Contacts of the helix formed by residues 126 - 139 (chain J) in PDB entry 6QXT
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 PHE 126 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121J LEU* 2.9 17.4 + - + +
122J GLY* 4.6 2.1 + - - -
124J CYS* 4.7 5.2 - - + +
125J SER* 1.3 75.6 - - - +
127J PHE* 1.3 59.3 + - - +
128J GLU 3.5 1.1 - - - +
129J LYS* 4.0 22.0 - - + +
130J SER* 3.2 28.1 + - - -
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Residues in contact with PHE 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J SER 3.9 2.2 + - - -
126J PHE* 1.3 71.2 - - - +
128J GLU* 1.3 62.0 + - - +
130J SER* 4.5 1.3 - - - -
131J GLN* 2.8 32.2 + - - +
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Residues in contact with GLU 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J PHE* 3.5 0.4 - - - +
127J PHE* 1.3 78.8 - - - +
129J LYS* 1.3 58.4 + - - +
131J GLN* 3.8 4.2 - - - +
132J SER* 2.9 29.6 + - - -
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Residues in contact with LYS 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J LEU* 4.7 6.3 - - + -
126J PHE* 4.0 20.0 + - + +
127J PHE 3.4 0.4 - - - -
128J GLU* 1.3 78.0 - - - +
130J SER* 1.3 60.8 + - - +
132J SER* 3.3 5.6 + - - -
133J ILE* 2.9 29.9 + - - +
155J ILE 5.8 0.2 - - - +
159J THR* 4.6 20.2 - - - -
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Residues in contact with SER 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J SER* 3.5 28.9 - - - +
121J LEU* 3.6 15.1 - - - +
122J GLY* 3.8 7.2 - - - -
126J PHE 3.2 20.6 + - - -
127J PHE* 4.5 1.6 - - - -
129J LYS* 1.3 77.4 - - - +
131J GLN* 1.3 58.7 + - - +
133J ILE* 4.5 4.9 - - - -
134J MET* 2.9 29.8 + - - +
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Residues in contact with GLN 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J PHE 2.8 23.9 + - - +
128J GLU* 3.8 5.6 - - - +
130J SER* 1.3 74.4 - - - +
132J SER* 1.3 60.0 + - - +
134J MET* 3.5 7.0 + - - +
135J GLU* 2.9 27.4 + - - +
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Residues in contact with SER 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J GLU 2.9 18.5 + - - -
129J LYS* 3.3 6.3 + - - -
131J GLN* 1.3 74.6 - - - +
133J ILE* 1.3 60.4 + - - +
135J GLU* 3.1 9.5 + - - +
136J LEU* 2.9 27.2 + - - +
155J ILE* 6.4 2.2 - - - -
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Residues in contact with ILE 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J ILE* 4.8 9.0 - - + +
117J GLN* 5.2 6.1 - - + -
118J SER* 4.4 18.6 - - - +
121J LEU* 6.2 0.7 - - + -
129J LYS 2.9 17.2 + - - +
130J SER* 4.1 4.9 - - - +
132J SER* 1.3 75.9 - - - +
134J MET* 1.3 58.6 + - - +
136J LEU* 3.3 8.1 + - - +
137J TYR* 2.9 26.7 + - - +
152J SER* 5.2 16.1 - - - +
155J ILE* 6.5 0.7 - - + -
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Residues in contact with MET 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J SER* 4.2 11.6 - - - -
130J SER 2.9 20.8 + - - +
131J GLN* 3.7 7.4 - - - +
132J SER 3.2 0.2 - - - -
133J ILE* 1.3 75.3 - - - +
135J GLU* 1.3 59.1 + - - +
137J TYR* 3.2 9.6 + - - +
138J HIS* 2.9 28.6 + - - +
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Residues in contact with GLU 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J GLN 2.9 15.1 + - - +
132J SER* 3.1 12.3 + - - +
134J MET* 1.3 77.0 - - - +
136J LEU* 1.3 56.1 - - - +
138J HIS* 3.3 7.6 + - - +
139J GLY* 2.9 24.8 + - - -
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Residues in contact with LEU 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J ILE* 5.6 1.8 - - + -
132J SER 2.9 13.0 + - - +
133J ILE* 3.7 11.0 - - - +
135J GLU* 1.3 76.1 - - - +
137J TYR* 1.3 57.8 + - - +
139J GLY* 3.6 3.0 - - - +
140J LEU* 3.0 28.1 + - - +
148J ARG* 3.9 34.0 - - + +
151J HIS* 6.1 1.8 - - + -
152J SER* 4.9 7.6 - - - +
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Residues in contact with TYR 137 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111J ALA* 5.0 12.3 - - + +
114J ILE* 4.2 23.0 - - + +
115J LEU* 4.7 11.9 - - + +
133J ILE 2.9 14.1 + - - +
134J MET* 3.2 13.2 + - - +
136J LEU* 1.3 77.0 - - - +
138J HIS* 1.3 60.3 + - - +
139J GLY 3.4 0.2 + - - -
140J LEU* 3.5 18.4 + - - +
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Residues in contact with HIS 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J MET 2.9 16.0 + - - +
135J GLU* 3.8 7.0 - - - +
137J TYR* 1.3 76.5 - - - +
139J GLY* 1.3 57.5 + - - +
140J LEU 3.5 3.4 + - - +
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Residues in contact with GLY 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J GLU 2.9 15.4 + - - -
136J LEU* 3.3 5.6 + - - -
137J TYR 3.2 0.6 - - - -
138J HIS* 1.3 77.0 - - - +
140J LEU* 1.3 63.6 + - - +
141J GLU* 3.5 6.8 + - - +
146J SER* 5.5 5.9 - - - -
148J ARG* 5.2 4.6 - - - +
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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