - +
432C GLN* 2.8 30.8 + - - +
442C THR* 3.7 2.9 - - - +
444C LEU* 3.9 11.4 - - + -
468C LEU* 3.7 28.0 - - + +
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Residues in contact with LEU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 4.5 2.5 - - + -
45C ILE* 3.9 20.2 - - + -
47C THR* 4.9 4.9 - - + -
52C ALA* 5.9 0.2 - - + -
56C ALA* 4.3 12.3 - - + -
425C PHE* 3.0 13.1 + - + +
426C GLY* 3.2 10.3 + - - +
428C ALA* 1.3 75.5 - - - +
430C GLY* 1.3 63.2 + - - +
432C GLN* 3.2 7.7 + - - +
433C VAL* 3.2 19.6 + - - +
457C GLU* 4.0 21.8 - - + +
460C THR* 3.8 28.3 - - + -
461C LEU* 3.9 26.2 - - + -
466C LEU* 3.8 19.4 - - + +
468C LEU* 4.1 7.1 - - + +
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Residues in contact with GLY 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.9 10.8 - - - -
56C ALA* 3.2 31.3 - - - +
60C TYR* 3.6 14.8 - - - +
426C GLY 3.0 10.9 + - - -
427C THR 3.8 0.2 - - - -
429C LEU* 1.3 74.7 - - - +
431C ALA* 1.3 64.3 + - - +
433C VAL* 3.1 5.7 + - - +
434C ALA 3.1 18.0 + - - -
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Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLY 3.6 14.3 - - - +
60C TYR* 4.5 0.4 - - - +
63C ALA* 3.9 18.4 - - + -
388C THR* 4.4 5.2 - - + -
390C VAL* 4.4 0.7 - - + -
413C LEU* 4.2 10.8 - - + -
427C THR 2.9 16.8 + - - +
428C ALA* 3.5 7.4 - - - +
430C GLY* 1.3 75.7 - - - +
432C GLN* 1.3 57.0 + - - +
434C ALA* 3.2 3.3 + - - +
435C ASP* 2.8 33.7 + - - -
442C THR* 3.8 16.2 - - + -
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Residues in contact with GLN 432 (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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428C ALA 2.8 19.8 + - - +
429C LEU* 3.6 6.1 - - - +
430C GLY 3.2 0.2 - - - -
431C ALA* 1.3 73.1 - - - +
433C VAL* 1.3 62.2 + - - +
435C ASP* 3.6 2.8 - - - +
436C LEU* 3.1 26.3 + - + +
440C ARG 3.2 23.6 + - - -
441C ARG* 3.8 11.5 - - - +
442C THR* 2.8 45.4 + - - +
466C LEU* 4.4 9.9 - - + -
467C PRO* 3.8 33.6 - - + +
468C LEU* 4.1 14.1 - - + +
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Residues in contact with VAL 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C HIS* 3.7 35.2 + - + +
23C PHE* 3.8 24.5 - - + -
45C ILE* 4.2 10.5 - - + -
60C TYR* 4.0 11.1 - - + -
429C LEU 3.2 13.8 + - - +
430C GLY 3.1 7.9 + - - +
432C GLN* 1.3 76.1 - - - +
434C ALA* 1.3 62.3 + - - +
436C LEU* 3.3 28.4 - - + +
437C GLU* 4.4 1.0 + - - +
466C LEU* 3.7 27.1 - - + -
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Residues in contact with ALA 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C HIS* 6.1 0.2 - - - -
60C TYR* 3.7 43.7 - - + +
63C ALA* 4.3 3.6 - - + -
64C GLY* 4.1 17.8 - - - +
66C LYS* 5.2 3.9 + - + +
430C GLY 3.1 9.4 + - - +
431C ALA 3.7 7.2 - - - +
433C VAL* 1.3 75.9 - - - +
435C ASP* 1.3 61.2 + - - +
436C LEU 3.4 0.7 + - - -
437C GLU* 3.7 12.1 + - - +
438C ALA* 4.1 8.0 + - - +
440C ARG* 5.7 0.8 + - - -
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Residues in contact with ASP 435 (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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63C ALA* 4.1 7.9 - - - +
388C THR* 2.6 29.0 + - - +
431C ALA 2.8 21.1 + - - +
432C GLN* 3.6 8.5 - - - +
433C VAL 3.2 0.4 - - - -
434C ALA* 1.3 71.2 - - - +
436C LEU* 1.3 66.2 + - - +
437C GLU 3.4 0.2 - - - -
438C ALA* 3.0 6.8 + - - -
439C GLY 2.9 4.2 + - - -
440C ARG* 2.9 74.8 + - + +
442C THR* 2.8 19.6 + - - -
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Residues in contact with LEU 436 (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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21C HIS* 6.2 1.1 - - - +
432C GLN* 3.1 34.2 + - + +
433C VAL* 3.3 21.8 - - + +
434C ALA 3.3 0.2 - - - -
435C ASP* 1.3 75.8 - - - +
437C GLU* 1.3 57.6 + - - +
439C GLY* 3.1 18.6 + - - -
440C ARG 5.0 1.1 - - - +
466C LEU* 4.0 20.9 - - + -
467C PRO* 4.5 15.5 - - + -
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Residues in contact with GLU 437 (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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21C HIS* 6.5 0.9 - - + -
433C VAL 4.4 1.3 + - - +
434C ALA 3.7 8.9 + - - +
435C ASP 3.4 0.6 - - - -
436C LEU* 1.3 78.3 - - - +
438C ALA* 1.3 58.8 + - - +
439C GLY 3.4 0.4 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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