Contacts of the helix formed by residues 69 - 75 (chain O) 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 VAL 69 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13O PHE* 3.8 3.4 - - - -
63O THR 5.9 0.4 - - - +
65O THR* 4.1 11.7 - - + +
67O THR 3.8 9.9 - - - +
68O THR* 1.3 82.5 - - - +
70O TRP* 1.3 64.5 + - - +
71O THR* 3.4 18.6 + - - +
72O ASP* 3.4 35.5 + - - +
1479O EDO 3.3 9.4 + - - +
175V LYS* 3.9 22.9 - - + -
176V PRO* 4.2 2.5 - - + -
404V GLY* 4.1 5.2 - - - -
407V LEU* 3.3 31.0 - - + +
408V GLY 4.1 2.2 - - - +
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Residues in contact with TRP 70 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C MET* 3.7 23.1 - - + -
78C LEU* 3.5 29.0 - - + +
79C PRO* 3.9 16.4 - - + -
81C PHE* 3.5 30.4 - + + -
13O PHE* 3.5 42.0 - + + +
69O VAL* 1.3 72.3 - - - +
71O THR* 1.3 81.8 + - + +
72O ASP* 3.2 0.4 - - - +
73O GLY* 3.2 11.8 + - - -
74O LEU* 3.7 25.8 - - + -
187V ARG* 5.2 5.8 - - + -
188V ALA* 5.2 2.5 - - + -
191V GLU* 5.7 3.6 - - + -
407V LEU 3.2 28.5 + - - -
409V HIS 4.7 0.2 - - - -
412V GLY* 4.1 8.1 - - - -
413V ASN* 2.7 41.0 + - - +
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Residues in contact with THR 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69O VAL* 3.6 8.0 - - - +
70O TRP* 1.3 110.2 - - + +
72O ASP* 1.3 65.5 + - - +
73O GLY 3.0 2.5 - - - -
74O LEU* 3.0 25.6 + - + +
75O THR 3.9 1.9 + - - -
175V LYS 2.5 29.6 + - - +
176V PRO* 3.4 6.4 - - - +
180V LEU* 3.9 15.1 - - + +
188V ALA* 4.5 10.1 - - + -
407V LEU* 3.8 19.0 - - + +
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Residues in contact with ASP 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68O THR* 5.0 1.4 - - - +
69O VAL* 3.4 25.2 - - - +
71O THR* 1.3 78.3 + - - +
73O GLY* 1.3 58.0 + - - +
75O THR* 3.0 32.8 + - - +
77O LEU* 3.5 25.9 + - + +
1479O EDO 2.6 39.5 + - - -
176V PRO* 3.5 22.0 - - - +
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Residues in contact with GLY 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ILE* 3.5 12.5 - - - +
81C PHE* 3.4 25.7 - - - -
112C ASN* 3.4 19.2 + - - +
70O TRP 3.2 6.0 + - - -
71O THR 3.0 1.6 - - - -
72O ASP* 1.3 78.3 - - - +
74O LEU* 1.3 59.5 + - - +
75O THR 3.2 2.1 - - - +
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Residues in contact with LEU 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ILE* 5.0 1.6 - - + -
79C PRO* 4.1 6.7 - - + -
81C PHE* 3.8 17.9 - - + -
110C PHE* 4.0 36.9 - - + +
111C ASP 4.6 0.9 - - - +
112C ASN* 3.6 14.0 - - - -
115C GLN* 3.3 19.5 - - - +
70O TRP* 3.7 29.8 - - + -
71O THR* 3.0 19.2 + - + +
73O GLY* 1.3 76.0 - - - +
75O THR* 1.3 58.5 + - - +
180V LEU* 4.5 4.5 - - + -
184V ASN* 3.7 40.7 + - + +
187V ARG* 4.6 7.4 - - - -
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Residues in contact with THR 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ASN* 3.2 26.7 + - - +
115C GLN* 3.4 13.2 + - - +
71O THR 4.2 4.0 - - - +
72O ASP* 3.0 21.2 + - - +
73O GLY* 3.8 1.7 - - - +
74O LEU* 1.3 78.7 - - - +
76O SER* 1.3 72.4 + - - +
77O LEU* 3.9 5.0 + - + +
80O TYR* 3.3 13.9 - - + -
176V PRO* 4.1 24.0 - - + -
178V LEU 5.3 0.2 - - - +
179V GLY* 2.8 31.0 + - - +
180V LEU* 4.4 1.8 - - + -
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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