Contacts of the helix formed by residues 89 - 96 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59T GLU* 4.1 7.9 - - + +
60T MET* 4.3 8.3 - - - +
63T ALA* 3.6 28.5 - - + -
80T PHE* 3.7 21.1 - - + -
86T SER* 2.9 10.6 + - - +
88T GLN* 1.3 76.2 - - - +
90T ILE* 1.3 66.1 + - - +
91T ASP 3.1 2.7 - - - -
92T GLN* 3.0 17.0 + - - +
93T VAL* 3.1 13.7 + - + +
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Residues in contact with ILE 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87R MET* 3.7 24.9 - - + +
90R ILE* 4.1 11.0 - - + -
135R TRP* 3.7 20.0 - - + -
86T SER 3.1 10.5 + - - +
87T MET* 3.4 17.0 - - + +
88T GLN 3.3 1.6 - - - -
89T ALA* 1.3 79.2 - - - +
91T ASP* 1.3 66.1 + - - +
93T VAL* 3.2 5.3 + - - -
94T ILE* 2.9 33.5 + - + +
132T PHE* 5.6 0.2 - - + -
135T TRP* 4.0 22.4 - - + -
136T TYR* 3.4 39.9 - - + +
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Residues in contact with ASP 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84R ASN 5.0 0.9 - - - +
87R MET* 4.0 24.8 + - + +
88R GLN* 3.6 16.2 - - - +
137S ILE* 3.4 43.6 - - - +
140S ALA* 3.8 13.8 - - - +
60T MET* 3.8 21.1 - - + +
88T GLN 4.9 0.2 + - - -
90T ILE* 1.3 81.5 - - - +
92T GLN* 1.3 57.6 + - - +
95T ASN* 2.8 44.1 + - - +
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Residues in contact with GLN 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140S ALA* 3.5 25.9 + - - +
143S PRO* 3.9 5.3 - - - +
144S LEU* 4.6 2.5 - - - +
174S GLN* 3.5 20.5 + - - -
60T MET* 3.7 20.6 + - - +
63T ALA* 4.4 8.1 - - + -
64T GLY* 3.3 40.2 - - - +
67T VAL* 4.7 5.7 - - + +
89T ALA 3.0 10.2 + - - +
91T ASP* 1.3 77.3 - - - +
93T VAL* 1.3 58.0 + - - +
96T SER* 2.9 54.4 + - - -
97T ALA* 3.1 5.6 + - - +
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Residues in contact with VAL 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80T PHE* 4.7 9.4 - - + -
86T SER 5.5 0.4 - - - +
89T ALA* 3.1 16.8 + - + +
90T ILE* 3.2 7.2 + - - +
92T GLN* 1.3 75.7 - - + +
94T ILE* 1.3 58.3 + - - +
97T ALA* 3.4 7.7 - - - +
98T ALA* 2.9 27.9 + - - +
114T PHE* 3.6 49.8 - - + -
136T TYR* 4.4 20.6 - - + +
142T LEU* 4.1 18.1 - - + +
168T VAL* 4.4 9.4 - - + -
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Residues in contact with ILE 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87R MET* 4.0 15.5 - - + -
130R GLN* 3.7 27.1 - - - +
135R TRP* 3.9 19.7 - - + -
90T ILE* 2.9 25.6 + - + +
93T VAL* 1.3 75.8 - - + +
95T ASN* 1.3 59.7 + - - +
98T ALA* 3.4 12.4 - - + +
99T LYS* 3.4 31.1 + - - +
136T TYR* 4.6 5.8 - - + -
139T CYS* 3.3 36.8 - - + -
142T LEU* 4.4 14.4 - - + -
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Residues in contact with ASN 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84R ASN* 4.5 1.4 + - - +
87R MET* 2.9 30.2 - - - +
127R GLN* 2.5 56.4 + - - +
137S ILE* 3.5 26.0 - - + +
91T ASP* 2.8 25.4 + - - +
94T ILE* 1.3 74.0 - - - +
96T SER* 1.3 56.6 - - - +
99T LYS* 2.9 33.8 + - - +
100T THR* 4.5 3.1 + - - -
103T MET* 4.6 2.6 - - - +
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Residues in contact with SER 96 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127R GLN* 4.6 2.7 + - - +
135S ASN* 5.1 3.5 + - - +
140S ALA* 4.5 7.8 - - - +
144S LEU* 3.5 21.6 - - - +
67T VAL* 4.3 17.5 - - - +
71T MET* 4.8 4.7 - - - +
91T ASP 3.7 0.6 + - - -
92T GLN* 2.9 38.6 + - - -
95T ASN* 1.3 80.3 + - - +
97T ALA* 1.3 58.6 + - - +
100T THR* 2.5 28.0 + - - +
110T VAL* 4.4 2.3 - - - +
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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