Contacts of the helix formed by residues 503 - 511 (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 503 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502C GLY* 1.3 70.3 - - - -
504C TYR* 1.3 63.7 + - - +
505C HIS* 3.1 25.3 + - - -
506C GLY* 3.1 19.7 + - - -
507C VAL* 3.0 23.6 + - - +
541C ASN* 4.8 0.7 - - - -
510D ALA* 2.9 20.6 + - - +
511D PHE* 5.1 0.4 - - - -
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Residues in contact with TYR 504 (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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448C ASP* 3.4 36.2 + - + +
451C VAL* 3.9 6.5 - - + -
452C GLY* 5.2 0.9 - - - -
455C ILE* 3.7 24.4 - - + +
458C PHE* 5.0 0.5 - - - -
472C ILE* 3.3 27.1 - - + -
474C ASN* 3.6 29.2 - - - -
499C LEU* 4.8 5.1 + - - +
501C ASN 3.9 14.4 + - - -
502C GLY 4.2 9.2 - - - -
503C SER* 1.3 72.3 - - - +
505C HIS* 1.3 57.9 + - - +
507C VAL* 3.2 7.9 + - - +
508C ALA* 3.0 27.9 + - - +
539C CYS* 3.9 3.7 - - - -
541C ASN* 3.8 10.6 + - - +
48D ARG* 3.0 32.1 + - - -
511D PHE* 4.1 21.5 - + - -
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Residues in contact with HIS 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C SER* 3.1 22.1 + - - -
504C TYR* 1.3 76.8 + - - +
506C GLY* 1.3 64.1 + - - +
508C ALA* 3.4 3.8 + - - +
509C ALA* 2.9 30.8 + - - +
515C GLY* 4.1 7.2 - - - -
516C TYR 3.5 31.0 - - - +
517C HIS* 3.4 46.2 - + + +
539C CYS* 4.1 11.3 - - - +
541C ASN* 3.1 22.7 + - + +
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Residues in contact with GLY 506 (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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503C SER* 3.0 22.6 + - - -
505C HIS* 1.3 77.4 - - - +
507C VAL* 1.3 58.2 + - - +
509C ALA* 3.4 7.4 + - - +
510C ALA* 2.9 29.3 + - - +
506D GLY 4.7 0.2 - - - +
510D ALA* 3.6 12.7 - - - +
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Residues in contact with VAL 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C ILE* 3.7 31.0 - - + -
503C SER 3.0 14.3 + - - +
504C TYR* 3.5 10.3 - - - +
506C GLY* 1.3 73.0 - - - +
508C ALA* 1.3 66.2 + - - +
510C ALA* 3.1 15.8 + - - +
511C PHE* 3.2 25.6 + - + -
507D VAL* 3.8 21.3 - - + +
510D ALA* 3.8 14.6 - - + -
511D PHE* 3.6 33.4 - - + -
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Residues in contact with ALA 508 (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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458C PHE* 4.0 28.4 - - + -
504C TYR 3.0 9.4 + - - +
505C HIS 3.4 6.9 + - - +
507C VAL* 1.3 76.0 - - - +
509C ALA* 1.3 60.1 + - - +
511C PHE* 3.0 11.8 + - - +
512C GLY 3.2 0.3 + - - -
513C ALA* 3.0 28.7 + - + +
514C ASP 4.8 1.6 - - - +
515C GLY* 5.0 0.2 - - - -
539C CYS* 3.3 34.5 - - + -
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Residues in contact with ALA 509 (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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505C HIS 2.9 20.2 + - - +
506C GLY* 3.7 8.5 - - - +
508C ALA* 1.3 73.4 - - - +
510C ALA* 1.3 58.4 + - - +
512C GLY* 2.8 20.6 + - - -
513C ALA 3.3 15.4 + - - +
515C GLY* 5.0 6.3 - - - +
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Residues in contact with ALA 510 (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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506C GLY 2.9 17.8 + - - +
507C VAL 3.1 6.0 + - - +
509C ALA* 1.3 76.5 - - - +
511C PHE* 1.3 59.2 + - - +
512C GLY 3.3 0.8 + - - -
502D GLY* 3.7 0.7 - - - -
503D SER* 2.9 39.9 + - - +
506D GLY* 3.6 9.4 - - - +
507D VAL* 3.6 31.2 - - + +
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Residues in contact with PHE 511 (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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48C ARG* 5.0 2.0 - - - -
455C ILE 3.9 12.1 - - - -
456C GLY* 4.0 15.0 - - - -
458C PHE* 3.8 24.9 - - + +
459C ASP* 3.6 34.1 - - + +
462C VAL* 3.3 11.1 - - - +
507C VAL* 3.2 32.6 + - + -
508C ALA 3.0 9.8 + - - +
510C ALA* 1.3 78.0 - - - +
512C GLY* 1.3 56.5 + - - +
513C ALA 3.4 1.3 - - - -
452D GLY* 5.9 1.6 - - - -
455D ILE* 4.2 16.4 - - + -
501D ASN* 2.9 26.9 + - - +
502D GLY* 4.2 10.3 - - - -
504D TYR* 4.1 22.7 - + - -
507D VAL* 3.5 26.5 - - + -
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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