Contacts of the helix formed by residues 423 - 439 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D HIS* 3.4 46.4 - - + +
62D ARG* 6.0 2.0 - - - +
83D THR* 4.3 3.6 - - + -
87D ASN* 4.2 18.4 - - - +
415D HIS* 3.8 20.2 - - + +
420D SER* 3.1 38.1 - - - +
421D MET 4.8 0.7 - - - +
422D GLY* 1.3 76.4 - - - +
424D GLY* 1.3 61.0 + - - +
425D PHE 3.3 0.8 + - - -
426D GLY 3.7 1.1 + - - -
427D THR* 2.7 33.8 + - - +
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Residues in contact with GLY 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390D VAL* 3.8 6.4 - - - +
391D ALA 5.2 1.3 - - - -
392D ASP* 2.7 28.9 + - - -
423D VAL* 1.3 76.1 - - - +
425D PHE* 1.3 54.8 + - - +
427D THR* 3.6 7.3 - - - -
428D ALA* 2.8 36.7 + - - +
444D LEU* 3.5 15.9 - - - +
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Residues in contact with PHE 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D ASP* 4.2 1.6 + - - -
422D GLY 3.8 4.0 + - - +
423D VAL 3.3 1.0 - - - -
424D GLY* 1.3 71.7 - - - +
426D GLY* 1.3 67.8 + - - +
428D ALA* 3.2 3.3 + - - +
429D LEU* 3.0 22.3 + - + +
444D LEU* 3.7 13.7 - - + +
450D SER 6.1 0.4 - - - +
451D VAL* 4.0 26.7 - - + -
454D SER* 3.5 40.2 - - - +
455D ILE* 4.1 2.5 - - - -
457D GLU* 3.7 17.3 - - + -
458D PHE* 3.6 57.0 - + - -
461D LEU* 4.0 21.1 - - + -
468D LEU* 4.2 7.9 - - + -
470D VAL* 4.0 8.3 - - + -
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Residues in contact with GLY 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ALA* 3.5 32.6 - - - +
55D HIS* 3.8 6.8 - - - +
56D ALA* 3.0 15.3 - - - +
423D VAL 3.7 3.0 + - - -
424D GLY 3.5 0.2 - - - -
425D PHE* 1.3 78.0 - - - +
427D THR* 1.3 62.9 + - - +
429D LEU* 3.2 7.3 + - - +
430D GLY 3.0 19.2 + - - -
454D SER* 4.9 2.4 + - - -
457D GLU* 5.3 1.3 - - - +
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Residues in contact with THR 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D HIS* 3.2 21.6 + - - +
58D GLU* 5.0 3.7 + - - +
59D GLY* 3.3 23.8 - - - +
62D ARG* 3.6 27.8 + - - +
87D ASN* 5.3 0.7 + - - -
390D VAL* 4.0 10.5 - - + -
413D LEU* 3.8 12.8 - - + -
423D VAL* 2.7 29.6 + - - +
424D GLY* 3.6 9.2 - - - -
426D GLY* 1.3 76.1 - - - +
428D ALA* 1.3 56.2 + - - +
431D ALA* 2.9 25.6 + - - +
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Residues in contact with ALA 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D VAL* 3.8 21.7 - - + +
424D GLY 2.8 22.3 + - - +
425D PHE 3.7 3.1 - - - +
427D THR* 1.3 70.3 - - - +
429D LEU* 1.3 60.3 + - - +
431D ALA* 3.3 2.0 + - - +
432D GLN* 2.9 30.1 + - - +
442D THR* 3.6 3.7 - - - +
444D LEU* 3.8 15.3 - - + -
468D LEU* 3.6 28.3 - - + +
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Residues in contact with LEU 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PHE* 4.4 2.5 - - + -
45D ILE* 3.9 20.4 - - + -
47D THR* 4.7 6.3 - - + -
52D ALA* 6.1 0.2 - - + -
56D ALA* 4.2 12.6 - - + -
425D PHE* 3.0 13.2 + - + +
426D GLY* 3.2 10.1 + - - +
428D ALA* 1.3 77.0 - - - +
430D GLY* 1.3 62.3 + - - +
432D GLN* 3.3 7.8 + - - +
433D VAL* 3.2 24.4 + - - +
457D GLU* 4.1 20.6 - - + +
460D THR* 3.7 29.4 - - + -
461D LEU* 3.7 27.6 - - + -
466D LEU* 3.9 18.1 - - + +
468D LEU* 4.0 6.6 - - + +
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Residues in contact with GLY 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PHE* 3.8 11.0 - - - -
56D ALA* 3.2 31.9 - - - +
60D TYR* 3.6 14.5 - - - +
426D GLY 3.0 10.7 + - - -
429D LEU* 1.3 73.4 - - - +
431D ALA* 1.3 65.8 + - - +
433D VAL* 3.1 5.7 + - - +
434D ALA 3.0 17.5 + - - -
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Residues in contact with ALA 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLY 3.6 13.9 - - - +
