Contacts of the helix formed by residues 403 - 408 (chain H) in PDB entry 1UW9
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 GLY 403 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H CYS* 4.0 1.1 - - - -
173H THR* 3.2 33.5 - - - +
175H LYS* 4.5 2.5 - - - -
401H GLN 4.0 0.4 - - - -
402H PHE* 1.3 69.4 - - - +
404H GLY* 1.3 60.8 + - - +
405H GLY 3.1 1.0 - - - +
406H THR 2.9 3.3 + - - -
407H LEU* 2.9 32.6 + - - +
1478O CAP 2.9 22.0 + - - -
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Residues in contact with GLY 404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175H LYS* 4.4 0.2 - - - +
403H GLY* 1.3 71.6 - - - +
405H GLY* 1.3 57.0 + - - +
408H GLY* 2.8 30.5 + - - -
462H TRP* 3.6 0.7 - - - -
1478O CAP 2.8 20.7 + - - -
65R THR* 4.0 13.1 - - - +
66R TRP* 3.9 3.8 - - - +
67R THR* 3.3 25.1 - - - +
69R VAL* 4.2 8.3 - - - -
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Residues in contact with GLY 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382H ILE 4.0 10.9 + - - -
383H HIS* 4.9 1.7 - - - -
402H PHE* 4.0 7.2 - - - -
403H GLY 3.1 4.9 - - - +
404H GLY* 1.3 74.4 - - - +
406H THR* 1.3 59.2 + - - +
409H HIS* 5.6 0.2 - - - -
416H GLY* 4.4 3.6 - - - +
420H ASN* 3.2 19.6 + - - +
462H TRP* 3.5 28.5 - - - -
66R TRP* 3.8 19.0 - - - +
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Residues in contact with THR 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H CYS* 3.8 4.0 - - - -
192H CYS* 4.0 15.3 - - - -
197H LEU* 3.9 23.6 - - + +
402H PHE* 2.7 24.2 + - - +
403H GLY 2.9 2.3 + - - -
405H GLY* 1.3 77.6 - - - +
407H LEU* 1.3 58.5 + - - +
408H GLY 3.1 3.8 - - - -
409H HIS* 3.2 24.5 + - - +
412H GLY 3.8 8.0 - - - +
413H ASN* 3.5 23.6 - - - +
416H GLY* 4.4 3.1 - - - -
417H ALA 3.7 8.7 - - - +
420H ASN* 3.1 17.4 + - - -
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Residues in contact with LEU 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H CYS* 3.6 16.8 - - - -
173H THR 3.6 19.7 - - - +
174H ILE* 4.1 5.2 - - + -
175H LYS* 3.6 28.3 - - + +
188H ALA* 4.3 8.7 - - + -
192H CYS* 4.1 5.4 - - - -
403H GLY 2.9 28.3 + - - +
406H THR* 1.3 71.7 - - - +
408H GLY* 1.3 56.3 + - - +
409H HIS 3.5 0.7 - - - -
413H ASN* 3.4 34.5 - - - +
69R VAL* 3.4 16.6 - - + -
70R TRP* 3.1 35.1 + - - +
71R THR* 3.8 16.4 - - + +
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Residues in contact with GLY 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404H GLY 2.8 19.5 + - - -
407H LEU* 1.3 78.0 - - - +
409H HIS* 1.3 64.6 + - - +
410H PRO* 3.9 0.7 - - - +
461H VAL* 4.8 0.2 - - - +
462H TRP* 3.5 18.5 - - - -
13R PHE* 3.9 1.7 - - - -
15R ALA* 3.5 20.1 - - - +
16R GLY 4.5 0.9 + - - -
67R THR* 4.4 0.9 - - - -
68R THR 3.2 23.2 - - - +
69R VAL* 4.1 0.4 - - - +
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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