Contacts of the helix formed by residues 105 - 115 (chain D) in PDB entry 2GF2
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 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D LEU* 3.4 2.4 + - - +
104D PRO* 1.3 87.3 + - - +
106D SER* 1.3 76.0 - - - +
107D ILE* 3.6 24.1 - - + +
108D ASN* 3.2 21.0 + - - +
109D ALA* 3.1 24.8 + - - +
135D ILE* 3.9 7.1 - - - +
284D LYS* 4.6 10.1 - - + +
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Residues in contact with SER 106 (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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105D THR* 1.3 79.5 - - - +
107D ILE* 1.3 60.2 + - - +
109D ALA* 3.3 2.8 + - - +
110D ILE* 3.0 34.2 + - - +
134D THR 5.0 1.2 + - - -
135D ILE* 3.6 29.9 - - - +
136D ASP* 3.6 16.8 + - - +
139D VAL* 4.3 13.2 - - - +
284D LYS* 5.4 1.4 - - - +
288D LEU* 4.7 5.7 - - - +
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Residues in contact with ILE 107 (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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105D THR* 3.6 21.0 - - + +
106D SER* 1.3 79.3 - - - +
108D ASN* 1.3 76.3 + - - +
110D ILE* 3.2 18.3 - - + +
111D GLU* 3.0 25.1 + - - +
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Residues in contact with ASN 108 (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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103D LEU* 3.7 22.5 - - + +
104D PRO* 3.9 13.5 - - + +
105D THR* 3.2 34.5 + - - +
106D SER 3.4 0.4 - - - -
107D ILE* 1.3 86.4 - - - +
109D ALA* 1.3 57.2 + - - +
111D GLU* 3.4 7.1 + - - +
112D ALA* 3.0 29.5 + - - +
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Residues in contact with ALA 109 (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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103D LEU* 3.7 16.1 - - + +
105D THR 3.1 17.9 + - - +
106D SER 3.5 4.9 - - - +
107D ILE 3.2 0.2 - - - -
108D ASN* 1.3 77.3 - - - +
110D ILE* 1.3 62.7 + - + +
112D ALA* 3.2 2.4 + - - +
113D TYR* 3.2 30.7 + - + -
131D ASP* 4.4 15.0 - - - +
133D SER* 4.4 4.3 - - - +
135D ILE* 4.1 22.2 - - + -
143D LEU* 4.8 4.0 - - + -
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Residues in contact with ILE 110 (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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106D SER* 3.0 17.2 + - - +
107D ILE* 3.2 25.8 - - + +
109D ALA* 1.3 71.6 - - - +
111D GLU* 1.3 57.6 + - + +
114D SER* 2.6 41.2 + - - -
115D GLY 3.5 0.3 + - - -
139D VAL* 3.5 28.5 - - + -
143D LEU* 3.8 20.9 - - + -
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Residues in contact with GLU 111 (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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107D ILE 3.0 18.4 + - - +
108D ASN* 3.6 9.0 - - - +
109D ALA 3.2 0.2 - - - -
110D ILE* 1.3 79.7 - - + +
112D ALA* 1.3 59.7 + - - +
114D SER 4.9 0.2 - - - -
115D GLY* 2.9 43.1 + - - +
116D ALA* 4.1 6.9 + - - +
117D ASN 5.2 1.6 + - - -
118D GLY* 3.9 4.3 + - - -
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Residues in contact with ALA 112 (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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45D ILE* 4.6 14.4 - - + -
89D PRO* 3.6 13.3 - - + +
101D THR* 4.9 3.4 - - + -
103D LEU* 3.5 24.5 - - + -
108D ASN 3.0 17.5 + - - +
109D ALA 3.2 3.3 + - - +
111D GLU* 1.3 76.9 - - - +
113D TYR* 1.3 62.4 + - + +
118D GLY* 3.3 2.1 - - - -
119D ILE* 2.8 30.4 + - - +
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Residues in contact with TYR 113 (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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99D ILE* 5.2 0.7 + - - +
101D THR* 2.7 44.9 + - + +
109D ALA* 3.2 27.6 + - - +
111D GLU 3.2 0.2 - - - -
112D ALA* 1.3 81.1 - - + +
114D SER* 1.3 60.0 + - - +
115D GLY 3.5 1.2 - - - +
118D GLY* 3.5 3.6 - - - -
119D ILE* 3.4 21.9 + - + +
120D LEU* 3.1 51.5 + - + +
121D LYS 4.8 0.2 + - - -
129D LEU* 3.9 22.7 - - + +
130D ILE 3.8 4.5 + - - -
131D ASP* 3.6 18.2 + - + +
143D LEU* 3.7 31.6 - - + -
147D VAL* 4.3 7.0 - - + -
154D PHE* 3.7 20.5 - + - -
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Residues in contact with SER 114 (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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110D ILE* 2.6 22.4 + - - -
113D TYR* 1.3 72.4 - - - +
115D GLY* 1.3 64.8 + - - +
120D LEU* 4.7 9.8 - - - +
121D LYS* 5.0 4.5 - - - -
143D LEU* 4.2 14.4 - - - +
146D GLU* 4.6 20.2 + - - +
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Residues in contact with GLY 115 (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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110D ILE 3.5 2.4 + - - -
111D GLU* 2.9 39.8 + - - -
113D TYR 3.5 1.6 - - - +
114D SER* 1.3 82.7 - - - +
116D ALA* 1.3 65.9 + - - -
117D ASN 3.2 3.1 - - - -
118D GLY* 3.0 10.4 + - - -
121D LYS* 3.6 11.4 - - - +
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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