Contacts of the helix formed by residues 125 - 131 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50F LYS* 3.5 2.7 - - - -
52F SER* 1.3 51.8 - - - -
54F VAL* 3.0 7.9 - - - +
111Q LEU* 3.8 3.8 - - - -
124Q ILE* 1.3 64.7 - - - +
126Q ALA* 1.3 64.0 + - - -
127Q GLU 3.1 3.8 + - - -
128Q GLU* 3.2 17.3 + - - +
129Q ILE* 3.4 13.2 + - - +
136Q MET* 4.8 0.2 - - - +
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Residues in contact with ALA 126 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F GLN 4.7 0.4 - - - +
50F LYS* 4.1 3.4 - - + +
52F SER* 3.1 4.8 + - - +
104Q ILE* 3.9 17.7 - - + +
107Q VAL* 3.5 26.5 - - + -
108Q ASN* 3.0 35.7 - - - +
111Q LEU* 3.4 5.0 - - - +
125Q GLY* 1.3 70.5 - - - -
127Q GLU* 1.3 58.0 + - - +
129Q ILE* 3.1 2.4 + - - +
130Q VAL* 2.8 35.0 + - - +
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Residues in contact with GLU 127 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F MET* 3.1 5.7 - - - +
48F GLY 3.7 1.7 + - - -
50F LYS* 1.3 99.9 - - + +
53F TYR* 3.4 4.2 - - - -
57F GLU* 4.5 2.6 - - - +
146H GLY 4.6 0.9 - - - +
147H ARG* 4.0 2.9 - - - -
148H THR* 1.4 49.3 + - + +
149H THR* 4.5 1.2 + - - -
167H GLU* 4.5 0.7 - - - +
100Q ARG* 3.9 9.4 + - - +
104Q ILE* 5.1 2.7 - - - +
126Q ALA* 1.3 72.6 - - - +
128Q GLU* 1.3 59.1 + - + +
130Q VAL* 3.2 6.5 + - - +
131Q ASP* 2.8 49.4 + - - +
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Residues in contact with GLU 128 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LYS* 1.9 44.7 + - - -
54F VAL* 3.3 8.3 - - - +
57F GLU* 2.7 20.6 - - - +
125Q GLY 3.2 16.8 + - - +
127Q GLU* 1.3 81.1 - - + +
129Q ILE* 1.3 60.2 + - - +
131Q ASP* 3.3 8.1 + - - -
132Q GLY 3.1 3.5 + - - -
133Q ASN* 2.9 39.5 + - + +
136Q MET* 3.0 49.3 - - + +
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Residues in contact with ILE 129 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73Q PHE* 3.9 22.0 - - + +
74Q ARG* 3.5 13.2 + - - +
79Q LEU* 4.5 0.9 - - + -
107Q VAL* 3.7 26.9 - - + -
111Q LEU* 4.7 3.4 - - + -
124Q ILE* 4.3 10.3 - - + -
125Q GLY 3.4 15.7 - - - +
126Q ALA* 3.1 5.7 + - - +
128Q GLU* 1.3 73.0 - - - +
130Q VAL* 1.3 67.4 + - - +
132Q GLY* 3.1 11.1 + - - -
136Q MET* 4.1 24.0 - - + +
137Q THR* 4.2 15.4 + - - +
140Q MET* 3.8 36.1 - - + -
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Residues in contact with VAL 130 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Q ARG* 3.1 34.8 + - - +
100Q ARG* 4.3 30.1 - - + +
103Q LYS* 3.8 29.6 + - + +
104Q ILE* 3.7 34.8 - - + +
107Q VAL* 4.1 4.5 - - + -
126Q ALA 2.8 24.0 + - - +
127Q GLU* 3.6 6.3 - - - +
129Q ILE* 1.3 71.4 - - - +
131Q ASP* 1.3 58.0 + - - +
132Q GLY 3.1 0.2 - - - -
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Residues in contact with ASP 131 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Q ARG* 4.4 3.6 - - - -
100Q ARG* 2.6 30.6 + - - -
127Q GLU* 2.8 34.5 + - - +
128Q GLU* 3.6 9.1 + - - +
130Q VAL* 1.3 77.8 - - - +
132Q GLY* 1.3 60.0 + - - +
133Q 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