63D ALA* 3.8 18.6 - - + +
388D THR* 4.4 4.7 - - + -
390D VAL* 4.4 0.2 - - + -
413D LEU* 4.1 11.4 - - + -
427D THR 2.9 18.1 + - - +
428D ALA* 3.6 7.4 - - - +
429D LEU 3.3 0.2 - - - -
430D GLY* 1.3 73.6 - - - +
432D GLN* 1.3 53.2 + - - +
434D ALA* 3.1 4.7 + - - +
435D ASP* 2.7 36.9 + - - -
442D THR* 3.8 16.2 - - + -
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Residues in contact with GLN 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428D ALA 2.9 17.1 + - - +
429D LEU* 3.7 6.3 - - - +
431D ALA* 1.3 73.0 - - - +
433D VAL* 1.3 64.9 + - - +
435D ASP* 3.6 2.0 - - - +
436D LEU* 3.1 27.9 + - + +
440D ARG 3.2 24.2 + - - -
441D ARG* 3.8 11.9 - - - +
442D THR* 2.9 44.0 + - - +
466D LEU* 4.5 11.0 - - + -
467D PRO* 3.9 33.2 - - + +
468D LEU* 3.9 12.3 + - + +
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Residues in contact with VAL 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D HIS* 3.7 36.4 + - + +
23D PHE* 3.8 23.3 - - + -
45D ILE* 4.3 11.0 - - + -
60D TYR* 4.0 10.9 - - + -
429D LEU 3.2 15.1 + - - +
430D GLY 3.1 7.7 + - - +
432D GLN* 1.3 78.6 - - - +
434D ALA* 1.3 62.9 + - - +
436D LEU* 3.3 25.7 + - + +
437D GLU 4.3 1.2 + - - -
466D LEU* 3.7 26.2 - - + -
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Residues in contact with ALA 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D TYR* 3.8 38.9 - - + +
63D ALA* 4.0 6.1 - - + -
64D GLY* 4.0 18.0 - - - +
66D LYS* 5.5 2.2 - - + +
430D GLY 3.0 10.9 + - - +
431D ALA 3.4 7.9 - - - +
433D VAL* 1.3 76.8 - - - +
435D ASP* 1.3 62.6 + - - +
436D LEU 3.3 1.0 + - - -
437D GLU* 3.5 9.4 + - - -
438D ALA* 3.8 8.7 + - - +
440D ARG* 4.9 1.5 + - - -
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Residues in contact with ASP 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ALA* 4.2 5.5 - - - +
388D THR* 2.8 28.1 + - - +
431D ALA 2.7 19.0 + - - +
432D GLN* 3.6 9.4 - - - +
433D VAL 3.2 0.2 - - - -
434D ALA* 1.3 72.9 - - - +
436D LEU* 1.3 59.7 + - - +
437D GLU 3.3 0.2 - - - -
438D ALA* 2.9 5.0 + - - -
439D GLY 2.9 25.6 + - - -
440D ARG* 2.8 62.6 + - + +
442D THR* 2.7 19.6 + - - -
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Residues in contact with LEU 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D HIS* 6.2 0.7 - - - +
432D GLN* 3.1 27.4 + - + +
433D VAL* 3.5 17.7 - - + +
434D ALA 3.2 0.4 - - - -
435D ASP* 1.3 75.8 - - - +
437D GLU* 1.3 61.9 + - - +
439D GLY* 3.2 12.5 + - - +
440D ARG 4.9 1.6 - - - +
465D GLN 6.0 0.2 - - - +
466D LEU* 4.0 21.3 - - + -
467D PRO* 4.5 19.1 - - + -
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Residues in contact with GLU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433D VAL 4.3 1.4 + - - -
434D ALA 3.5 7.3 + - - -
435D ASP 3.3 0.6 - - - -
436D LEU* 1.3 78.2 - - - +
438D ALA* 1.3 57.7 + - - +
439D GLY 3.3 0.7 + - - -
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Residues in contact with ALA 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D ALA 3.8 6.9 + - - +
435D ASP 2.9 7.7 + - - +
437D GLU* 1.3 76.3 - - - +
439D GLY* 1.3 61.2 + - - +
440D ARG* 3.4 45.0 + - - +
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Residues in contact with GLY 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D GLY* 4.2 7.1 - - - +
435D ASP 2.9 4.3 + - - -
436D LEU* 3.2 10.8 + - - -
437D GLU 3.3 2.0 + - - -
438D ALA* 1.3 77.2 - - - +
440D ARG* 1.3 60.8 + - - +
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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
------------------------------------------------------------
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