Contacts of the helix formed by residues 550 - 555 (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 PRO 550 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395D LEU* 3.7 17.0 - - + -
398D LEU* 3.9 29.6 - - + +
399D TRP* 3.3 36.5 - - + +
548D PRO 3.7 3.4 - - - +
549D ILE* 1.4 84.2 - - - +
551D PRO* 1.3 76.6 - - + +
552D GLU 4.4 2.0 - - - +
553D GLU* 2.9 38.7 + - + +
554D LEU 2.9 10.4 + - - -
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Residues in contact with PRO 551 (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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356D ARG* 4.1 12.1 - - + +
360D ILE* 3.6 28.0 - - + -
399D TRP* 3.8 18.2 - - + -
402D GLU* 3.5 25.6 - - + +
549D ILE 3.6 1.5 - - - +
550D PRO* 1.3 85.1 - - + +
552D GLU* 1.3 53.1 + - - +
554D LEU* 3.0 9.7 + - + +
555D ILE* 2.8 43.6 + - + +
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Residues in contact with GLU 552 (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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239D TYR* 5.5 1.5 + - - +
258D GLN* 3.5 41.4 + - - +
356D ARG* 3.2 25.3 + - - -
398D LEU* 3.8 34.2 + - + +
401D SER* 4.6 3.8 - - - +
402D GLU* 4.2 6.9 + - - +
550D PRO* 3.2 1.4 - - - +
551D PRO* 1.3 80.3 - - - +
553D GLU* 1.3 60.0 + - - +
555D ILE* 3.6 29.3 + - - +
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Residues in contact with GLU 553 (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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395D LEU* 3.5 13.9 - - - +
398D LEU* 4.5 9.3 - - + +
480D ALA* 4.0 9.7 - - - +
483D HIS* 2.5 49.7 + - - +
484D PHE 5.0 0.2 + - - -
487D LEU* 4.7 7.9 - - + -
549D ILE* 3.4 15.7 - - + +
550D PRO* 2.9 23.5 + - + +
552D GLU* 1.3 76.5 - - - +
554D LEU* 1.3 65.5 + - - +
555D ILE 3.0 10.1 - - - +
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Residues in contact with LEU 554 (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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549D ILE* 3.7 16.7 - - + +
550D PRO 2.9 12.0 + - - +
551D PRO* 3.0 12.3 + - + +
553D GLU* 1.3 76.4 - - - +
555D ILE* 1.3 61.4 + - + +
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Residues in contact with ILE 555 (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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261D TYR* 3.7 54.1 - - + +
356D ARG* 3.9 17.5 - - - +
551D PRO* 2.8 25.1 + - + +
552D GLU* 3.6 37.9 - - - +
553D GLU 3.0 15.8 - - - +
554D LEU* 1.3 74.4 - - + +
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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
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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