Contacts of the helix formed by residues 138 - 150 (chain B) in PDB entry 4OUH
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 ILE 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B LEU* 5.0 9.6 - - + -
30B VAL* 5.4 4.3 - - + -
91B LEU* 4.3 17.9 - - + +
93B VAL* 3.5 36.8 - - + -
102B ALA* 4.2 16.7 - - - +
103B ASP 4.3 0.7 - - - -
104B LEU* 4.0 29.6 - - + -
134B ILE* 2.8 22.7 + - + +
137B GLY* 1.3 85.5 - - - +
139B ILE* 1.3 79.7 + - + +
140B THR 3.6 0.4 - - - -
141B PRO* 3.3 9.1 - - - +
142B ILE* 3.1 24.3 + - + +
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 4.1 19.1 - - - +
30B VAL* 4.4 17.3 - - + -
33B HIS* 3.6 42.0 - - + +
35B TYR* 6.1 6.1 - - + -
134B ILE* 3.1 19.6 + - + +
135B VAL* 3.5 18.8 - - + +
138B ILE* 1.3 86.2 - - + +
140B THR* 1.3 66.1 + - - +
142B ILE* 3.1 9.7 + - + +
143B HIS* 3.0 24.6 + - + +
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Residues in contact with THR 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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135B VAL* 2.6 37.0 + - - +
136B SER* 4.1 8.4 - - - +
139B ILE* 1.3 73.1 - - - +
141B PRO* 1.3 67.9 - - + +
143B HIS* 3.2 8.1 + - + +
144B GLU* 2.9 54.5 + - + +
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Residues in contact with PRO 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ALA* 3.9 15.3 - - + -
136B SER 3.3 22.2 - - - +
137B GLY* 3.4 17.7 - - - +
138B ILE 3.3 13.2 - - - +
140B THR* 1.3 89.7 - - + +
142B ILE* 1.3 61.5 + - + +
144B GLU* 3.4 9.7 + - + +
145B GLN* 3.0 24.7 + - - +
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Residues in contact with ILE 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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35B TYR* 3.6 21.5 - - + +
76B ARG* 2.8 39.3 + - - +
78B LEU* 3.8 15.7 - - + -
93B VAL* 3.8 36.8 - - + +
95B GLU* 3.7 9.0 - - + +
101B VAL 5.8 1.8 - - - +
102B ALA* 4.5 11.0 - - + +
138B ILE* 3.1 20.6 + - + +
139B ILE* 3.1 9.7 + - + +
141B PRO* 1.3 76.5 - - - +
143B HIS* 1.3 61.7 + - - +
145B GLN* 3.3 16.3 + - - +
146B TRP 3.1 7.6 + - - -
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Residues in contact with HIS 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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76B ARG* 4.7 3.0 + - - +
139B ILE* 3.0 16.6 + - + +
140B THR* 3.7 11.4 - - + +
142B ILE* 1.3 79.3 - - - +
144B GLU* 1.3 58.8 + - + +
146B TRP* 3.2 27.4 - + - +
147B GLU* 3.1 48.6 + - + +
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Residues in contact with GLU 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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140B THR* 2.9 43.1 + - + +
141B PRO* 3.9 8.5 - - + +
143B HIS* 1.3 76.8 - - + +
145B GLN* 1.3 64.8 + - - +
146B TRP 3.0 1.6 - - - -
147B GLU* 3.1 22.7 + - - +
148B LYS* 3.1 25.2 + - - +
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Residues in contact with GLN 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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76B ARG* 4.5 0.2 - - - -
95B GLU* 2.9 46.5 + - - +
101B VAL 5.4 8.6 + - - +
141B PRO 3.0 13.0 + - - +
142B ILE* 3.5 15.8 - - - +
144B GLU* 1.3 76.2 - - - +
146B TRP* 1.3 61.0 + - - +
148B LYS* 3.2 39.4 - - - +
149B ALA* 3.6 12.1 + - + +
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Residues in contact with TRP 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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71B TYR* 6.2 2.0 - - - -
76B ARG* 3.1 56.1 - - + +
95B GLU* 4.6 2.2 - - - -
142B ILE 3.1 4.0 + - - +
143B HIS* 3.2 35.2 - + - +
144B GLU 3.0 0.2 - - - -
145B GLN* 1.3 78.5 - - - +
147B GLU* 1.3 59.5 + - + +
149B ALA* 4.0 4.2 - - + -
150B ASN* 3.1 49.0 + - - -
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Residues in contact with GLU 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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143B HIS* 3.1 37.4 + - + +
144B GLU* 3.1 28.1 + - - +
146B TRP* 1.3 81.7 - - + +
148B LYS* 1.3 57.6 + - - +
150B ASN* 2.9 28.6 + - - +
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Residues in contact with LYS 148 (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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144B GLU 3.1 12.1 + - - +
145B GLN* 3.2 40.1 - - - +
147B GLU* 1.3 78.3 - - - +
149B ALA* 1.3 62.8 + - + +
150B ASN* 3.3 8.8 + - - +
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Residues in contact with ALA 149 (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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145B GLN* 3.6 14.8 + - + +
146B TRP* 4.6 3.6 - - + +
147B GLU 3.4 0.2 - - - -
148B LYS* 1.3 82.9 - - + +
150B ASN* 1.3 72.0 + - - +
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Residues in contact with ASN 150 (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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146B TRP* 3.1 47.0 + - - -
147B GLU* 2.9 23.1 + - - +
148B LYS 3.3 9.8 + - - +
149B ALA* 1.3 83.7 - - - +
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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