Contacts of the helix formed by residues 123 - 126 (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 ASN 123 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177O LYS* 3.8 3.6 - - - +
204O GLU* 3.1 21.9 + - - -
294O HIS* 3.3 20.6 - - - -
296O ALA* 4.5 0.5 - - - -
298O HIS* 6.0 1.5 - - - -
299O ALA* 5.1 1.7 - - - +
335O LEU* 3.4 25.1 - - + +
1476O CAP 3.0 49.4 + - - +
60V GLU* 4.6 10.8 + - - +
119V SER 5.0 2.0 + - - -
122V GLY* 1.3 81.6 - - - +
124V VAL* 1.3 68.3 + - - +
125V PHE 3.1 4.1 + - - -
126V GLY* 3.2 10.6 + - - -
127V PHE* 3.7 7.3 - - + -
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Residues in contact with VAL 124 (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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40V PHE* 4.5 0.7 - - + -
56V ALA 4.4 0.4 - - - +
57V VAL* 3.4 44.4 - - + +
60V GLU* 3.9 28.9 - - + +
61V SER* 3.9 4.3 - - - +
120V ILE 3.7 21.1 - - - +
121V VAL* 4.7 0.4 - - - -
122V GLY 3.9 0.4 - - - +
123V ASN* 1.3 77.9 - - - +
125V PHE* 1.3 70.8 + - + +
126V GLY 3.2 2.2 + - - -
127V PHE* 3.5 19.3 + - + +
130V LEU* 3.6 18.7 - - - +
133V LEU* 3.7 20.6 - - + -
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Residues in contact with PHE 125 (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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299O ALA* 3.4 25.3 - - + +
300O VAL* 3.8 19.5 - - + +
303O ARG* 2.9 27.9 + - - +
40V PHE* 4.1 6.7 - + - -
121V VAL* 3.6 43.1 - - + +
123V ASN 3.1 1.4 + - - -
124V VAL* 1.3 87.2 - - + +
126V GLY* 1.3 56.7 + - - +
127V PHE 3.5 0.4 - - - -
130V LEU* 4.0 1.8 - - - +
133V LEU* 3.1 56.5 - - + -
134V ARG 4.0 0.2 - - - -
135V LEU* 4.0 10.5 - - + -
307V HIS* 3.8 13.5 - + + -
308V GLY 3.2 22.7 - - - -
309V ILE* 4.6 0.4 - - + -
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Residues in contact with GLY 126 (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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298O HIS* 5.7 2.9 - - - -
299O ALA* 3.3 17.1 - - - +
303O ARG* 3.4 10.8 - - - -
335O LEU* 3.5 11.9 - - - +
336O GLU* 2.9 32.7 + - - +
123V ASN 3.2 7.9 + - - -
124V VAL 3.2 1.0 - - - -
125V PHE* 1.3 76.5 - - - +
127V PHE* 1.3 61.5 + - - +
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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