Contacts of the helix formed by residues 69 - 75 (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 VAL 69 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175O LYS* 3.9 26.9 - - + -
176O PRO* 4.1 2.5 - - + -
404O GLY* 4.2 6.1 - - - -
407O LEU* 3.4 26.7 - - + +
408O GLY 4.2 1.6 - - - +
13V PHE* 3.8 3.4 - - - -
63V THR 5.9 0.2 - - - +
65V THR* 4.0 11.2 - - + -
67V THR 3.8 9.0 - - - +
68V THR* 1.3 82.5 - - - +
70V TRP* 1.3 64.3 + - - +
71V THR* 3.5 17.5 - - - +
72V ASP* 3.4 36.1 + - - +
1478V EDO 3.2 8.3 + - - +
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Residues in contact with TRP 70 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75M MET* 3.9 22.9 - - + -
78M LEU* 3.6 27.2 - - + +
79M PRO* 3.9 15.5 - - + -
81M PHE* 3.5 28.6 - + + -
187O ARG* 5.2 5.6 - - + -
188O ALA* 5.2 3.6 - - + -
191O GLU* 5.8 2.7 - - + -
407O LEU 3.2 27.3 + - - -
409O HIS 4.7 0.7 - - - -
412O GLY* 3.9 10.0 - - - -
413O ASN* 2.8 38.7 + - + -
13V PHE* 3.5 41.2 - + + +
69V VAL* 1.3 74.4 - - - +
71V THR* 1.3 82.9 + - + +
72V ASP 3.1 1.4 + - - -
73V GLY* 3.2 11.1 + - - -
74V LEU* 3.7 26.0 - - + -
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Residues in contact with THR 71 (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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175O LYS 2.6 29.3 + - - +
176O PRO* 3.4 5.3 - - - +
180O LEU* 3.9 16.1 - - + +
184O ASN 5.9 0.4 - - - +
188O ALA* 4.5 9.6 - - + -
407O LEU* 3.8 17.9 - - + +
69V VAL* 3.5 10.4 - - - +
70V TRP* 1.3 109.0 - - + +
72V ASP* 1.3 64.6 + - - +
73V GLY 3.0 2.5 - - - -
74V LEU* 3.1 25.5 + - + +
75V THR* 4.0 0.9 + - - +
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Residues in contact with ASP 72 (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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176O PRO* 3.5 22.0 - - - +
68V THR* 4.9 1.6 - - - +
69V VAL* 3.4 24.7 - - - +
70V TRP 3.1 0.6 + - - +
71V THR* 1.3 77.2 + - - +
73V GLY* 1.3 57.8 + - - +
75V THR* 2.9 34.4 + - - +
77V LEU* 3.5 27.4 + - + +
1478V EDO 2.6 41.6 + - - -
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Residues in contact with GLY 73 (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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39M ILE* 3.4 13.5 - - - +
81M PHE* 3.5 24.2 - - - -
112M ASN* 3.2 22.8 + - - +
70V TRP 3.2 5.7 + - - -
71V THR 3.0 1.6 - - - -
72V ASP* 1.3 78.0 - - - +
74V LEU* 1.3 57.2 + - - +
75V THR 3.2 2.0 - - - +
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Residues in contact with LEU 74 (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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39M ILE* 4.9 1.3 - - + -
79M PRO* 4.3 5.6 - - + -
81M PHE* 3.9 18.8 - - + -
110M PHE* 4.0 36.8 - - + +
111M ASP 4.4 0.5 - - - +
112M ASN* 3.4 15.4 - - - -
115M GLN* 3.3 22.1 - - - +
180O LEU* 4.5 2.5 - - + -
184O ASN* 3.7 40.2 + - + +
187O ARG* 4.7 8.1 - - - -
70V TRP* 3.7 29.2 - - + -
71V THR* 3.1 19.1 + - + +
73V GLY* 1.3 75.8 - - - +
75V THR* 1.3 57.8 + - - +
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Residues in contact with THR 75 (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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112M ASN* 3.0 28.4 + - - +
115M GLN* 3.3 15.8 + - - +
176O PRO* 4.2 18.8 - - + -
178O LEU 5.4 0.4 - - - +
179O GLY* 2.9 30.4 + - - +
180O LEU* 4.4 2.0 - - + -
71V THR 4.2 5.6 - - - +
72V ASP* 2.9 24.4 + - - +
73V GLY* 3.9 0.9 - - - +
74V LEU* 1.3 77.6 - - - +
76V SER* 1.3 70.9 + - - +
77V LEU* 3.9 5.2 + - + +
80V TYR* 3.4 13.4 - - + -
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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