Contacts of the helix formed by residues 125 - 131 (chain O) in PDB entry 3LUE
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 GLY 125 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D LYS* 3.4 2.2 - - - -
52D SER* 1.3 52.7 - - - -
54D VAL* 3.0 7.1 - - - +
111O LEU* 3.8 4.0 - - - -
124O ILE* 1.3 64.4 - - - +
126O ALA* 1.3 64.9 + - - -
127O GLU 3.1 3.8 + - - -
128O GLU* 3.2 17.6 + - - +
129O ILE* 3.4 13.5 + - - +
136O MET* 4.8 0.4 - - - +
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Residues in contact with ALA 126 (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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49D GLN 4.7 0.7 - - - +
50D LYS* 4.1 3.0 - - + +
51D ASP 5.3 0.2 - - - +
52D SER* 3.1 3.6 + - - +
104O ILE* 3.9 17.5 - - + +
107O VAL* 3.5 25.8 - - + -
108O ASN* 3.0 35.5 - - - +
111O LEU* 3.4 5.3 - - - +
125O GLY* 1.3 71.6 - - - -
127O GLU* 1.3 58.7 + - - +
129O ILE* 3.1 3.0 + - - +
130O VAL* 2.8 35.2 + - - +
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Residues in contact with GLU 127 (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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47D MET* 3.1 5.5 - - - +
48D GLY 3.6 1.7 + - - -
49D GLN 5.2 0.2 + - - -
50D LYS* 1.3 99.0 - - + +
53D TYR* 3.4 4.7 - - - -
57D GLU* 4.5 2.6 - - - +
146F GLY 4.6 0.7 - - - +
147F ARG* 3.8 3.3 - - - -
148F THR* 1.4 49.6 + - + +
149F THR* 4.5 1.4 + - - -
167F GLU* 4.3 0.7 - - - +
100O ARG* 3.9 9.9 + - - +
104O ILE* 5.1 2.5 - - - -
126O ALA* 1.3 73.0 - - - +
128O GLU* 1.3 58.5 + - + +
130O VAL* 3.2 7.1 + - - +
131O ASP* 2.8 49.4 + - - +
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Residues in contact with GLU 128 (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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50D LYS* 1.9 44.6 + - - -
54D VAL* 3.3 9.0 - - - +
57D GLU* 2.7 21.6 - - - +
125O GLY 3.2 16.2 + - - +
127O GLU* 1.3 82.1 - - + +
129O ILE* 1.3 61.1 + - - +
131O ASP* 3.3 8.3 + - - -
132O GLY 3.2 3.3 + - - -
133O ASN* 2.9 40.0 + - + +
136O MET* 3.0 47.6 - - + +
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Residues in contact with ILE 129 (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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73O PHE* 3.9 22.0 - - + +
74O ARG* 3.5 13.2 + - - +
79O LEU* 4.5 1.1 - - + -
107O VAL* 3.7 26.7 - - + -
111O LEU* 4.7 3.4 - - + -
124O ILE* 4.3 10.1 - - + -
125O GLY 3.4 15.9 - - - +
126O ALA* 3.1 5.3 + - - +
128O GLU* 1.3 73.4 - - - +
130O VAL* 1.3 66.6 + - - +
132O GLY* 3.1 11.8 + - - -
136O MET* 4.1 23.3 - - + +
137O THR* 4.2 15.8 + - - +
140O MET* 3.8 37.0 - - + -
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Residues in contact with VAL 130 (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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74O ARG* 3.1 35.8 + - - +
100O ARG* 4.3 30.1 - - + +
103O LYS* 3.8 29.7 + - + +
104O ILE* 3.7 35.9 - - + +
107O VAL* 4.1 4.0 - - + -
126O ALA 2.8 23.5 + - - +
127O GLU* 3.6 6.3 - - - +
129O ILE* 1.3 72.7 - - - +
131O ASP* 1.3 59.0 - - - +
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Residues in contact with ASP 131 (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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74O ARG* 4.4 3.5 - - - -
100O ARG* 2.6 30.7 + - - -
127O GLU* 2.8 34.7 + - - +
128O GLU* 3.6 9.4 + - - +
129O ILE 3.2 0.2 - - - -
130O VAL* 1.3 76.8 - - - +
132O GLY* 1.3 60.3 + - - +
133O ASN* 3.5 3.7 + - + +
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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