Contacts of the helix formed by residues 298 - 303 (chain Q) in PDB entry 1HI0
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 TYR 298 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133Q LEU* 3.4 41.3 + - + +
293Q LYS* 4.6 4.6 - - + -
294Q ILE* 3.0 33.7 + - + +
297Q LYS* 1.3 111.4 + - + +
299Q ALA* 1.3 66.0 + - - +
300Q TYR 3.0 4.6 + - - +
301Q THR 3.1 4.2 + - - -
302Q PHE* 3.1 31.1 + - + +
437Q ASP* 2.8 44.5 + - - -
440Q TRP* 3.5 42.0 - + + -
441Q GLN* 4.0 9.0 - - + +
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Residues in contact with ALA 299 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294Q ILE 3.3 1.0 + - - -
295Q TYR 3.1 25.6 - - - +
296Q SER* 2.9 11.6 + - - +
297Q LYS 3.4 1.4 + - - -
298Q TYR* 1.3 76.5 - - - +
300Q TYR* 1.3 64.4 + - - +
303Q HIS* 3.1 29.9 + - + +
313Q LYS* 2.8 15.1 + - - -
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Residues in contact with TYR 300 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298Q TYR 3.0 1.6 + - - -
299Q ALA* 1.3 77.0 - - - +
301Q THR* 1.3 73.2 + - + +
304Q HIS* 3.9 0.2 - - - -
313Q LYS* 2.8 61.5 + - + +
316Q GLU* 5.9 1.3 - - - -
317Q TRP* 2.8 35.4 + + - -
440Q TRP 3.7 1.1 - - - +
441Q GLN* 3.5 25.5 - - - +
442Q GLY* 3.4 22.0 - - - -
447Q ARG* 3.2 33.8 + - + -
448Q GLN 4.0 7.6 - - - -
449Q ILE* 3.5 5.9 - - + +
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Residues in contact with THR 301 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298Q TYR 3.1 2.5 + - - -
300Q TYR* 1.3 90.3 - - + +
302Q PHE* 1.3 75.7 + - - +
304Q HIS* 3.0 7.4 + - - -
439Q TYR* 4.1 4.7 - - + +
440Q TRP* 3.0 46.1 + - - +
447Q ARG* 5.7 0.2 - - + -
448Q GLN* 2.7 44.0 - - + +
449Q ILE* 4.0 0.9 - - - +
450Q SER 2.7 30.7 + - - +
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Residues in contact with PHE 302 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134Q MET* 4.5 4.0 - - + -
294Q ILE* 3.7 35.2 - - + +
295Q TYR* 3.5 26.2 - - + -
298Q TYR* 3.1 20.1 + - + +
301Q THR* 1.3 93.9 - - - +
303Q HIS* 1.3 60.8 + - - +
304Q HIS* 3.4 17.9 + - - -
403Q THR* 3.4 30.5 - - + -
407Q SER* 3.7 7.9 - - - -
440Q TRP* 3.6 53.6 - + - -
448Q GLN* 4.1 0.4 - - - -
450Q SER* 3.8 25.6 - - - +
451Q LYS* 5.3 2.9 - - - +
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Residues in contact with HIS 303 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295Q TYR* 3.2 48.8 + + + +
299Q ALA* 3.1 17.4 + - + +
302Q PHE* 1.3 75.4 - - - +
304Q HIS* 1.3 69.3 + - - +
305Q THR* 3.4 24.7 - - + +
309Q ASN* 3.4 8.7 + - - +
313Q LYS* 3.4 14.2 + - - -
633Q THR* 4.3 9.7 - - + +
635Q ALA* 5.4 2.2 - - - +
636Q ASP* 3.2 26.8 + - - -
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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