Contacts of the helix formed by residues 128 - 140 (chain B) in PDB entry 6WNX
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 THR 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B ASP 4.1 1.2 + - - -
127B PHE* 1.3 76.4 - - - +
129B GLU* 1.3 68.9 + - + +
130B GLU* 3.5 22.2 - - + +
131B GLU* 3.4 22.6 + - - -
132B GLU* 3.2 19.9 + - - +
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Residues in contact with GLU 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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127B PHE 3.8 0.4 + - - +
128B THR* 1.3 78.1 - - + +
130B GLU* 1.3 61.6 + - - +
132B GLU* 3.8 9.1 - - - +
133B ALA* 3.2 22.5 + - - +
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Residues in contact with GLU 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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128B THR* 3.1 15.1 - - + +
129B GLU* 1.3 73.3 - - - +
131B GLU* 1.3 68.4 + - - +
132B GLU 2.9 2.6 + - - -
133B ALA* 3.1 16.8 + - - +
134B GLN* 3.2 13.3 + - + +
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Residues in contact with GLU 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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39A LYS* 3.0 37.7 + - - +
42A GLN* 5.5 1.6 - - - +
126B ASP 4.8 1.0 - - - +
127B PHE* 4.0 18.3 - - + -
128B THR* 3.4 36.0 + - - +
130B GLU* 1.3 81.2 - - - +
132B GLU* 1.3 60.1 + - - +
134B GLN* 3.4 9.4 - - - +
135B VAL* 3.3 29.3 + - + +
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Residues in contact with GLU 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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36A LEU* 4.0 20.3 - - + +
118B ARG* 4.2 8.2 + - - -
125B ASN* 3.0 32.4 + - - -
127B PHE* 4.1 12.6 - - + +
128B THR 3.2 15.7 + - - +
129B GLU* 3.8 9.8 - - - +
130B GLU 2.9 2.2 + - - -
131B GLU* 1.3 76.8 - - - +
133B ALA* 1.3 61.2 + - - +
134B GLN 3.1 1.1 - - - -
135B VAL* 3.1 5.2 + - - +
136B ARG* 2.9 59.7 + - + +
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Residues in contact with ALA 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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129B GLU 3.2 11.0 + - - +
130B GLU* 3.1 11.6 + - - +
132B GLU* 1.3 78.0 - - - +
134B GLN* 1.3 55.2 + - - +
136B ARG* 3.5 10.0 + - - +
137B LYS* 3.0 30.8 + - - +
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Residues in contact with GLN 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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130B GLU* 3.2 10.5 + - + +
131B GLU* 3.4 15.3 - - - +
133B ALA* 1.3 78.4 - - - +
135B VAL* 1.3 58.4 + - + +
137B LYS* 3.5 17.4 + - - +
138B GLU* 3.0 60.9 + - - +
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Residues in contact with VAL 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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35A GLU* 4.3 10.5 - - + +
36A LEU* 3.8 28.3 - - + -
42A GLN* 3.9 22.4 - - - +
93A ARG* 3.7 17.0 - - - +
127B PHE* 5.3 7.0 - - + -
131B GLU* 3.3 17.7 - - + +
132B GLU* 3.1 6.1 + - - +
134B GLN* 1.3 74.6 - - + +
136B ARG* 1.3 67.5 + - - +
138B GLU* 3.0 16.4 + - - +
139B ASN* 2.9 29.9 + - - +
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Residues in contact with ARG 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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36A LEU* 4.0 27.5 - - + +
114B PRO* 4.0 16.0 - - - +
115B GLU* 3.0 31.5 + - - -
118B ARG* 5.3 0.6 - - - +
132B GLU* 2.9 46.5 + - - +
133B ALA* 3.6 9.2 - - - +
135B VAL* 1.3 77.0 - - - +
137B LYS* 1.3 54.4 - - - +
139B ASN* 3.4 2.5 + - - +
140B GLN* 2.9 52.9 + - - +
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Residues in contact with LYS 137 (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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133B ALA 3.0 17.3 + - - +
134B GLN* 3.5 20.2 - - - +
136B ARG* 1.3 73.9 - - - +
138B GLU* 1.3 66.1 + - + +
139B ASN 3.1 1.7 + - - -
140B GLN* 3.2 25.0 + - - +
141B TRP 4.8 0.5 + - - -
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Residues in contact with GLU 138 (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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93A ARG* 2.6 43.7 + - - +
97A PRO* 5.4 1.4 - - - +
134B GLN* 3.0 41.0 + - - +
135B VAL* 3.0 19.0 + - - +
137B LYS* 1.3 81.9 - - + +
139B ASN* 1.3 57.4 + - - +
140B GLN 3.6 0.2 - - - -
141B TRP* 3.2 19.1 + - - -
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Residues in contact with ASN 139 (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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32A CYS* 3.2 41.9 + - + +
35A GLU* 2.7 23.9 + - - +
36A LEU* 4.5 5.9 - - + +
51A TRP* 5.6 0.5 - - - -
93A ARG* 2.7 28.6 + - - +
135B VAL* 2.9 20.4 + - - +
136B ARG* 3.7 4.5 - - - +
137B LYS 3.1 0.2 - - - -
138B GLU* 1.3 76.7 - - - +
140B GLN* 1.3 56.2 + - - +
141B TRP* 3.0 18.4 + - - +
142B CYS* 3.0 31.0 + - - -
143B GLU* 5.6 0.5 - - - +
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Residues in contact with GLN 140 (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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136B ARG* 2.9 49.1 + - - +
137B LYS* 3.2 15.9 + - - +
138B GLU 3.6 0.2 - - - -
139B ASN* 1.3 76.3 - - - +
141B TRP* 1.3 62.0 + - - +
142B CYS 3.2 0.4 - - - -
143B GLU* 3.1 28.7 + - + +
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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