Contacts of the helix formed by residues 297 - 303 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117O PHE* 4.4 18.6 - - + -
121O VAL* 3.4 27.4 - - + +
122O GLY 2.7 14.7 + - - -
270O LEU* 6.5 0.2 - - + -
274O PHE* 6.0 0.4 - - - -
301O ILE* 4.2 23.3 - - + -
309O ILE* 4.1 25.8 - - + -
314O LEU* 5.8 0.4 - - + -
1484O EDO 4.0 22.0 - - - -
270V LEU* 4.0 13.5 - - + +
271V THR* 3.8 21.8 - - + -
296V ALA* 1.3 73.3 - - - +
298V HIS* 1.3 64.7 + - - +
299V ALA 3.2 3.4 - - - -
300V VAL* 3.0 28.8 + - + +
301V ILE* 3.8 10.5 + - + +
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Residues in contact with HIS 298 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122O GLY 5.1 4.3 - - - -
123O ASN* 6.0 1.3 - - - -
126O GLY* 5.7 2.7 - - - -
270V LEU* 3.7 18.3 - - + +
295V ARG* 2.9 78.3 + - + +
296V ALA* 3.4 1.2 + - - -
297V MET* 1.3 76.8 - - - +
299V ALA* 1.3 72.2 + - + +
301V ILE* 2.8 10.7 + - - +
302V ASP* 2.4 62.4 + - - +
311V PHE* 4.0 5.9 - - + -
314V LEU* 4.0 9.6 - - + -
335V LEU* 6.0 2.6 - - - +
336V GLU 5.7 0.9 - - - -
1476V CAP 4.0 6.9 + - - -
1482V EDO 3.7 12.1 - - - -
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Residues in contact with ALA 299 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122O GLY 5.5 1.7 + - - +
123O ASN 5.2 2.0 - - - +
125O PHE* 3.4 10.3 - - + +
126O GLY* 3.4 37.7 - - - +
307O HIS* 2.8 21.1 + - - -
297V MET 3.2 1.4 - - - -
298V HIS* 1.3 87.3 - - + +
300V VAL* 1.3 62.5 + - - +
301V ILE 3.1 1.5 + - - -
302V ASP* 3.2 14.6 - - - +
303V ARG* 3.3 14.3 + - + +
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Residues in contact with VAL 300 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121O VAL* 3.8 24.5 - - + +
125O PHE* 3.7 30.9 - - + +
300O VAL 4.9 4.9 - - - +
301O ILE* 3.8 20.2 - - + +
307O HIS* 3.5 22.9 - - - -
308O GLY* 3.9 11.1 - - - -
309O ILE* 3.7 29.2 - - + -
297V MET* 3.0 23.0 + - + +
299V ALA* 1.3 77.4 - - - +
301V ILE* 1.3 58.3 + - - +
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Residues in contact with ILE 301 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297O MET* 4.2 16.6 - - + -
300O VAL* 3.8 17.0 - - + -
301O ILE* 3.9 25.4 - - + -
1484O EDO 4.7 8.7 - - - -
270V LEU* 4.9 7.2 - - + -
297V MET* 4.2 25.8 - - + +
298V HIS 2.8 7.4 + - - +
300V VAL* 1.3 81.4 - - + +
302V ASP* 1.3 57.7 + - - +
303V ARG 3.7 1.5 + - - -
304V GLN 5.5 0.2 - - - -
307V HIS 3.9 4.0 - - - +
308V GLY* 3.3 11.3 - - - -
309V ILE* 3.1 54.2 + - + +
314V LEU* 4.1 19.1 - - + -
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Residues in contact with ASP 302 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134V ARG* 3.0 22.8 + - - +
298V HIS* 2.4 44.7 + - - +
299V ALA* 3.2 15.8 - - - +
301V ILE* 1.3 77.1 - - - +
303V ARG* 1.3 65.5 + - - +
304V GLN 3.6 2.0 - - - -
309V ILE 3.0 22.7 - - - +
310V HIS* 4.0 0.4 - - - -
311V PHE* 3.3 33.7 + - - +
314V LEU* 4.0 3.5 - - + +
473V ASP* 4.1 8.1 - - - +
1482V EDO 4.3 6.7 + - - -
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Residues in contact with ARG 303 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O GLN* 4.5 0.8 - - - +
125O PHE 2.9 24.6 + - - +
126O GLY* 3.4 15.0 - - - -
127O PHE 2.9 23.7 + - - -
128O LYS* 4.0 8.7 + - - +
130O LEU* 2.8 31.3 + - - +
131O ARG 4.7 2.2 - - - +
307O HIS* 3.5 11.6 + - + +
299V ALA* 3.3 22.4 + - - +
301V ILE 3.7 1.0 - - - -
302V ASP* 1.3 83.5 + - - +
304V GLN* 1.3 76.4 + - - +
336V GLU* 3.0 43.9 + - - +
472V ILE* 3.6 22.1 - - + +
473V ASP* 3.5 22.0 + - - +
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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