Contacts of the helix formed by residues 84 - 88 (chain D) 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 ASN 84 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ILE* 4.7 6.3 - - + +
91B ASP* 4.5 4.9 - - - +
95B ASN* 4.5 0.7 + - - -
99B LYS* 5.0 0.3 + - - -
82D THR* 3.1 23.2 + - - +
83D PHE* 1.3 79.8 - - - +
85D PHE* 1.3 61.9 - - + +
87D MET* 3.3 30.9 + - + +
88D GLN* 5.7 0.2 - - - +
118D ASN* 6.3 0.2 - - - +
119D GLY 5.2 2.8 + - - +
127D GLN 3.3 24.9 - - - +
128D HIS* 2.9 28.6 + - - +
129D SER* 3.6 0.4 + - - +
130D GLN* 3.0 42.1 + - - +
132D PHE* 4.0 8.7 - - - -
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Residues in contact with PHE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLY 4.2 7.2 - - - -
137A ILE* 3.7 35.2 - - + -
138A VAL* 5.1 7.0 - - + -
59D GLU* 3.6 38.6 - - + +
80D PHE* 4.8 3.6 - - + -
81D MET* 3.5 28.7 - - + +
82D THR* 3.2 41.5 + - + +
83D PHE 3.1 0.6 - - - -
84D ASN* 1.3 74.9 - - + +
86D SER* 1.3 59.4 + - - +
87D MET 3.0 6.9 + - - -
88D GLN* 3.4 17.7 + - - +
128D HIS* 3.6 28.3 - + - -
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Residues in contact with SER 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D PHE* 3.6 41.9 - - - -
82D THR 4.0 1.6 + - - -
83D PHE* 2.4 37.2 + - - -
85D PHE* 1.3 75.0 - - - +
87D MET* 1.3 60.8 + - - +
88D GLN 2.9 7.6 + - - -
89D ALA 2.9 12.5 + - - +
90D ILE* 3.0 13.9 + - - +
93D VAL* 6.0 0.2 - - - -
132D PHE* 4.9 1.9 - - - -
136D TYR* 3.0 25.4 + - - -
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Residues in contact with MET 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B MET 4.0 4.5 - - - +
88B GLN 5.1 1.2 - - - +
90B ILE* 3.4 23.8 + - + +
91B ASP* 3.8 24.2 + - + +
94B ILE* 4.0 25.6 - - + -
95B ASN* 2.8 36.8 - - - +
99B LYS* 4.6 0.4 - - - +
84D ASN* 3.5 19.5 - - + +
85D PHE 3.0 2.0 - - - -
86D SER* 1.3 78.0 + - - +
88D GLN* 1.3 60.2 + - - +
89D ALA 3.3 0.2 - - - -
90D ILE* 3.7 12.4 + - + -
130D GLN* 3.5 20.6 - - - +
132D PHE* 3.7 31.9 - - + -
135D TRP* 4.4 12.1 - - + -
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Residues in contact with GLN 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ILE* 3.9 11.0 - - + +
138A VAL 4.2 0.6 - - - +
172A GLN* 3.3 20.4 + - - +
174A GLN* 3.2 25.1 + - - -
60B MET* 3.5 14.8 - - + +
87B MET 5.1 1.0 - - - +
88B GLN 5.1 6.8 - - - +
91B ASP* 3.7 21.5 - - + +
177C GLU* 5.2 1.8 + - - -
59D GLU* 3.6 29.4 + - + +
60D MET* 3.4 36.7 - - + +
84D ASN 5.7 0.2 - - - +
85D PHE* 3.7 15.5 - - - +
86D SER 2.9 0.2 - - - -
87D MET* 1.3 82.8 - - + +
89D ALA* 1.3 58.1 + - - +
90D ILE 3.2 2.4 + - - -
91D ASP 4.9 0.2 + - - -
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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