Contacts of the helix formed by residues 229 - 235 (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 229 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100Q TRP* 4.0 7.0 - - - -
227Q VAL 4.0 0.6 + - - -
228Q ALA* 1.3 74.7 - - - +
230Q PHE* 1.3 65.5 + - - +
231Q GLU* 4.1 6.1 - - - +
232Q TYR* 2.9 18.5 + - - +
233Q ALA* 3.0 18.4 + - - +
240Q GLY* 3.6 4.2 - - - -
241Q SER* 2.9 40.9 + - - -
243Q PHE* 4.0 16.1 - - + -
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Residues in contact with PHE 230 (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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3Q ARG* 4.4 7.9 - - - -
6Q ALA* 3.7 18.2 - - + -
100Q TRP* 3.5 51.7 - + + +
229Q ASP* 1.3 74.8 - - - +
231Q GLU* 1.3 80.1 + - + +
233Q ALA* 3.3 1.3 + - - +
234Q VAL* 3.0 58.1 + - + +
377Q THR* 4.0 8.7 - - + -
379Q LEU* 3.8 13.5 - - + -
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Residues in contact with GLU 231 (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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3Q ARG* 2.7 41.5 + - - -
229Q ASP* 3.3 5.6 + - - +
230Q PHE* 1.3 88.8 - - + +
232Q TYR* 1.3 66.4 + - - +
234Q VAL* 3.2 1.2 + - - +
235Q THR* 2.9 31.0 + - - +
239Q GLN* 3.6 21.2 - - + +
240Q GLY* 3.3 20.4 - - - +
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Residues in contact with TYR 232 (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* 3.5 26.5 - - + -
108Q LYS* 6.1 1.5 - - + +
228Q ALA* 3.7 10.3 - - + -
229Q ASP* 2.9 22.2 + - - +
231Q GLU* 1.3 78.9 - - - +
233Q ALA* 1.3 62.8 + - - +
236Q GLY* 3.1 4.2 + - - -
237Q GLY* 3.0 52.0 + - - -
239Q GLN 3.4 16.8 - - - -
240Q GLY* 3.4 1.0 - - - -
241Q SER* 3.3 30.3 - - - +
242Q LEU* 3.4 41.8 - - + +
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Residues in contact with ALA 233 (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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100Q TRP* 3.6 23.8 - - + +
101Q PRO 3.4 21.3 - - - +
102Q LEU* 3.7 12.1 - - - +
103Q ALA* 2.9 25.9 + - - +
228Q ALA* 4.2 0.8 - - + +
229Q ASP 3.0 17.2 + - - +
230Q PHE* 3.6 4.5 - - - +
232Q TYR* 1.3 78.3 - - - +
234Q VAL* 1.3 62.1 + - + +
235Q THR 3.4 0.7 + - - -
236Q GLY 3.6 5.2 + - - -
379Q LEU* 4.8 6.3 - - + -
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Residues in contact with VAL 234 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Q ARG* 4.4 2.1 + - - +
3Q ARG* 3.4 29.6 - - - +
4Q ALA* 2.7 53.3 + - + +
6Q ALA* 4.5 2.0 - - + -
103Q ALA* 4.4 1.8 - - - +
230Q PHE* 3.0 56.9 + - + +
231Q GLU* 3.3 11.0 - - - +
233Q ALA* 1.3 75.2 - - - +
235Q THR* 1.3 64.1 + - + +
236Q GLY 3.5 0.8 + - - -
379Q LEU* 3.8 18.8 - - + -
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Residues in contact with THR 235 (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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2Q ARG 5.0 4.7 - - - +
3Q ARG* 3.9 23.1 - - + +
107Q LYS* 4.9 0.2 - - - +
231Q GLU* 2.9 37.3 + - - +
232Q TYR 3.2 4.7 + - - -
234Q VAL* 1.3 87.0 - - + +
236Q GLY* 1.3 59.3 + - - +
237Q GLY 2.9 5.8 + - - -
238Q GLU* 3.0 28.3 + - - +
239Q GLN* 2.9 36.8 + - + +
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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