Contacts of the helix formed by residues 520 - 534 (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 SER 520 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370D LEU* 4.0 13.7 - - - +
519D ASP* 1.3 88.0 + - - +
521D VAL* 1.3 65.0 + - - +
522D GLU* 3.6 6.7 + - - +
523D SER* 2.7 30.7 + - - -
524D PHE* 2.9 26.3 + - - +
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Residues in contact with VAL 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D SER* 4.7 5.2 - - - +
370D LEU* 3.6 24.4 - - + +
374D HIS* 4.0 18.8 - - + +
378D VAL* 4.0 23.2 - - + +
381D LYS* 5.9 1.1 - - - +
520D SER* 1.3 72.7 - - - +
522D GLU* 1.3 58.8 + - - +
524D PHE* 3.9 1.1 - - - +
525D SER* 2.9 33.0 + - - -
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Residues in contact with GLU 522 (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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520D SER* 3.2 7.1 + - - +
521D VAL* 1.3 80.7 - - - +
523D SER* 1.3 62.5 + - - +
525D SER* 3.8 5.5 - - - -
526D ALA* 3.1 23.9 + - - +
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Residues in contact with SER 523 (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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517D HIS 5.5 0.2 - - - -
518D VAL* 3.4 19.5 - - - +
519D ASP* 3.2 14.2 + - - -
520D SER* 2.7 38.0 + - - -
522D GLU* 1.3 72.8 - - - +
524D PHE* 1.3 60.1 + - - +
526D ALA* 3.4 6.8 + - - +
527D ALA* 3.0 24.6 + - - +
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Residues in contact with PHE 524 (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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370D LEU* 4.5 4.3 - - + -
375D ALA* 3.2 38.1 - - + -
378D VAL* 3.6 20.2 - - + -
379D ILE* 3.7 21.3 - - + -
471D ILE* 3.7 27.6 - - + -
473D MET* 4.2 2.7 - - + -
518D VAL* 3.7 18.8 - - + +
520D SER 2.9 20.0 + - - +
521D VAL* 3.9 2.5 - - - +
523D SER* 1.3 75.4 + - - +
525D SER* 1.3 63.4 + - - +
527D ALA* 3.2 1.6 + - - +
528D LEU* 2.9 35.0 + - + +
540D ILE* 4.0 11.9 - - + -
542D VAL* 3.8 24.2 - - + -
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Residues in contact with SER 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D VAL* 3.8 14.3 - - - +
381D LYS* 2.7 32.0 + - - +
382D HIS* 4.9 2.1 + - - -
521D VAL* 2.9 24.6 + - - -
522D GLU* 3.8 5.8 - - - -
524D PHE* 1.3 72.5 - - - +
526D ALA* 1.3 63.3 + - - +
528D LEU* 3.9 1.7 - - - +
529D ALA* 3.0 26.4 + - - +
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Residues in contact with ALA 526 (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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522D GLU 3.1 17.5 + - - +
523D SER* 3.6 7.4 - - - +
525D SER* 1.3 75.2 - - - +
527D ALA* 1.3 64.2 + - - +
529D ALA* 3.8 4.1 - - - +
530D GLN* 3.0 25.0 + - - +
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Residues in contact with ALA 527 (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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516D TYR* 3.8 33.5 - - + -
518D VAL* 3.7 19.3 - - + -
523D SER 3.0 17.4 + - - +
524D PHE 3.7 2.9 - - - +
526D ALA* 1.3 76.0 - - - +
528D LEU* 1.3 56.7 + - - +
530D GLN* 3.3 3.8 + - - +
531D ALA* 2.9 30.3 + - - +
540D ILE* 4.0 10.7 - - + +
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Residues in contact with LEU 528 (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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378D VAL* 3.8 19.5 - - + +
379D ILE* 3.9 23.1 - - + -
382D HIS* 3.6 30.3 - - + +
443D ILE* 4.7 7.4 - - + -
469D ILE* 4.5 9.6 - - + -
471D ILE* 4.0 18.2 - - + -
524D PHE* 2.9 25.8 + - + +
525D SER* 4.0 3.8 - - - +
527D ALA* 1.3 74.7 - - - +
529D ALA* 1.3 59.4 + - - +
531D ALA* 3.3 0.7 + - - +
532D LEU* 2.9 49.3 + - + +
540D ILE* 3.8 12.7 - - + +
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Residues in contact with ALA 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D HIS* 4.5 19.6 + - + -
525D SER* 3.0 20.7 + - - +
526D ALA* 3.8 5.4 - - - +
528D LEU* 1.3 77.6 - - - +
530D GLN* 1.3 61.6 + - - +
532D LEU* 3.3 4.0 + - - +
533D ALA* 3.0 24.0 + - - +
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Residues in contact with GLN 530 (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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516D TYR* 3.2 33.3 + - + +
526D ALA 3.0 17.8 + - - +
527D ALA* 3.6 4.0 - - - +
529D ALA* 1.3 76.6 - - - +
531D ALA* 1.3 61.7 + - - +
533D ALA* 3.2 10.6 + - - +
534D HIS* 3.0 41.3 + - + +
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Residues in contact with ALA 531 (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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441D ARG* 3.3 9.0 + - - -
469D ILE* 3.8 17.3 - - + -
516D TYR* 4.0 10.9 + - + -
527D ALA 2.9 19.7 + - - +
528D LEU 3.3 4.5 + - - +
530D GLN* 1.3 73.6 - - - +
532D LEU* 1.3 58.0 + - - +
533D ALA 3.4 0.2 + - - -
534D HIS* 3.1 26.7 + - - +
536D ARG 4.7 1.4 - - - +
538D ALA* 4.1 19.7 - - + -
540D ILE* 4.0 17.5 - - + -
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Residues in contact with LEU 532 (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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382D HIS* 3.3 46.7 - - + +
387D VAL* 5.5 5.2 - - + -
441D ARG* 3.2 33.7 + - + +
443D ILE* 4.0 17.7 - - + -
469D ILE* 3.6 20.2 - - + -
528D LEU* 2.9 30.4 + - + +
529D ALA* 3.8 4.3 - - - +
531D ALA* 1.3 76.3 - - - +
533D ALA* 1.3 60.2 + - - +
534D HIS 4.5 0.2 - - - -
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Residues in contact with ALA 533 (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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529D ALA 3.0 17.0 + - - +
530D GLN* 3.2 9.8 + - - +
532D LEU* 1.3 78.2 - - - +
534D HIS* 1.3 67.0 + - + +
535D ASN 4.4 0.2 + - - -
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Residues in contact with HIS 534 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D ARG* 3.0 28.6 + - - -
514D ASP* 5.5 1.1 - - - +
516D TYR* 5.2 2.5 - - - -
530D GLN* 3.0 43.7 + - + +
531D ALA* 3.1 8.7 + - - +
532D LEU 3.3 0.4 - - - -
533D ALA* 1.3 87.9 + - + +
535D ASN* 1.3 59.4 + - - +
536D ARG* 3.1 33.1 + - + +
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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