Contacts of the helix formed by residues 125 - 131 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LYS* 3.4 2.5 - - - -
52A SER* 1.4 52.5 - - - -
54A VAL* 3.1 7.7 - - - +
111K LEU* 3.8 3.8 - - - -
124K ILE* 1.3 64.1 - - - +
126K ALA* 1.3 64.8 + - - -
127K GLU 3.1 3.7 + - - -
128K GLU* 3.2 17.6 + - - +
129K ILE* 3.4 13.2 + - - +
136K MET* 4.8 0.2 - - - +
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Residues in contact with ALA 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLN 4.7 0.7 - - - +
50A LYS* 4.1 3.7 - - + +
52A SER* 3.1 4.2 + - - +
104K ILE* 3.9 17.5 - - + +
107K VAL* 3.5 26.2 - - + -
108K ASN* 3.0 35.5 - - - +
111K LEU* 3.4 4.6 - - - +
125K GLY* 1.3 71.7 - - - -
127K GLU* 1.3 57.6 + - - +
129K ILE* 3.1 2.6 + - - +
130K VAL* 2.8 35.1 + - - +
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Residues in contact with GLU 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A MET* 3.1 6.6 - - - +
48A GLY 3.6 1.6 + - - -
49A GLN 5.2 0.2 + - - -
50A LYS* 1.3 100.0 - - + +
53A TYR* 3.4 4.3 - - - -
57A GLU* 4.6 2.4 - - - +
146C GLY 4.5 0.9 - - - +
147C ARG* 4.0 3.1 - - - -
148C THR* 1.5 48.6 + - + +
149C THR* 4.5 1.6 + - - -
167C GLU* 4.5 0.3 - - - +
100K ARG* 3.9 9.6 + - - +
104K ILE* 5.1 2.9 - - - -
126K ALA* 1.3 71.6 - - - +
128K GLU* 1.3 58.3 + - + +
130K VAL* 3.2 6.5 + - - +
131K ASP* 2.8 50.1 + - - +
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Residues in contact with GLU 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LYS* 1.9 44.9 + - - -
54A VAL* 3.4 8.7 - - - +
57A GLU* 2.7 21.5 - - - +
125K GLY 3.2 15.9 + - - +
127K GLU* 1.3 83.8 - - + +
129K ILE* 1.3 61.1 + - - +
131K ASP* 3.3 7.3 + - - -
132K GLY 3.2 3.6 + - - -
133K ASN* 2.9 40.6 + - + +
136K MET* 3.0 48.6 - - + +
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Residues in contact with ILE 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73K PHE* 3.9 21.7 - - + +
74K ARG* 3.5 13.0 - - - +
79K LEU* 4.5 1.1 - - + -
107K VAL* 3.7 26.5 - - + -
111K LEU* 4.7 3.4 - - + -
124K ILE* 4.3 10.3 - - + -
125K GLY 3.4 16.4 - - - +
126K ALA* 3.1 5.5 + - - +
128K GLU* 1.3 73.8 - - - +
130K VAL* 1.3 65.7 + - - +
132K GLY* 3.1 11.4 + - - -
136K MET* 4.1 22.9 - - + +
137K THR* 4.2 17.4 + - + +
140K MET* 3.8 37.9 - - + -
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Residues in contact with VAL 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74K ARG* 3.1 35.3 + - - +
100K ARG* 4.3 30.5 - - + +
103K LYS* 3.8 30.1 + - + +
104K ILE* 3.7 35.4 - - + +
107K VAL* 4.1 4.3 - - + -
126K ALA 2.8 23.3 + - - +
127K GLU* 3.6 5.8 - - - +
129K ILE* 1.3 71.7 - - - +
131K ASP* 1.3 58.5 + - - +
132K GLY 3.1 0.2 - - - -
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Residues in contact with ASP 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C GLY 5.4 0.2 - - - +
74K ARG* 4.4 3.7 - - - -
100K ARG* 2.6 30.8 + - - -
127K GLU* 2.8 33.7 + - - +
128K GLU* 3.6 9.0 + - - +
129K ILE 3.2 0.2 - - - -
130K VAL* 1.3 78.4 - - - +
132K GLY* 1.3 59.9 + - - +
133K ASN* 3.3 4.2 + - + +
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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