Contacts of the helix formed by residues 115 - 126 (chain A) in PDB entry 3LX9
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 HIS 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A GLU* 2.7 35.1 + - - +
114A PRO* 1.3 85.4 - - + +
116A GLY* 1.3 64.2 + - - +
118A ARG* 5.8 0.2 - - - +
119A GLN* 3.3 53.7 + - + +
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Residues in contact with GLY 116 (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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66A GLU* 4.0 3.5 + - - +
108A ALA* 4.5 7.0 - - - -
113A PHE* 3.0 19.7 + - - +
114A PRO 3.3 1.4 + - - -
115A HIS* 1.3 84.0 - - - +
117A ILE* 1.3 67.0 + - - -
118A ARG* 3.4 2.4 + - - -
120A LEU* 3.4 17.8 + - - +
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Residues in contact with ILE 117 (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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91A ILE* 4.4 15.0 - - + -
95A TRP* 3.9 15.3 - - + -
108A ALA* 3.8 25.5 - - + +
113A PHE* 4.2 19.5 - - + -
116A GLY* 1.3 70.5 - - - -
118A ARG* 1.3 58.8 + - - +
120A LEU* 3.2 6.3 + - + +
121A ALA* 2.8 28.1 + - - +
131A LEU* 4.1 18.6 - - + -
133A ILE* 4.1 9.6 - - + -
162A TRP* 3.4 53.3 - - + +
164A VAL* 4.7 2.2 - - + -
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Residues in contact with ARG 118 (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 HIS 5.8 0.2 - - - +
116A GLY* 3.4 1.2 - - - -
117A ILE* 1.3 78.0 - - - +
119A GLN* 1.3 61.7 + - + +
121A ALA* 3.3 2.4 + - - +
122A ASN* 2.9 47.8 + - - +
161A ASP* 2.8 57.1 + - - -
162A TRP* 3.8 36.8 - - + +
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Residues in contact with GLN 119 (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 HIS* 3.3 55.7 + - + +
116A GLY 3.7 1.7 + - - +
117A ILE 3.4 0.4 - - - -
118A ARG* 1.3 80.0 - - + +
120A LEU* 1.3 61.3 + - - +
122A ASN* 3.4 11.5 + - - +
123A TYR* 2.8 29.5 + - - +
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Residues in contact with LEU 120 (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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66A GLU* 4.1 12.8 - - + +
69A PHE* 4.2 18.4 - - + -
70A MET* 3.8 31.4 - - + +
91A ILE* 3.8 28.9 - - + -
113A PHE* 4.1 22.0 - - + -
116A GLY 3.4 11.7 + - - +
117A ILE* 3.2 12.0 + - + +
119A GLN* 1.3 75.7 - - - +
121A ALA* 1.3 60.1 + - - +
123A TYR* 3.1 5.7 + - + +
124A VAL* 2.9 47.3 + - + +
131A LEU* 4.4 6.7 - - + -
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Residues in contact with ALA 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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117A ILE* 2.8 18.1 + - + +
118A ARG 3.5 0.9 - - - +
120A LEU* 1.3 73.0 - - - +
122A ASN* 1.3 55.9 + - - +
124A VAL* 3.3 1.6 + - - +
125A HIS* 2.8 40.7 + - + -
131A LEU* 3.5 26.3 - - + +
162A TRP 3.3 27.6 - - - +
163A GLY 4.1 13.2 - - - +
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Residues in contact with ASN 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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118A ARG* 2.9 39.0 + - - +
119A GLN* 3.6 11.1 - - - +
121A ALA* 1.3 78.8 - - - +
123A TYR* 1.3 58.2 + - - +
125A HIS* 3.3 14.3 + - - +
126A SER* 3.0 29.6 + - - -
162A TRP 4.8 2.6 + - - -
163A GLY* 6.1 0.2 - - - -
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Residues in contact with TYR 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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70A MET* 3.7 61.0 - - + +
73A ALA* 4.6 6.3 - - + -
74A GLU* 2.7 31.9 + - - +
119A GLN 2.8 17.6 + - - +
120A LEU* 3.1 8.5 + - - +
122A ASN* 1.3 75.1 - - - +
124A VAL* 1.3 66.7 + - + +
126A SER* 2.7 26.5 + - - -
127A LYS* 3.5 37.5 + - - +
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Residues in contact with VAL 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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73A ALA* 4.4 5.6 - - + -
89A LEU* 4.0 25.8 - - + -
120A LEU* 2.9 34.5 + - + +
121A ALA* 3.7 5.6 - - - +
123A TYR* 1.3 75.3 - - + +
125A HIS* 1.3 66.0 + - + +
127A LYS* 3.1 12.5 + - - +
129A LEU* 3.1 54.9 + - + +
130A LYS 3.8 17.0 - - - +
131A LEU* 4.2 12.6 - - + +
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Residues in contact with HIS 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 ALA* 2.8 29.6 + - + +
122A ASN* 3.7 13.6 + - - +
124A VAL* 1.3 76.7 - - + +
126A SER* 1.3 57.5 + - - +
127A LYS 3.1 0.2 - - - -
128A GLY* 3.0 19.2 + - - -
129A LEU 3.5 14.8 - - - -
130A LYS* 4.5 2.7 - - + -
131A LEU 4.5 2.8 + - - -
163A GLY* 3.0 26.8 + - - -
165A ASP* 2.7 31.2 + - - -
196A ARG* 3.5 14.6 - - - -
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Residues in contact with SER 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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122A ASN 3.0 14.1 + - - -
123A TYR* 2.7 27.8 + - - -
125A HIS* 1.3 75.4 - - - +
127A LYS* 1.3 66.1 + - - +
128A GLY 3.4 0.4 - - - -
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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