Contacts of the helix formed by residues 126 - 136 (chain B) in PDB entry 6W4E
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 ASP 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B ARG* 4.0 12.8 - - - +
124B THR 3.4 4.0 + - - +
125B VAL* 1.3 75.2 - - - +
127B THR* 1.3 79.7 + - - +
128B LYS* 2.7 53.5 + - + +
129B GLN* 2.8 31.2 + - + +
130B ALA* 3.2 9.2 + - - +
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ARG* 3.2 14.6 + - - +
126B ASP* 1.3 78.0 + - - +
128B LYS* 1.3 62.3 + - - +
130B ALA* 3.4 6.1 + - - +
131B GLN* 3.0 44.1 + - - +
141B PHE* 3.7 15.7 - - + -
143B GLU* 2.7 34.3 + - + +
154C ASP* 4.9 5.6 - - + +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ASP* 2.7 44.8 + - + +
127B THR* 1.3 79.1 - - - +
129B GLN* 1.3 66.7 + - + +
131B GLN* 3.4 5.4 + - - +
132B ASP* 2.9 30.4 + - - +
45C VAL* 5.5 4.9 + - - -
47C ASP* 3.1 55.6 + - + +
157C TYR* 6.1 4.8 - - + -
161C ARG* 4.9 1.1 - - - +
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B THR* 5.7 4.8 - - - +
90B PHE* 3.9 20.2 - - + -
124B THR 3.3 6.9 - - - +
125B VAL* 3.2 18.7 - - + -
126B ASP* 2.8 38.8 + - + +
128B LYS* 1.3 80.9 - - + +
130B ALA* 1.3 59.9 + - - +
132B ASP* 3.5 8.0 - - - +
133B LEU* 2.9 30.7 + - - +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 4.1 14.4 - - + -
90B PHE* 3.8 11.4 - - - -
113B LEU* 3.6 8.6 - - + +
125B VAL* 4.2 4.9 - - + -
126B ASP 3.2 16.9 + - - +
127B THR 3.7 4.3 - - - +
129B GLN* 1.3 79.5 - - - +
131B GLN* 1.3 58.3 + - - +
133B LEU* 3.5 1.6 + - - +
134B ALA* 3.1 27.5 + - - +
141B PHE* 3.7 32.8 - - + -
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B THR* 3.0 30.0 + - - +
128B LYS 4.0 2.2 - - - +
130B ALA* 1.3 74.5 - - - +
132B ASP* 1.3 60.3 + - - +
134B ALA* 3.8 6.6 - - - +
135B ARG* 2.9 32.7 + - - +
141B PHE* 3.4 35.3 + - + +
47C ASP* 5.4 0.2 - - - +
154C ASP* 2.7 33.8 + - - +
158C THR* 4.9 1.2 + - - -
161C ARG* 2.9 38.8 + - - +
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Residues in contact with ASP 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LYS 2.9 18.5 + - - +
129B GLN* 3.5 10.8 - - - +
130B ALA 3.2 0.2 - - - -
131B GLN* 1.3 79.1 - - - +
133B LEU* 1.3 62.2 + - - +
135B ARG* 2.7 54.9 + - - +
136B SER* 3.9 6.9 + - - -
47C ASP* 4.8 7.7 - - + +
164C ARG* 5.5 0.3 + - - -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PHE* 3.9 37.2 - - + +
91B GLU* 6.3 0.4 - - - -
93B ILE* 5.8 2.9 - - + -
94B HIS* 5.3 9.9 - - + +
113B LEU* 5.7 3.8 - - + -
129B GLN 2.9 17.5 + - - +
130B ALA 3.9 3.6 - - - +
132B ASP* 1.3 78.0 + - - +
134B ALA* 1.3 65.4 + - - +
135B ARG 3.2 0.9 + - - -
136B SER* 3.3 15.7 + - - -
137B TYR* 3.5 45.6 + - + +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 3.9 14.3 - - + +
130B ALA 3.1 15.8 + - - +
131B GLN* 4.0 7.0 - - - +
133B LEU* 1.3 76.3 - - - +
135B ARG* 1.3 58.8 + - - +
137B TYR* 3.0 13.2 + - - +
138B GLY 2.9 24.8 + - - -
139B ILE* 3.3 37.1 + - + +
141B PHE* 4.4 6.5 - - + -
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Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B GLN 2.9 17.3 + - - +
132B ASP* 2.7 59.0 + - - +
133B LEU 3.1 0.4 - - - -
134B ALA* 1.3 78.1 - - - +
136B SER* 1.3 63.8 + - - +
137B TYR 3.1 0.9 + - - -
138B GLY* 3.3 12.4 + - - +
139B ILE 5.2 0.4 - - - -
47C ASP* 3.5 26.7 + - - -
161C ARG* 3.9 20.0 + - - +
164C ARG* 4.2 10.9 - - - +
165C LYS* 3.7 45.7 + - + +
168C GLU* 5.8 6.0 + - - -
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ARG* 4.9 4.5 + - - -
132B ASP 3.9 8.2 + - - -
133B LEU* 3.3 10.7 + - - -
134B ALA 3.3 0.6 - - - -
135B ARG* 1.3 79.9 + - - +
137B TYR* 1.3 69.5 + - - +
168C GLU* 5.5 2.3 + - - -
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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