Contacts of the helix formed by residues 125 - 130 (chain A) in PDB entry 6BSL
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 GLN 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ILE* 3.8 7.2 - - + -
122A GLN* 3.0 37.9 + - + +
123A PRO 4.6 2.5 - - - +
124A GLY* 1.3 76.3 - - - +
126A GLU* 1.3 63.4 + - - +
127A TYR* 3.2 3.4 - - - -
128A ASN* 3.0 40.5 + - - +
129A PHE* 3.7 5.2 - - - -
157A PHE* 3.5 34.6 - - + -
305A EDO 2.6 44.5 + - - -
180B GLY 5.4 2.1 + - - +
181B GLN* 5.1 5.3 - - - +
182B ARG 5.7 0.8 - - - +
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Residues in contact with GLU 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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118A ARG 5.1 3.6 - - - +
121A ILE* 3.7 29.1 - - + +
122A GLN 4.1 4.2 - - - -
123A PRO* 3.7 15.6 - - - +
124A GLY* 2.9 23.3 + - - -
125A GLN* 1.3 78.7 + - - +
127A TYR* 1.3 57.1 + - - +
129A PHE* 2.9 29.5 + - - +
159A ARG* 5.8 0.5 + - - -
155B ASN* 2.9 24.4 + - - +
161B ILE* 3.9 32.0 - - + +
162B PHE* 3.4 24.3 - - + -
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Residues in contact with TYR 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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124A GLY 3.4 22.7 - - - -
125A GLN 4.1 0.9 - - - -
126A GLU* 1.3 78.5 + - - +
128A ASN* 1.3 86.7 + - - +
129A PHE 3.1 2.1 + - - -
130A LEU* 3.3 30.0 + - + +
304A EVV 4.1 32.9 - - + +
305A EDO 2.5 35.1 + - - -
154B ARG* 3.4 46.4 - - - +
155B ASN* 5.8 0.4 - - - +
161B ILE 5.6 0.4 + - - -
162B PHE* 4.0 13.6 - - + -
178B PRO* 4.6 4.1 - - + +
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Residues in contact with ASN 128 (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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103A HIS* 5.4 1.0 + - - -
105A HIS* 2.8 29.5 + - - -
106A THR* 4.2 5.4 - - - +
125A GLN* 3.0 45.3 + - - +
126A GLU 3.1 0.8 + - - -
127A TYR* 1.3 99.0 + - - +
129A PHE* 1.3 54.2 + - + +
130A LEU 3.5 0.9 - - - -
152A TYR* 3.4 16.6 + - - +
157A PHE* 3.5 28.4 - - + -
304A EVV 4.9 10.7 - - - +
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Residues in contact with PHE 129 (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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105A HIS* 3.8 16.8 - + + -
110A ARG* 2.7 35.1 + - - -
116A ILE* 3.8 20.0 - - + -
121A ILE* 3.7 32.8 - - + -
125A GLN 3.7 8.1 - - - -
126A GLU 2.9 13.1 + - - +
128A ASN* 1.3 81.3 - - + +
130A LEU* 1.3 60.2 + - - +
152A TYR* 3.9 11.9 - + - -
156A THR 3.4 22.9 - - - -
157A PHE* 3.8 17.3 - + + -
165A THR* 3.9 14.1 - - - -
166A ILE* 3.8 26.7 - - + -
301A SCN 4.1 18.8 - - - -
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Residues in contact with LEU 130 (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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106A THR* 3.4 18.2 - - - +
110A ARG* 4.3 0.4 - - - -
126A GLU 3.9 0.8 + - - -
127A TYR* 3.3 24.0 + - + +
128A ASN 4.7 0.2 - - - +
129A PHE* 1.3 79.4 - - - +
131A LYS* 1.3 71.1 + - - +
132A MET* 5.5 1.0 - - - +
301A SCN 3.8 10.3 - - - +
162B PHE* 3.6 51.1 - - + -
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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