Contacts of the helix formed by residues 520 - 534 (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 SER 520 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370C LEU* 4.0 13.7 - - - +
519C ASP* 1.3 86.5 + - - +
521C VAL* 1.3 59.1 + - - +
522C GLU* 3.8 7.6 + - - +
523C SER* 2.7 30.3 + - - -
524C PHE* 2.8 31.4 + - - +
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Residues in contact with VAL 521 (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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366C SER* 4.8 5.2 - - - +
370C LEU* 3.6 22.7 - - + +
374C HIS* 4.0 20.2 - - + +
378C VAL* 4.1 17.3 - - + -
520C SER* 1.3 71.8 - - - +
522C GLU* 1.3 58.4 + - + +
524C PHE* 3.9 1.4 - - - +
525C SER* 2.7 46.7 + - - +
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Residues in contact with GLU 522 (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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520C SER* 3.3 7.5 + - - +
521C VAL* 1.3 81.3 - - + +
523C SER* 1.3 57.4 + - - +
525C SER* 3.8 4.4 - - - -
526C ALA* 3.0 29.6 + - - +
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Residues in contact with SER 523 (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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517C HIS 5.5 0.4 - - - -
518C VAL* 3.5 20.2 - - - +
519C ASP* 3.1 13.7 + - - -
520C SER* 2.7 39.8 + - - -
522C GLU* 1.3 78.4 - - - +
524C PHE* 1.3 56.4 + - - +
526C ALA* 3.3 5.9 + - - +
527C ALA* 2.9 25.5 + - - +
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Residues in contact with PHE 524 (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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370C LEU* 4.4 5.4 - - + -
375C ALA* 3.2 42.4 - - + -
378C VAL* 3.6 22.0 - - + -
379C ILE* 3.7 21.5 - - + -
471C ILE* 3.7 25.4 - - + -
473C MET* 4.2 2.2 - - + -
518C VAL* 3.8 15.2 - - + +
520C SER 2.8 19.5 + - - +
521C VAL* 4.0 2.0 - - - +
523C SER* 1.3 74.6 + - - +
525C SER* 1.3 65.0 + - - +
527C ALA* 3.2 1.6 + - - -
528C LEU* 2.9 32.3 + - + +
540C ILE* 3.9 16.8 - - + -
542C VAL* 3.7 25.4 - - + -
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Residues in contact with SER 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C VAL* 3.6 27.6 - - - +
381C LYS* 6.2 0.2 - - - +
382C HIS* 4.9 4.2 + - - -
521C VAL* 2.7 34.8 + - - +
522C GLU* 3.8 5.6 - - - -
524C PHE* 1.3 71.3 - - - +
526C ALA* 1.3 57.8 + - - +
528C LEU* 4.0 1.3 - - - +
529C ALA* 3.0 31.4 + - - +
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Residues in contact with ALA 526 (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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522C GLU 3.0 18.5 + - - +
523C SER* 3.6 6.1 - - - +
525C SER* 1.3 77.9 - - - +
527C ALA* 1.3 63.1 + - - +
529C ALA* 3.7 5.3 - - - +
530C GLN* 3.1 24.9 + - - +
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Residues in contact with ALA 527 (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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516C TYR* 3.6 37.0 - - + -
518C VAL* 3.7 17.9 - - + -
523C SER 2.9 16.1 + - - +
524C PHE 3.7 3.4 - - - +
526C ALA* 1.3 76.5 - - - +
528C LEU* 1.3 57.1 + - - +
530C GLN* 3.2 3.5 + - - +
531C ALA* 2.9 30.7 + - - +
540C ILE* 4.0 11.2 - - + +
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Residues in contact with LEU 528 (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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378C VAL* 4.1 7.9 - - + +
379C ILE* 4.0 33.4 - - + -
382C HIS* 3.7 30.3 - - + +
443C ILE* 4.8 6.1 - - + -
469C ILE* 4.4 11.4 - - + -
471C ILE* 4.0 20.0 - - + -
524C PHE* 2.9 21.4 + - + +
525C SER* 4.1 3.8 - - - +
527C ALA* 1.3 77.0 - - - +
529C ALA* 1.3 63.1 + - - +
531C ALA 3.3 0.3 + - - -
532C LEU* 2.9 43.0 + - + +
540C ILE* 3.7 16.3 - - + +
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Residues in contact with ALA 529 (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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382C HIS* 4.3 20.0 + - + +
525C SER 3.0 19.2 + - - +
526C ALA* 3.7 6.1 - - - +
528C LEU* 1.3 76.0 - - - +
530C GLN* 1.3 62.6 + - - +
532C LEU* 3.4 3.9 + - - +
533C ALA* 3.1 22.5 + - - +
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Residues in contact with GLN 530 (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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516C TYR* 3.1 32.7 + - + +
526C ALA 3.1 17.8 + - - +
527C ALA* 3.7 4.0 - - - +
529C ALA* 1.3 74.3 - - - +
531C ALA* 1.3 65.6 + - - +
533C ALA* 3.1 10.2 + - - +
534C HIS* 3.0 42.4 + - + +
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Residues in contact with ALA 531 (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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441C ARG* 3.1 9.2 + - - -
469C ILE* 3.9 15.0 - - + -
516C TYR* 3.9 11.6 + - + +
527C ALA 2.9 20.5 + - - +
528C LEU 3.8 3.1 - - - +
530C GLN* 1.3 73.7 - - - +
532C LEU* 1.3 57.6 + - - +
533C ALA 3.4 0.2 + - - -
534C HIS* 3.0 26.3 + - - +
536C ARG 4.7 1.2 - - - +
538C ALA* 4.1 23.3 - - + -
540C ILE* 4.2 13.7 - - + -
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Residues in contact with LEU 532 (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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382C HIS* 3.3 46.9 - - + +
387C VAL* 5.5 4.3 - - + -
441C ARG* 3.3 36.1 + - + +
443C ILE* 4.1 13.2 - - + -
469C ILE* 3.5 22.4 - - + -
528C LEU* 2.9 30.0 + - + +
529C ALA* 3.8 4.3 - - - +
531C ALA* 1.3 77.3 - - - +
533C ALA* 1.3 60.5 + - - +
534C HIS 3.2 0.4 - - - -
535C ASN* 5.2 0.3 - - - +
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Residues in contact with ALA 533 (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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529C ALA 3.1 13.6 + - - +
530C GLN* 3.1 14.1 + - - +
532C LEU* 1.3 78.7 - - - +
534C HIS* 1.3 68.5 + - + +
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Residues in contact with HIS 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C ARG* 3.0 27.8 + - - -
514C ASP* 5.5 1.1 - - - +
516C TYR* 5.4 1.3 - - - -
530C GLN* 3.0 44.1 - - + +
531C ALA* 3.0 7.4 + - - +
532C LEU 3.2 0.2 - - - -
533C ALA* 1.3 88.5 + - + +
535C ASN* 1.3 62.9 + - - +
536C ARG* 3.1 32.9 + - + +
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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