Contacts of the helix formed by residues 225 - 229 (chain D) in PDB entry 1USK
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 225 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124D GLN* 3.9 6.3 - - - +
150D TYR* 3.2 20.6 - - + +
154D LEU* 3.5 21.5 - - + -
198D TYR* 3.4 17.7 - - - +
199D TYR 3.0 17.7 - - - +
200D GLY* 4.1 0.7 - - - -
201D GLY 3.7 22.0 - - - +
224D GLY* 1.3 88.6 - - - +
226D GLU* 1.3 67.3 + - - +
227D GLY 3.0 1.4 + - - -
228D VAL* 3.1 13.1 + - + +
246D VAL* 3.2 8.2 - - - +
247D THR* 3.5 13.7 - - - +
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Residues in contact with GLU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D TRP* 3.2 17.1 - - + -
102D THR* 3.9 2.2 - - - +
124D GLN* 2.8 34.1 + - - +
150D TYR* 2.5 27.9 + - - -
225D PRO* 1.3 72.4 - - - +
227D GLY* 1.3 57.0 + - - +
229D GLY* 3.1 17.4 + - - -
247D THR 3.1 19.0 + - - +
248D MET* 3.8 15.2 - - - +
249D PRO* 4.2 15.9 - - + -
275D PRO* 5.6 0.9 - - + -
276D TYR* 2.5 40.7 + - + +
331D PHE* 4.4 5.2 - - + -
1347D LEU* 2.7 23.3 + - - +
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Residues in contact with GLY 227 (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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18D TRP* 3.1 28.6 + - - -
150D TYR* 2.9 18.4 + - - -
201D GLY 3.9 8.1 - - - -
202D TYR* 3.5 5.7 - - - -
203D TYR* 3.1 15.4 + - - -
225D PRO 3.0 0.6 + - - -
226D GLU* 1.3 76.9 - - - +
228D VAL* 1.3 59.7 - - - +
229D GLY 3.5 0.2 - - - -
1347D LEU* 3.7 13.9 - - - -
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D TYR* 4.4 4.9 - - + -
201D GLY 3.3 22.0 - - - +
202D TYR 3.8 6.7 - - - +
203D TYR* 3.7 9.6 - - - +
206D MET* 3.8 33.0 - - + -
224D GLY* 4.1 10.5 - - - -
225D PRO* 3.1 24.6 + - + +
227D GLY* 1.3 75.3 - - - +
229D GLY* 1.3 61.0 + - - +
230D ASN 2.9 8.9 + - - -
233D LEU* 3.4 23.7 - - + +
244D MET* 4.0 21.3 - - + -
246D VAL* 3.9 11.4 - - + -
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Residues in contact with GLY 229 (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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18D TRP* 3.3 18.4 - - - -
21D MET* 5.5 0.5 - - - +
225D PRO 3.9 0.4 + - - -
226D GLU 3.1 10.3 + - - -
228D VAL* 1.3 76.8 - - - +
230D ASN* 1.3 58.4 + - - -
233D LEU* 5.0 0.7 - - - -
246D VAL* 4.2 5.2 - - - -
248D MET* 3.4 25.2 - - - +
275D PRO* 5.3 1.0 - - - +
336D TRP* 3.6 28.3 - - - -
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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