Contacts of the helix formed by residues 82 - 87 (chain N) 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 THR 82 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N TYR* 3.3 20.9 - - - +
80N PHE* 3.6 14.9 - - - +
81N MET* 1.3 88.6 - - + +
83N PHE* 1.3 60.0 + - - +
84N ASN* 2.9 33.4 + - - +
85N PHE* 2.9 32.4 + - + -
117N PRO* 3.4 22.2 - - + -
118N ASN* 5.7 0.4 - - - -
128N HIS* 5.4 7.1 - - + +
173N GLU* 5.9 0.4 - - - +
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Residues in contact with PHE 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N PHE* 3.8 23.6 - + + -
82N THR* 1.3 69.5 - - - +
84N ASN* 1.3 69.4 + - - +
86N SER* 2.9 44.2 + - - -
87N MET 3.7 0.7 + - - -
114N PHE* 4.3 4.3 - - + -
115N ARG* 4.1 8.7 - - - -
116N GLY* 3.6 25.4 - - - -
117N PRO 3.0 20.3 + - - +
118N ASN* 3.8 10.7 - - + +
132N PHE* 3.4 25.2 - - + -
136N TYR* 3.7 16.6 - + - -
168N VAL* 3.4 30.7 - - + -
169N VAL 3.6 8.7 - - - -
170N LEU* 3.5 21.8 - - + -
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Residues in contact with ASN 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82N THR* 2.9 23.9 + - - +
83N PHE* 1.3 80.1 - - - +
85N PHE* 1.3 69.7 + - + +
87N MET* 3.4 30.2 + - + +
88N GLN 4.8 0.2 + - - -
118N ASN* 6.3 0.4 - - - +
119N GLY 4.8 3.2 + - - +
127N GLN 3.2 27.4 - - - +
128N HIS* 3.0 29.6 + - - +
129N SER 3.6 0.9 + - - +
130N GLN* 3.2 35.3 + - - +
132N PHE* 3.6 9.8 - - - -
137O ILE* 5.0 3.5 - - + +
95P ASN* 4.8 1.0 + - - -
99P LYS* 5.2 1.0 + - - -
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Residues in contact with PHE 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N GLU* 5.0 2.2 - - - -
59N GLU* 3.5 37.0 - - + +
80N PHE* 4.7 3.4 - - + -
81N MET* 3.3 44.4 - - + +
82N THR* 2.9 25.4 + - + +
84N ASN* 1.3 72.6 - - + +
86N SER* 1.3 64.9 + - - +
88N GLN* 3.2 25.3 + - - +
128N HIS* 3.9 29.6 - + - -
136O GLY 4.3 5.4 - - - -
137O ILE* 3.6 33.7 - - + -
138O VAL* 5.6 4.3 - - + -
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Residues in contact with SER 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N PHE* 3.5 33.5 - - - -
82N THR 3.7 2.4 + - - -
83N PHE* 2.9 38.5 + - - -
85N PHE* 1.3 75.3 - - - +
87N MET* 1.3 56.6 + - - +
89N ALA 2.6 25.1 + - - -
90N ILE* 2.7 12.6 + - - +
93N VAL* 5.7 0.4 - - - -
132N PHE* 5.1 2.3 - - - -
136N TYR* 2.6 27.3 + - - -
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Residues in contact with MET 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84N ASN* 3.4 18.2 + - + +
85N PHE 3.2 1.4 - - - -
86N SER* 1.3 78.7 + - - +
88N GLN* 1.3 61.2 + - - +
89N ALA 3.3 0.7 + - - -
90N ILE* 3.4 25.2 + - + +
130N GLN* 4.2 6.1 - - - +
132N PHE* 3.6 35.9 - - + -
135N TRP* 4.1 9.9 - - + -
87P MET 3.9 5.0 - - - +
88P GLN 5.3 0.5 - - - +
90P ILE* 3.9 28.1 - - + +
91P ASP* 4.4 13.6 + - + -
94P ILE* 4.1 23.8 - - + -
95P ASN* 2.8 39.9 - - - +
99P LYS* 4.9 0.4 - - - +
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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