Contacts of the helix formed by residues 89 - 96 (chain L) in PDB entry 3EXG
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 ALA 89 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59L GLU* 3.6 15.7 - - + +
60L MET* 3.9 10.3 - - - +
63L ALA* 3.5 30.3 - - + -
80L PHE* 3.9 14.1 - - + -
86L SER 2.8 8.8 + - - +
88L GLN* 1.3 76.1 - - - +
90L ILE* 1.3 55.7 + - - +
91L ASP 3.2 3.1 - - - -
92L GLN* 2.7 26.4 + - + +
93L VAL* 3.2 11.9 + - - +
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Residues in contact with ILE 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J MET* 4.0 17.7 - - + +
90J ILE* 3.9 18.8 - - + -
135J TRP* 3.8 22.4 - - + -
86L SER 2.9 9.8 + - - +
87L MET* 3.7 18.6 - - + +
88L GLN 3.3 2.6 - - - -
89L ALA* 1.3 75.3 - - - +
91L ASP* 1.3 64.0 + - - +
93L VAL* 4.0 3.8 - - + +
94L ILE* 3.0 32.7 + - + +
132L PHE* 5.5 0.4 - - + -
135L TRP* 4.1 19.7 - - + -
136L TYR* 3.4 42.8 - - + +
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Residues in contact with ASP 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J ASN 5.3 0.5 - - - +
87J MET* 3.6 20.7 + - + +
88J GLN* 4.2 12.1 - - + +
137K ILE* 3.5 27.3 - - - +
140K ALA* 3.8 14.0 - - - +
174K GLN* 4.8 0.2 + - - -
60L MET* 3.9 24.3 - - + +
88L GLN 4.7 0.4 + - - -
89L ALA 3.2 0.6 - - - -
90L ILE* 1.3 80.0 - - - +
92L GLN* 1.3 70.9 + - - +
95L ASN* 3.0 46.8 + - - +
96L SER* 3.6 3.7 + - - -
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Residues in contact with GLN 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140K ALA* 3.7 18.7 + - - +
143K PRO* 4.1 1.6 - - - +
144K LEU* 3.9 3.5 - - - +
174K GLN* 3.1 25.9 + - - -
60L MET* 3.5 29.3 + - - +
63L ALA* 4.2 10.5 - - + +
64L GLY* 3.6 30.9 - - - +
67L VAL* 4.5 6.5 - - + +
89L ALA 2.7 16.7 + - - +
91L ASP* 1.3 81.1 - - - +
93L VAL* 1.3 61.0 + - + +
96L SER* 2.9 48.0 + - - -
97L ALA* 3.1 6.8 + - - +
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Residues in contact with VAL 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L PHE* 4.8 7.9 - - + -
86L SER 5.8 0.2 - - - +
89L ALA 3.2 12.4 + - - +
90L ILE* 4.0 8.7 - - - +
92L GLN* 1.3 77.0 - - - +
94L ILE* 1.3 62.5 + - + +
97L ALA* 3.3 7.4 - - + +
98L ALA* 3.2 24.3 + - - +
114L PHE* 3.6 46.4 - - + -
136L TYR* 4.2 22.7 - - + +
142L LEU* 4.0 28.5 - - + -
168L VAL* 4.5 1.8 - - + -
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Residues in contact with ILE 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J MET* 4.0 12.1 - - - -
130J GLN* 3.6 24.9 - - - +
135J TRP* 3.9 20.2 - - + -
90L ILE* 3.0 23.7 + - + +
93L VAL* 1.3 90.0 - - + +
95L ASN* 1.3 65.3 + - - +
96L SER 3.6 0.3 + - - -
98L ALA* 3.4 16.5 - - + +
99L LYS* 3.5 22.3 + - - +
136L TYR* 4.8 3.4 - - + -
139L CYS* 3.3 34.1 - - + -
142L LEU* 4.0 19.3 - - + -
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Residues in contact with ASN 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J ASN* 4.2 7.7 + - - +
87J MET* 3.0 25.3 - - - +
127J GLN* 2.6 50.6 + - - +
130J GLN* 5.4 0.2 + - - -
137K ILE* 3.5 23.5 - - + +
91L ASP* 3.0 23.9 + - - +
94L ILE* 1.3 78.5 - - - +
96L SER* 1.3 60.2 + - - +
99L LYS* 3.2 36.8 + - - +
100L THR* 4.2 4.3 + - - -
103L MET* 4.4 0.5 - - - +
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Residues in contact with SER 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J GLN* 4.7 2.6 + - - +
135K ASN* 5.4 1.7 + - - -
140K ALA* 4.5 9.5 - - - +
144K LEU* 3.9 17.3 - - - +
67L VAL* 4.1 19.1 - - - +
71L MET* 5.3 2.8 - - - +
91L ASP* 3.6 1.5 + - - -
92L GLN* 2.9 37.5 + - - -
95L ASN* 1.3 80.0 - - - +
97L ALA* 1.3 60.6 + - - +
100L THR* 2.3 30.4 + - - +
110L VAL* 4.5 1.6 - - - +
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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