Contacts of the helix formed by residues 120 - 127 (chain A) in PDB entry 5LXG
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 SER 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A MET 2.8 8.1 + - - -
119A PRO* 1.3 75.6 - - - +
121A PHE* 1.3 59.2 + - - +
122A ARG* 3.6 7.1 + - - +
123A ALA* 3.5 26.2 + - - +
124A CYS* 3.0 29.6 + - - -
196A HIS* 3.3 4.8 - - - -
402A SO4 2.7 21.9 + - - -
30L HIS* 3.9 9.5 - - - +
32L PHE* 3.8 16.6 - - - -
92L TRP* 3.9 5.7 - - - -
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Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A SER* 1.3 68.4 - - - +
122A ARG* 1.4 55.4 + - - +
124A CYS* 3.2 3.5 + - + +
125A PHE* 2.8 57.2 + + + -
193A VAL* 3.9 25.6 - - + -
196A HIS* 3.7 28.9 - + - -
200A VAL* 3.9 29.8 - - + -
204A PHE* 4.8 10.5 - + - -
402A SO4 3.1 28.8 + - - +
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU* 4.4 14.5 + - - -
120A SER* 3.8 5.8 - - - +
121A PHE* 1.4 74.8 - - - +
123A ALA* 1.4 55.0 + - - +
125A PHE* 3.5 4.2 + - - +
126A LYS* 2.9 39.9 + - + +
402A SO4 2.9 20.4 + - - +
30L HIS* 3.5 19.8 + - - -
92L TRP* 4.5 14.3 - - + -
201L SO4 3.0 40.6 + - - -
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLY* 4.7 11.0 - - - +
92A TRP* 4.4 7.6 + - + +
118A MET* 4.5 24.4 - - + +
120A SER* 3.5 23.0 + - - +
121A PHE 3.4 0.2 - - - -
122A ARG* 1.4 78.9 - - - +
124A CYS* 1.4 57.5 + - - +
126A LYS* 3.9 8.2 - - - +
127A SER* 3.2 27.9 + - - -
32L PHE* 4.6 7.6 - - + -
92L TRP* 4.7 6.5 - - + -
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Residues in contact with CYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ARG* 4.1 0.6 + - - +
118A MET* 3.7 18.2 - - - -
120A SER 3.0 23.8 + - - +
121A PHE* 3.2 7.6 + - - +
123A ALA* 1.4 76.6 - - - +
125A PHE* 1.3 60.6 + - + +
127A SER* 2.7 23.5 + - - -
128A ILE* 4.0 6.2 + - - +
192A THR* 3.4 25.0 - - - +
193A VAL* 4.2 9.2 - - + -
195A CYS* 3.7 24.5 - - - -
196A HIS* 3.8 19.5 - - - -
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Residues in contact with PHE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PHE* 2.8 55.1 + + + +
122A ARG* 4.1 4.3 - - - +
124A CYS* 1.3 71.0 - - - +
126A LYS* 1.3 63.7 + - - +
127A SER 3.3 0.4 - - - -
128A ILE* 3.3 39.8 - - + +
129A PHE* 4.3 7.3 - - - -
188A TRP* 4.0 23.3 - + - -
189A LEU* 4.0 17.3 - - + -
192A THR* 4.2 7.4 - - - -
193A VAL* 4.5 11.4 - - + -
204A PHE* 6.6 0.2 - + - -
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1A GLY* 3.9 28.1 + - - -
89A GLU 4.2 14.3 + - - +
90A GLY 5.8 0.4 + - - -
92A TRP* 6.0 0.7 - - - +
122A ARG* 2.9 24.9 + - + +
123A ALA* 3.9 8.5 - - - +
125A PHE* 1.3 76.3 - - - +
127A SER* 1.4 61.4 + - - +
128A ILE 3.3 1.2 + - - -
129A PHE* 3.4 25.1 + - + +
130A ARG* 4.5 9.3 - - - +
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TRP* 3.6 25.1 - - - +
115A ARG* 3.0 27.0 + - - -
118A MET* 5.5 0.9 - - - -
123A ALA 3.2 16.0 + - - -
124A CYS* 2.7 20.5 + - - -
125A PHE 3.3 0.2 - - - -
126A LYS* 1.4 74.3 - - - +
128A ILE* 1.4 55.1 + - - +
129A PHE 3.2 0.4 - - - -
130A ARG* 3.0 26.3 + - - +
132A HIS* 2.8 25.3 + - - -
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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