Contacts of the helix formed by residues 141 - 146 (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 PRO 141 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33V ASP 3.3 25.8 - - - +
34V THR* 3.2 26.2 - - - +
35V ASP 3.5 11.7 - - - +
36V ILE* 3.8 19.5 - - + -
139V ARG* 3.3 17.9 - - - +
140V ILE* 1.3 87.6 - - + +
142V PRO* 1.3 72.4 - - + +
143V ALA 4.3 2.2 - - - +
144V TYR* 2.9 22.1 + - + +
145V VAL* 2.9 11.1 + - - +
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Residues in contact with PRO 142 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R THR* 4.3 13.9 - - + -
143R ALA* 4.3 1.3 - - + -
33V ASP 4.7 5.8 - - - +
139V ARG* 5.5 2.7 - - - +
140V ILE 3.8 0.9 - - - +
141V PRO* 1.3 83.3 - - + +
143V ALA* 1.3 56.6 + - - +
145V VAL* 3.6 9.8 - - + +
146V LYS* 2.9 37.7 + - - +
367V ASP* 3.8 41.9 - - + +
369V SMC 3.9 26.0 - - + -
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Residues in contact with ALA 143 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142R PRO* 4.3 1.6 - - + -
143R ALA* 3.7 31.7 - - + +
146R LYS* 3.4 28.9 - - + +
369R SMC 5.5 0.2 - - - -
33V ASP 5.6 0.2 + - - -
34V THR* 4.0 22.9 - - + -
105V ILE* 3.7 18.6 - - + -
141V PRO* 3.1 2.2 + - - +
142V PRO* 1.3 79.0 - - - +
144V TYR* 1.3 59.6 + - - +
146V LYS* 4.1 3.8 + - - +
147V THR* 3.6 5.2 - - - +
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Residues in contact with TYR 144 (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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146R LYS* 5.6 1.3 - - - -
36V ILE* 4.3 14.4 - - + -
105V ILE* 3.7 20.0 - - + +
108V PHE* 3.5 28.9 - + + +
109V GLU 2.8 32.8 + - - -
110V GLU* 4.2 2.2 - - + -
112V SER 3.4 15.6 + - - -
116V MET* 4.1 17.9 + - + +
140V ILE* 4.0 15.3 - - + -
141V PRO* 2.9 24.0 + - + +
143V ALA* 1.3 76.6 - - - +
145V VAL* 1.3 65.0 + - - +
146V LYS 3.1 1.6 - - - -
147V THR* 2.7 40.2 + - + -
148V PHE* 3.2 29.2 - + - -
320V MET* 4.0 7.2 - - + -
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Residues in contact with VAL 145 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140V ILE* 3.7 30.5 - - + +
141V PRO 2.9 18.6 + - - +
142V PRO* 3.6 9.6 - - + +
144V TYR* 1.3 75.9 - - - +
146V LYS* 1.3 59.7 + - + +
147V THR 3.1 0.2 - - - -
148V PHE* 3.1 32.4 + - - +
320V MET* 5.7 0.7 - - + -
366V GLN* 4.4 0.2 - - - +
367V ASP 4.0 11.4 - - - +
368V TRP* 3.3 36.3 - - + +
369V SMC 4.7 4.0 - - + +
371V MET* 3.7 27.8 - - + +
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Residues in contact with LYS 146 (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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210H PRO* 3.7 18.0 - - - +
105R ILE* 4.2 25.5 + - + +
106R ASP* 5.3 1.2 + - - -
108R PHE 5.2 1.0 + - - -
110R GLU* 2.9 47.8 + - - +
143R ALA* 3.4 28.7 - - + +
144R TYR* 5.6 0.9 - - - -
147R THR* 3.6 23.5 - - + +
142V PRO 2.9 21.6 + - - +
143V ALA 4.1 4.0 - - - +
144V TYR 3.1 0.6 - - - -
145V VAL* 1.3 78.3 - - + +
147V THR* 1.3 59.3 + - + +
148V PHE 3.3 4.9 + - - +
369V SMC 4.2 30.9 + - + +
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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