Contacts of the helix formed by residues 297 - 303 (chain K) 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 MET 297 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E PHE* 4.4 17.5 - - + -
121E VAL* 3.4 26.2 - - + +
122E GLY 2.7 14.2 + - - -
270E LEU* 6.5 0.2 - - + -
274E PHE* 6.1 1.1 - - - -
301E ILE* 4.3 19.1 - - + -
309E ILE* 4.1 26.7 - - + -
314E LEU* 5.8 0.7 - - + -
1482E EDO 4.2 20.6 - - - -
270K LEU* 3.9 14.4 - - + +
271K THR* 3.8 21.5 - - + -
296K ALA* 1.3 74.0 - - - +
298K HIS* 1.3 63.5 + - - +
299K ALA 3.2 3.1 - - - -
300K VAL* 3.0 31.5 + - + +
301K ILE* 3.9 11.2 + - + +
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Residues in contact with HIS 298 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E GLY 5.0 4.3 - - - -
123E ASN* 5.9 1.6 - - - -
126E GLY* 5.6 3.4 - - - -
270K LEU* 3.7 19.7 - - + +
295K ARG* 2.9 76.0 + - + +
296K ALA 3.4 1.0 + - - -
297K MET* 1.3 77.5 - - - +
299K ALA* 1.3 71.8 + - + +
301K ILE* 2.9 11.7 + - - +
302K ASP* 2.4 61.5 + - - +
311K PHE* 3.9 6.5 - - + -
314K LEU* 4.1 8.5 - - + -
335K LEU* 5.9 2.6 - - - +
336K GLU 5.7 0.7 - - - -
1481K EDO 3.6 12.1 - - - -
1478R CAP 4.1 7.3 + - - -
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Residues in contact with ALA 299 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E GLY 5.5 2.0 + - - +
123E ASN* 5.2 2.2 - - - +
125E PHE* 3.4 10.3 - - + +
126E GLY* 3.3 37.9 - - - +
307E HIS* 2.8 21.3 + - - -
297K MET 3.2 1.0 - - - -
298K HIS* 1.3 88.1 - - + +
300K VAL* 1.3 61.5 + - - +
301K ILE 3.1 1.9 + - - -
302K ASP* 3.1 13.9 - - - +
303K ARG* 3.3 14.5 + - + +
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Residues in contact with VAL 300 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E VAL* 3.8 24.5 - - + +
125E PHE* 3.7 31.7 - - + +
300E VAL 4.9 4.9 - - - +
301E ILE* 3.8 20.0 - - + +
307E HIS* 3.5 22.7 - - - -
308E GLY* 3.9 11.7 - - - -
309E ILE* 3.8 28.5 - - + -
297K MET* 3.0 23.0 + - + +
299K ALA* 1.3 76.9 - - - +
301K ILE* 1.3 57.4 + - + +
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Residues in contact with ILE 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E MET* 4.4 15.9 - - + -
300E VAL* 3.9 17.3 - - + -
301E ILE* 4.0 23.6 - - + -
307E HIS* 5.8 0.4 - - - -
1482E EDO 4.9 7.6 - - - -
270K LEU* 4.8 9.4 - - + -
297K MET* 4.2 27.1 - - + +
298K HIS 2.9 6.7 + - - +
300K VAL* 1.3 82.3 - - + +
302K ASP* 1.3 60.6 + - - +
303K ARG 3.7 1.3 + - - -
304K GLN 5.1 0.2 + - - -
307K HIS 3.9 5.2 - - - +
308K GLY* 3.3 10.0 - - - -
309K ILE* 3.2 54.1 + - + +
314K LEU* 4.1 17.7 - - + -
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Residues in contact with ASP 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134K ARG* 3.0 22.9 + - - +
298K HIS* 2.4 44.3 + - - +
299K ALA* 3.1 16.5 - - - +
301K ILE* 1.3 77.5 - - - +
303K ARG* 1.3 64.8 + - - +
304K GLN 3.6 1.6 - - - -
309K ILE 3.0 22.0 - - - +
310K HIS* 4.0 0.6 - - - -
311K PHE* 3.3 33.8 + - - +
314K LEU* 4.2 3.8 - - + -
473K ASP* 4.1 7.6 - - - +
1481K EDO 4.4 6.6 + - - -
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Residues in contact with ARG 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E GLN* 4.5 0.8 - - - +
125E PHE 2.9 25.6 + - - +
126E GLY* 3.4 15.4 - - - -
127E PHE 2.8 26.9 + - - -
128E LYS* 3.9 6.7 + - - +
130E LEU* 2.8 31.9 + - - +
131E ARG 4.8 1.7 - - - +
307E HIS* 3.5 11.4 + - + +
299K ALA* 3.3 20.5 + - - +
301K ILE 3.7 1.0 - - - -
302K ASP* 1.3 82.4 + - - +
304K GLN* 1.3 76.0 + - - +
336K GLU* 2.9 43.6 + - - +
472K ILE* 3.6 22.2 - - + +
473K ASP* 3.5 22.9 + - - +
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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