Contacts of the helix formed by residues 125 - 131 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H LYS* 3.5 2.2 - - - -
52H SER* 1.3 52.3 - - - -
54H VAL* 3.0 7.7 - - - +
111S LEU* 3.8 4.3 - - - -
124S ILE* 1.3 64.7 - - - +
126S ALA* 1.3 64.8 + - - -
127S GLU 3.1 3.8 + - - -
128S GLU* 3.2 17.4 + - - +
129S ILE* 3.4 13.2 + - - +
136S MET* 4.8 0.4 - - - +
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Residues in contact with ALA 126 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H GLN 4.7 0.7 - - - +
50H LYS* 4.1 3.2 - - + +
51H ASP 5.3 0.2 - - - +
52H SER* 3.1 3.6 + - - +
104S ILE* 3.9 16.8 - - + +
107S VAL* 3.5 25.8 - - + -
108S ASN* 3.0 35.9 - - - +
111S LEU* 3.4 5.5 - - - +
125S GLY* 1.3 72.2 - - - -
127S GLU* 1.3 58.0 + - - +
129S ILE* 3.1 3.0 + - - +
130S VAL* 2.8 34.8 + - - +
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Residues in contact with GLU 127 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H MET* 3.1 5.4 - - - +
48H GLY 3.7 1.4 + - - -
50H LYS* 1.3 100.6 - - + +
53H TYR* 3.4 4.7 - - - -
57H GLU* 4.5 3.0 - - - +
146J GLY 4.6 0.7 - - - +
147J ARG* 3.8 2.8 - - - -
148J THR* 1.4 50.1 + - + +
149J THR* 4.5 1.4 + - - -
167J GLU* 4.3 0.7 - - - +
100S ARG* 3.9 9.7 + - - +
104S ILE* 5.1 2.9 - - - +
126S ALA* 1.3 72.8 - - - +
128S GLU* 1.3 58.1 + - + +
130S VAL* 3.2 7.1 + - - +
131S ASP* 2.8 49.2 + - - +
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Residues in contact with GLU 128 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H LYS* 1.9 43.0 + - - -
54H VAL* 3.3 8.8 - - - +
57H GLU* 2.7 21.9 - - - +
125S GLY 3.2 17.0 + - - +
127S GLU* 1.3 80.9 - - + +
129S ILE* 1.3 61.0 + - - +
131S ASP* 3.3 8.1 + - - -
132S GLY 3.2 3.5 + - - -
133S ASN* 2.9 40.5 + - + +
136S MET* 3.0 47.9 - - + +
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Residues in contact with ILE 129 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73S PHE* 3.9 22.0 - - + +
74S ARG* 3.5 13.2 + - - +
79S LEU* 4.5 1.1 - - + -
107S VAL* 3.7 26.5 - - + -
111S LEU* 4.7 3.1 - - + -
124S ILE* 4.3 10.5 - - + -
125S GLY 3.4 16.2 - - - +
126S ALA* 3.1 5.6 + - - +
128S GLU* 1.3 73.0 - - - +
130S VAL* 1.3 66.1 + - - +
132S GLY* 3.1 11.6 + - - -
136S MET* 4.1 22.9 - - + +
137S THR* 4.2 15.8 + - - +
140S MET* 3.8 36.6 - - + -
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Residues in contact with VAL 130 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74S ARG* 3.1 36.1 + - - +
100S ARG* 4.3 29.8 - - + +
103S LYS* 3.8 30.2 + - + +
104S ILE* 3.7 35.7 - - + +
107S VAL* 4.1 3.8 - - + -
126S ALA 2.8 23.1 + - - +
127S GLU* 3.6 6.5 - - - +
129S ILE* 1.3 72.5 - - - +
131S ASP* 1.3 58.7 - - - +
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Residues in contact with ASP 131 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74S ARG* 4.4 3.6 - - - -
100S ARG* 2.6 30.8 + - - -
127S GLU* 2.8 33.7 + - - +
128S GLU* 3.6 9.2 + - - +
129S ILE 3.2 0.2 - - - -
130S VAL* 1.3 76.7 - - - +
132S GLY* 1.3 60.6 + - - +
133S ASN* 3.5 3.9 + - + +
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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