Contacts of the helix formed by residues 126 - 139 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121U LEU* 3.0 14.5 + - + +
122U GLY* 4.3 1.9 + - - -
124U CYS* 3.4 5.1 - - + +
125U SER* 1.3 75.8 - - - +
127U PHE* 1.3 59.8 + - - +
128U GLU 3.5 2.2 - - - +
129U LYS* 4.4 17.3 - - + +
130U SER* 3.2 26.9 + - - -
159U THR* 5.5 7.4 - - - -
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Residues in contact with PHE 127 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122U GLY* 6.0 1.1 - - - -
125U SER 3.9 3.6 + - - -
126U PHE* 1.3 71.6 - - - +
128U GLU* 1.3 60.6 + - - +
130U SER* 4.3 3.1 - - - -
131U GLN* 2.9 32.9 + - - +
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Residues in contact with GLU 128 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126U PHE* 3.5 0.8 - - - +
127U PHE* 1.3 75.1 - - - +
129U LYS* 1.3 60.1 + - - +
131U GLN* 3.4 5.5 + - - +
132U SER* 2.9 29.3 + - - -
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Residues in contact with LYS 129 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121U LEU* 4.8 4.7 - - + -
126U PHE* 4.1 14.9 + - + +
128U GLU* 1.3 78.1 - - - +
130U SER* 1.3 57.9 + - - +
132U SER* 3.3 7.1 + - - -
133U ILE* 2.9 30.0 + - - +
155U ILE* 4.8 15.0 - - + +
159U THR* 4.3 23.6 - - - -
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Residues in contact with SER 130 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118U SER* 3.2 34.6 - - - +
121U LEU* 3.6 12.7 - - - +
122U GLY* 3.7 8.3 - - - -
126U PHE 3.2 20.9 + - - -
127U PHE* 4.3 3.4 - - - -
129U LYS* 1.3 78.5 - - - +
131U GLN* 1.3 58.0 + - - +
133U ILE* 4.6 0.2 - - - -
134U MET* 2.9 29.6 + - - +
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Residues in contact with GLN 131 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127U PHE 2.9 21.9 + - - +
128U GLU* 3.7 4.9 - - - +
130U SER* 1.3 75.9 - - - +
132U SER* 1.3 58.9 + - - +
134U MET* 3.7 6.2 - - - +
135U GLU* 2.9 28.1 + - - +
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Residues in contact with SER 132 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128U GLU 2.9 17.4 + - - -
129U LYS* 3.3 7.4 + - - -
131U GLN* 1.3 74.5 - - - +
133U ILE* 1.3 60.3 + - - +
135U GLU* 3.1 8.5 + - - +
136U LEU* 2.9 28.1 + - - +
155U ILE* 5.7 6.3 - - - -
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Residues in contact with ILE 133 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114U ILE* 4.8 8.0 - - - +
117U GLN* 5.2 4.5 - - + -
118U SER* 3.8 24.9 - - - +
129U LYS 2.9 16.8 + - - +
132U SER* 1.3 77.5 - - - +
134U MET* 1.3 56.6 + - - +
136U LEU* 3.4 8.7 + - - +
137U TYR* 2.9 26.9 + - - +
152U SER* 4.7 20.1 - - - +
155U ILE* 5.6 5.8 - - + +
156U TYR* 6.3 1.8 - - + +
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Residues in contact with MET 134 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118U SER* 3.8 10.0 - - - -
130U SER 2.9 19.4 + - - +
131U GLN* 3.7 8.3 - - - +
132U SER 3.2 0.2 - - - -
133U ILE* 1.3 76.1 - - - +
135U GLU* 1.3 59.7 + - - +
137U TYR* 3.2 8.5 + - - +
138U HIS* 2.9 28.9 + - - +
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Residues in contact with GLU 135 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131U GLN 2.9 15.7 + - - +
132U SER* 3.1 11.6 + - - +
134U MET* 1.3 76.6 - - - +
136U LEU* 1.3 57.4 + - - +
138U HIS* 3.3 7.8 + - - +
139U GLY* 2.9 24.6 + - - -
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Residues in contact with LEU 136 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114U ILE* 5.8 0.4 - - - -
132U SER 2.9 13.7 + - - +
133U ILE* 3.7 11.0 - - - +
135U GLU* 1.3 75.9 - - - +
137U TYR* 1.3 62.1 + - - +
139U GLY* 3.3 3.0 + - - +
140U LEU* 3.1 19.9 + - - +
148U ARG* 3.7 37.8 - - + +
151U HIS* 5.9 2.0 - - + -
152U SER* 4.7 7.4 - - - +
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Residues in contact with TYR 137 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111U ALA* 5.0 12.4 - - + +
114U ILE* 4.3 21.5 - - + +
115U LEU* 4.7 13.2 - - + +
133U ILE 2.9 15.3 + - - +
134U MET* 3.2 12.5 + - - +
136U LEU* 1.3 77.7 - - - +
138U HIS* 1.3 61.1 + - - +
139U GLY 3.3 0.5 + - - -
140U LEU* 3.4 17.9 + - - +
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Residues in contact with HIS 138 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134U MET 2.9 15.4 + - - +
135U GLU* 3.9 7.0 - - - +
137U TYR* 1.3 77.1 - - - +
139U GLY* 1.3 57.5 + - - +
140U LEU 3.4 3.7 + - - +
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Residues in contact with GLY 139 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135U GLU 2.9 15.2 + - - -
136U LEU* 3.3 6.0 + - - -
137U TYR 3.2 0.4 - - - -
138U HIS* 1.3 77.2 - - - +
140U LEU* 1.3 63.2 + - - +
141U GLU* 3.6 6.4 + - - +
146U SER* 5.0 10.7 - - - -
148U ARG* 5.2 2.7 - - - -
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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