Contacts of the helix formed by residues 132 - 147 (chain B) in PDB entry 3W31
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 ASN 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B GLN* 2.8 37.7 + - + +
131B THR* 1.3 81.6 + - - +
133B GLU* 1.3 64.9 + - - +
134B ALA* 3.0 4.9 + - - -
135B GLN* 3.1 34.9 + - + +
136B ALA 2.9 17.5 + - - +
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Residues in contact with GLU 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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128B GLN 3.4 1.7 + - - -
129B TRP* 3.3 36.9 + - + +
130B LYS 5.4 1.1 - - - +
131B THR 3.0 9.7 + - - +
132B ASN* 1.3 73.4 - - - +
134B ALA* 1.3 68.1 + - - +
136B ALA* 3.2 4.6 + - - +
137B ILE* 3.0 35.7 + - + +
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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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132B ASN* 3.0 1.8 + - - +
133B GLU* 1.3 83.3 + - - +
135B GLN* 1.3 68.5 + - + +
137B ILE* 3.1 12.8 + - - +
138B GLU* 3.3 16.6 + - - +
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Residues in contact with GLN 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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128B GLN* 5.2 0.4 - - - +
132B ASN* 3.1 43.9 + - + +
134B ALA* 1.3 78.6 - - + +
136B ALA* 1.3 64.1 + - - +
138B GLU* 3.1 12.6 + - - +
139B THR* 2.9 29.1 + - - +
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Residues in contact with ALA 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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76B TYR* 3.5 25.1 - - + -
128B GLN* 3.7 8.7 - - + +
129B TRP* 3.7 43.8 - - + +
132B ASN* 2.9 13.0 + - - +
133B GLU* 3.4 8.7 - - - +
135B GLN* 1.3 77.5 - - - +
137B ILE* 1.3 61.6 + - - +
139B THR* 3.4 1.4 + - - -
140B ALA* 3.0 18.7 + - - +
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Residues in contact with ILE 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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46B PRO* 3.4 29.8 - - + -
129B TRP* 3.7 21.1 - - + +
133B GLU* 3.0 31.1 + - + +
134B ALA* 3.4 8.7 - - - +
136B ALA* 1.3 72.3 - - - +
138B GLU* 1.3 68.3 + - + +
140B ALA* 2.7 19.0 + - - +
141B ARG* 2.9 48.8 + - - +
203B IOD 4.5 3.1 - - + -
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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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134B ALA 3.3 11.2 + - - +
135B GLN* 3.2 14.4 - - - +
137B ILE* 1.3 79.5 - - + +
139B THR* 1.3 63.3 + - - +
141B ARG* 3.5 28.6 + - - +
142B ALA* 3.1 21.7 + - - +
145B ARG* 5.0 1.4 + - - -
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Residues in contact with THR 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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76B TYR* 3.9 27.4 + - + -
135B GLN* 2.9 16.2 + - - +
136B ALA* 3.5 9.3 - - - -
137B ILE 2.8 0.6 + - - -
138B GLU* 1.3 75.8 - - - +
140B ALA* 1.3 58.9 + - - +
142B ALA* 3.1 6.8 + - + +
143B TRP* 2.9 49.2 + - + +
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Residues in contact with ALA 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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46B PRO* 3.8 19.1 - - + -
47B PHE* 4.1 7.5 - - + -
76B TYR* 3.8 33.8 - - + +
129B TRP* 3.9 8.1 - - + -
136B ALA 3.0 12.6 + - - +
137B ILE 2.7 12.3 + - - +
139B THR* 1.3 67.9 - - - +
141B ARG* 1.3 66.1 + - - +
143B TRP* 3.1 3.2 + - - +
144B THR* 2.9 28.0 + - - -
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Residues in contact with ARG 141 (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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45B SER 4.9 1.2 + - - -
46B PRO* 3.5 24.7 + - - +
137B ILE* 2.9 34.5 + - + +
138B GLU* 3.5 28.7 + - - +
140B ALA* 1.3 77.9 - - - +
142B ALA* 1.3 61.2 + - - +
144B THR* 3.3 5.4 + - - -
145B ARG* 3.3 41.8 + - - +
203B IOD 3.0 31.3 - - - +
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Residues in contact with ALA 142 (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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138B GLU 3.1 13.8 + - - +
139B THR* 3.1 10.3 + - + +
141B ARG* 1.3 78.6 - - - +
143B TRP* 1.3 61.8 + - + +
145B ARG* 3.2 29.6 + - - +
146B LEU* 3.1 26.0 + - - +
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Residues in contact with TRP 143 (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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52B PHE* 5.8 0.6 - - - -
74B LYS* 4.9 8.9 - - + +
75B ILE* 3.7 19.5 - - - -
76B TYR* 3.4 53.8 - + + +
125B VAL* 6.1 1.1 - - + -
139B THR* 2.9 32.3 + - + +
140B ALA* 3.1 10.3 + - - +
142B ALA* 1.3 78.6 - - + +
144B THR* 1.3 60.4 + - - +
146B LEU* 3.7 4.9 - - + +
147B TYR* 2.9 62.6 + + + +
148B ALA* 3.6 0.5 + - - +
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Residues in contact with THR 144 (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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46B PRO 3.5 4.4 + - - -
47B PHE* 3.4 50.5 - - - +
48B GLU 4.2 4.3 - - - +
49B GLY 4.5 0.9 - - - -
50B GLY* 3.6 20.0 - - - +
52B PHE* 3.9 4.6 - - + -
140B ALA 2.9 15.9 + - - -
141B ARG 3.5 9.4 - - - -
142B ALA 3.2 0.2 - - - -
143B TRP* 1.3 78.8 - - - +
145B ARG* 1.3 58.6 + - - +
148B ALA* 3.1 29.3 + - + +
149B MET* 3.3 11.7 + - - +
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Residues in contact with ARG 145 (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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138B GLU 5.0 2.0 + - - -
141B ARG* 3.3 30.3 + - - +
142B ALA* 3.2 37.0 + - - +
143B TRP 3.2 0.4 - - - -
144B THR* 1.3 81.9 - - - +
146B LEU* 1.3 60.3 + - - +
149B MET* 3.7 43.6 - - + +
150B ASN* 5.2 1.7 + - - -
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Residues in contact with LEU 146 (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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142B ALA 3.1 15.3 + - - +
143B TRP* 4.0 5.6 - - + +
144B THR 3.3 0.2 - - - -
145B ARG* 1.3 80.4 - - - +
147B TYR* 1.3 102.6 + - + +
149B MET 3.9 9.0 - - - +
151B ASN* 5.5 0.3 - - - +
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Residues in contact with TYR 147 (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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73B THR* 3.7 10.4 - - + +
74B LYS* 3.9 57.7 - - + +
143B TRP* 2.9 53.2 + + + +
146B LEU* 1.3 107.0 - - + +
148B ALA* 1.3 60.8 + - - +
149B MET 3.4 1.1 - - - -
151B ASN* 3.2 25.7 + - - +
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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