Contacts of the helix formed by residues 126 - 139 (chain s) in PDB entry 6QY3
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 s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121s LEU* 3.0 16.2 + - + +
122s GLY* 4.6 2.1 + - - -
124s CYS* 4.7 4.9 - - + +
125s SER* 1.3 76.0 - - - +
127s PHE* 1.3 62.1 + - - +
128s GLU 3.6 0.4 - - - -
129s LYS* 4.0 21.8 - - + +
130s SER* 3.2 26.7 + - - -
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Residues in contact with PHE 127 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125s SER 3.9 3.4 + - - -
126s PHE* 1.3 70.8 - - - +
128s GLU* 1.3 61.5 + - - +
130s SER* 4.0 1.2 - - - -
131s GLN* 2.8 32.4 + - - +
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Residues in contact with GLU 128 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126s PHE 3.6 0.2 - - - -
127s PHE* 1.3 77.3 - - - +
129s LYS* 1.3 59.2 + - - +
131s GLN* 3.8 4.0 - - - +
132s SER* 2.9 30.5 + - - -
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Residues in contact with LYS 129 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121s LEU* 4.7 7.2 - - + -
126s PHE* 4.0 20.6 + - + +
128s GLU* 1.3 79.9 - - - +
130s SER* 1.3 56.9 + - - +
132s SER* 3.3 5.0 + - - -
133s ILE* 2.9 30.2 + - - +
159s THR* 4.6 20.6 - - - -
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Residues in contact with SER 130 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118s SER* 3.5 28.9 - - - +
121s LEU* 3.6 14.5 - - - +
122s GLY* 3.8 7.4 - - - -
126s PHE 3.2 19.5 + - - -
127s PHE* 4.5 1.3 - - - -
129s LYS* 1.3 78.2 - - - +
131s GLN* 1.3 58.3 + - - +
133s ILE* 4.4 4.7 - - - -
134s MET* 2.9 30.1 + - - +
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Residues in contact with GLN 131 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127s PHE 2.8 23.3 + - - +
128s GLU* 3.8 5.8 - - - +
130s SER* 1.3 76.3 - - - +
132s SER* 1.3 59.0 + - - +
134s MET* 3.7 5.4 - - - +
135s GLU* 2.9 27.0 + - - +
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Residues in contact with SER 132 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128s GLU 2.9 19.0 + - - -
129s LYS* 3.3 5.4 + - - -
131s GLN* 1.3 75.6 - - - +
133s ILE* 1.3 59.8 + - - +
135s GLU* 3.1 9.0 + - - +
136s LEU* 2.9 27.7 + - - +
155s ILE* 6.4 2.2 - - - -
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Residues in contact with ILE 133 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114s ILE* 4.8 9.5 - - + +
117s GLN* 5.2 5.4 - - + -
118s SER* 4.4 19.3 - - - +
121s LEU* 6.2 0.4 - - + -
129s LYS 2.9 16.8 + - - +
130s SER* 4.1 5.2 - - - +
132s SER* 1.3 76.0 - - - +
134s MET* 1.3 58.0 + - - +
136s LEU* 3.4 8.6 + - - +
137s TYR* 2.9 26.7 + - - +
152s SER* 5.2 15.4 - - - +
155s ILE* 6.5 0.7 - - + -
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Residues in contact with MET 134 (chain s).
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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118s SER* 4.2 10.9 - - - -
130s SER 2.9 21.0 + - - +
131s GLN* 3.7 7.2 - - - +
133s ILE* 1.3 75.4 - - - +
135s GLU* 1.3 59.5 + - - +
137s TYR* 3.2 9.3 + - - +
138s HIS* 2.9 28.1 + - - +
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Residues in contact with GLU 135 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131s GLN 2.9 16.3 + - - +
132s SER* 3.1 11.6 + - - +
134s MET* 1.3 76.2 - - - +
136s LEU* 1.3 56.8 + - - +
138s HIS* 3.3 7.8 + - - +
139s GLY* 2.9 24.3 + - - -
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Residues in contact with LEU 136 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114s ILE* 5.6 1.6 - - + -
132s SER 2.9 13.1 + - - +
133s ILE* 3.7 10.3 - - - +
134s MET 3.3 0.2 - - - -
135s GLU* 1.3 76.1 - - - +
137s TYR* 1.3 62.2 + - - +
139s GLY* 3.6 2.6 - - - +
140s LEU* 3.1 23.2 + - - +
148s ARG* 3.9 32.5 - - + +
151s HIS* 6.1 1.6 - - + -
152s SER* 4.9 8.1 - - - +
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Residues in contact with TYR 137 (chain s).
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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111s ALA* 5.0 12.4 - - + +
114s ILE* 4.2 21.7 - - + +
115s LEU* 4.7 11.7 - - + +
133s ILE 2.9 14.9 + - - +
134s MET* 3.2 12.5 + - - +
136s LEU* 1.3 77.9 - - - +
138s HIS* 1.3 60.8 + - - +
139s GLY 3.4 0.5 + - - -
140s LEU* 3.5 17.8 + - - +
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Residues in contact with HIS 138 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134s MET 2.9 16.0 + - - +
135s GLU* 3.8 6.3 - - - +
137s TYR* 1.3 75.8 - - - +
139s GLY* 1.3 57.9 + - - +
140s LEU 3.4 3.1 + - - +
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Residues in contact with GLY 139 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135s GLU 2.9 15.2 + - - -
136s LEU* 3.3 5.8 + - - -
137s TYR 3.2 0.4 - - - -
138s HIS* 1.3 78.1 - - - +
140s LEU* 1.3 62.9 + - - +
141s GLU* 3.5 6.6 + - - +
146s SER* 5.5 6.1 - - - -
148s ARG* 5.2 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