Contacts of the helix formed by residues 327 - 332 (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 ASP 327 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Q LYS* 3.9 10.9 + - - +
326Q SER* 1.3 75.7 - - - +
328Q HIS* 1.3 67.9 + - - +
329Q ASP* 3.3 1.0 + - - +
330Q THR* 2.8 46.6 + - - +
331Q PHE* 3.3 24.7 + - + -
667Q GTP 3.4 29.1 + - - -
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Residues in contact with HIS 328 (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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325Q VAL* 4.3 5.1 - - + +
326Q SER 3.1 5.0 + - - -
327Q ASP* 1.3 73.8 - - - +
329Q ASP* 1.3 89.2 + - - +
331Q PHE 3.2 1.7 + - - -
332Q TRP* 3.0 26.4 + + - +
391Q LEU* 4.0 5.7 - - - +
402Q GLY* 3.4 26.1 - - - -
405Q LEU* 3.8 17.5 - - + -
406Q MET* 3.7 30.4 - - + +
452Q SER* 4.7 1.5 - - - -
453Q ASP* 3.7 21.2 - - + +
486Q MET* 3.5 19.8 - - - +
667Q GTP 3.3 34.4 + - - +
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Residues in contact with ASP 329 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270Q ARG* 3.4 16.0 + - - +
327Q ASP 3.3 1.0 - - - -
328Q HIS* 1.3 102.4 + - - +
330Q THR* 1.3 65.8 + - + +
331Q PHE 3.4 0.3 + - - -
332Q TRP* 3.6 2.0 + - - +
389Q VAL 3.8 0.7 - - - +
390Q GLY* 3.5 1.2 - - - -
391Q LEU* 2.9 53.5 + - + +
393Q SER* 5.2 9.4 + - - -
398Q THR* 6.4 0.2 - - - -
667Q GTP 3.1 40.5 + - - +
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Residues in contact with THR 330 (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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102Q LEU* 5.8 7.2 - - - -
105Q ASN* 2.8 32.6 + - - +
108Q LYS* 3.3 17.6 - - - +
327Q ASP* 2.8 39.6 + - - +
329Q ASP* 1.3 82.2 - - + +
331Q PHE* 1.3 58.0 + - - +
389Q VAL 3.7 13.3 - - - +
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Residues in contact with PHE 331 (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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105Q ASN* 3.7 1.3 - - - +
108Q LYS* 3.3 49.8 - - + -
109Q ARG* 2.7 39.4 + - + -
112Q ALA* 3.9 18.8 - - + -
114Q LEU* 3.8 27.4 - - + -
326Q SER* 3.3 24.9 - - - -
327Q ASP* 3.3 24.8 + - + +
328Q HIS 3.2 0.4 + - - -
329Q ASP 3.2 0.6 - - - -
330Q THR* 1.3 80.7 + - - +
332Q TRP* 1.3 68.4 + - - +
486Q MET* 3.5 22.4 - - + -
487Q LYS* 4.8 13.2 - - + -
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Residues in contact with TRP 332 (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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105Q ASN* 3.2 15.2 + - - -
328Q HIS* 3.0 24.3 + + - +
329Q ASP* 3.7 14.1 - - - +
330Q THR 3.5 0.8 - - - -
331Q PHE* 1.3 74.3 - - - +
333Q PRO* 1.3 85.8 - - + +
334Q GLY* 3.6 2.8 + - - -
336Q LEU* 4.0 17.3 - - + -
337Q ARG* 3.8 36.8 - - + -
340Q ILE* 4.6 0.2 - - + -
361Q LEU* 4.5 9.4 - - + -
390Q GLY* 3.3 19.6 - - - -
391Q LEU* 3.7 28.3 - - + +
401Q MET* 3.0 60.2 + - + -
405Q LEU* 3.5 27.6 - - + +
486Q MET* 4.4 2.7 - - - -
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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