Contacts of the helix formed by residues 140 - 151 (chain B) in PDB entry 4XH9
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 LYS 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B ARG* 3.8 3.8 - - - +
128B ARG* 6.0 5.2 - - - +
137B GLU* 3.3 32.3 + - - -
138B PRO 4.2 5.4 - - - +
139B VAL* 1.3 80.0 - - - +
141B PRO* 1.3 72.9 - - + +
142B GLU* 3.2 24.5 - - - +
143B GLU* 2.7 42.7 + - + +
144B GLY 3.5 1.7 + - - -
156B TYR* 4.9 0.2 + - - -
158B GLU* 4.6 0.6 - - - +
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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
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122B ARG* 3.4 30.9 - - - +
140B LYS* 1.3 84.7 - - + +
142B GLU* 1.3 77.4 + - - +
144B GLY 3.2 2.4 + - - -
145B ARG* 3.1 40.2 + - - +
156B TYR* 3.5 8.7 - - + -
158B GLU* 3.4 20.4 - - - +
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Residues in contact with GLU 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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140B LYS* 3.2 29.2 - - - +
141B PRO* 1.3 95.5 - - - +
143B GLU* 1.3 58.5 + - + +
145B ARG* 3.3 28.5 + - - +
146B ASP* 2.9 41.7 + - - +
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Residues in contact with GLU 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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92B LEU* 4.3 17.3 - - + +
137B GLU* 5.3 2.8 - - - +
138B PRO 4.2 1.9 - - - +
139B VAL* 3.6 15.9 - - + +
140B LYS* 2.7 51.6 + - + +
142B GLU* 1.3 78.8 - - + +
144B GLY* 1.3 57.2 + - - +
146B ASP* 3.8 7.2 - - - +
147B MET* 2.9 30.3 + - - +
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Residues in contact with GLY 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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84B PHE* 4.5 6.7 - - - -
92B LEU* 5.4 0.2 - - - -
114B LEU* 3.3 10.2 - - - +
139B VAL* 4.6 1.4 - - - +
140B LYS 3.5 4.0 + - - -
141B PRO 3.2 3.6 + - - -
143B GLU* 1.3 76.7 - - - +
145B ARG* 1.3 58.8 + - - +
147B MET* 3.4 1.1 + - - -
148B ALA* 2.9 30.8 + - - +
156B TYR* 3.5 34.7 - - - -
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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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141B PRO* 3.1 28.3 + - - +
142B GLU* 3.3 42.8 + - - +
144B GLY* 1.3 75.4 - - - +
146B ASP* 1.3 64.9 + - - +
148B ALA* 3.4 3.6 + - - +
149B ASN* 3.2 29.3 + - - +
156B TYR* 3.8 22.1 - - + +
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Residues in contact with ASP 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 GLU* 2.9 28.8 + - - +
143B GLU* 3.8 6.1 - - - +
145B ARG* 1.3 77.0 - - - +
147B MET* 1.3 64.8 + - - +
149B ASN* 3.1 16.0 + - - +
150B ARG* 3.0 40.3 + - + +
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Residues in contact with MET 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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487A PHE* 5.6 0.2 - - - -
92B LEU* 4.1 30.5 - - + +
93B GLU* 5.5 1.6 - - - -
95B ILE* 4.4 7.2 - - + -
96B PRO* 3.8 42.8 - - + -
114B LEU* 3.8 18.8 - - + -
143B GLU 2.9 18.5 + - - +
146B ASP* 1.3 73.4 - - - +
148B ALA* 1.3 66.4 + - - +
150B ARG* 3.1 13.5 + - - +
151B ILE* 3.0 36.0 + - + +
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Residues in contact with ALA 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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114B LEU* 3.6 9.1 - - + +
144B GLY 2.9 18.3 + - - +
145B ARG 3.6 6.7 - - - +
146B ASP 3.2 0.2 - - - -
147B MET* 1.3 75.8 - - - +
149B ASN* 1.3 61.8 + - - +
151B ILE* 3.6 0.8 + - - -
152B GLY 3.2 2.9 + - - -
153B ALA* 2.8 51.7 + - + +
155B GLY* 4.3 2.7 - - - -
156B TYR* 3.7 24.5 - - + +
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Residues in contact with ASN 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 ARG* 3.2 20.4 + - - +
146B ASP* 3.1 16.0 + - - +
148B ALA* 1.3 76.5 - - - +
150B ARG* 1.3 78.4 + - - +
152B GLY* 3.3 12.0 + - - -
153B ALA 5.6 1.2 - - - +
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Residues in contact with ARG 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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487A PHE* 3.4 21.8 - - + -
146B ASP* 3.0 41.4 + - + +
147B MET* 3.1 20.6 + - - +
149B ASN* 1.3 91.1 - - - +
151B ILE* 1.3 61.6 + - + +
152B GLY 3.3 0.6 + - - -
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Residues in contact with ILE 151 (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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487A PHE* 4.0 17.7 - - + -
82B MET* 4.5 3.8 - - + -
95B ILE* 4.2 14.1 - - + -
96B PRO* 5.0 0.7 - - + -
100B THR* 3.5 33.4 - - + +
104B LYS* 2.9 28.1 + - - -
112B ILE* 4.3 18.5 - - + +
114B LEU* 4.3 17.0 - - + -
147B MET* 3.0 36.8 + - + +
148B ALA 3.7 6.5 - - - +
150B ARG* 1.3 77.4 - - - +
152B GLY* 1.3 59.9 + - - +
153B ALA* 3.8 17.3 - - + +
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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