Contacts of the helix formed by residues 136 - 150 (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 ASP 136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D SER* 3.6 7.5 + - - +
135D ILE* 1.3 74.9 - - - +
137D PRO* 1.4 76.8 - - - +
138D ALA* 2.9 36.8 + - - +
139D VAL* 2.9 33.7 + - + +
140D SER* 3.2 10.7 + - - -
288D LEU* 3.7 20.3 - - + +
291D ASP* 4.3 20.3 - - - +
292D SER* 4.6 7.7 + - - -
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Residues in contact with PRO 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 4.7 11.2 - - + -
135D ILE 3.3 1.1 - - - +
136D ASP* 1.4 91.6 - - - +
138D ALA* 1.3 61.8 + - - +
140D SER* 3.2 6.2 + - - -
141D LYS* 3.1 33.3 + - - +
203D GLY* 3.7 19.2 - - - +
206D GLN* 4.0 17.0 - - + -
207D ALA* 4.1 13.0 - - + +
210D ILE* 3.6 29.2 - - + -
288D LEU 5.7 0.2 - - - +
292D SER* 3.8 14.6 - - - +
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ASP* 2.9 15.9 + - - +
137D PRO* 1.3 79.2 - - - +
139D VAL* 1.3 56.8 + - + +
141D LYS* 3.4 20.4 + - - +
142D GLU* 3.0 27.6 + - - +
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Residues in contact with VAL 139 (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* 4.3 16.2 - - - +
110D ILE* 3.5 31.4 - - + -
135D ILE* 3.8 17.0 - - + -
136D ASP* 2.9 30.1 + - + +
138D ALA* 1.3 74.1 - - + +
140D SER* 1.3 61.2 + - - +
142D GLU* 3.3 7.7 + - + +
143D LEU* 2.8 31.0 + - + +
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Residues in contact with SER 140 (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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131D ASP* 5.2 0.2 + - - -
135D ILE* 3.4 17.7 - - - +
136D ASP 3.2 4.1 + - - -
137D PRO 3.3 10.3 - - - -
139D VAL* 1.3 77.0 - - - +
141D LYS* 1.3 54.4 + - - +
143D LEU* 3.4 4.2 + - - +
144D ALA* 2.9 29.1 + - - +
154D PHE* 3.8 9.2 - - - -
156D ASP* 3.9 12.1 - - - +
202D VAL* 3.6 18.2 - - - +
203D GLY* 4.2 5.4 - - - -
206D GLN* 3.3 24.9 + - - +
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Residues in contact with LYS 141 (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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233A LEU* 5.5 8.7 + - - +
137D PRO* 3.1 23.9 + - - +
138D ALA* 3.5 20.9 - - + +
139D VAL 3.2 0.2 - - - -
140D SER* 1.3 73.9 - - - +
142D GLU* 1.3 63.7 + - - +
144D ALA* 3.2 8.1 + - - +
145D LYS* 3.0 29.8 + - + +
202D VAL* 3.7 28.2 - - + +
203D GLY* 5.0 1.8 - - - -
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Residues in contact with GLU 142 (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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138D ALA 3.0 14.1 + - - +
139D VAL* 3.6 11.0 - - + +
141D LYS* 1.3 75.8 - - - +
143D LEU* 1.3 63.2 + - + +
145D LYS* 3.3 12.3 + - - +
146D GLU* 3.2 24.8 + - - +
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Residues in contact with LEU 143 (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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109D ALA* 4.5 8.7 - - + +
110D ILE* 3.8 29.2 - - + -
113D TYR* 3.7 47.6 - - + -
114D SER* 4.2 10.5 - - - +
120D LEU* 5.5 0.4 - - + +
131D ASP* 5.0 0.4 - - - +
135D ILE* 4.6 14.8 - - + -
139D VAL 2.8 16.8 + - - +
140D SER 3.6 4.9 - - - +
142D GLU* 1.3 78.1 - - + +
144D ALA* 1.3 61.5 + - - +
146D GLU* 3.1 7.9 + - + +
147D VAL* 3.0 29.0 + - + +
154D PHE* 3.7 23.6 - - + -
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Residues in contact with ALA 144 (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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140D SER 2.9 18.2 + - - +
141D LYS* 3.4 6.7 - - - +
143D LEU* 1.3 76.1 - - - +
145D LYS* 1.3 61.5 + - - +
147D VAL* 3.3 4.0 - - - +
148D GLU* 3.0 36.5 + - - +
154D PHE* 3.7 20.6 - - + +
202D VAL* 3.8 29.6 - - + -
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Residues in contact with LYS 145 (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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141D LYS* 3.0 16.6 + - + +
142D GLU* 3.3 13.4 + - - +
144D ALA* 1.3 75.9 - - + +
146D GLU* 1.3 62.1 + - + +
148D GLU* 3.5 11.4 + - - +
149D LYS* 3.2 34.5 + - - +
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Residues in contact with GLU 146 (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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114D SER* 4.6 16.1 + - - +
120D LEU* 3.5 28.7 - - + +
142D GLU 3.2 15.0 + - - +
143D LEU* 3.1 12.6 + - + +
145D LYS* 1.3 76.0 - - + +
147D VAL* 1.3 63.8 + - - +
149D LYS* 3.3 42.3 + - - +
150D MET* 3.6 10.8 + - - +
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Residues in contact with VAL 147 (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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113D TYR* 4.3 3.6 - - + -
120D LEU* 3.7 29.2 - - + -
123D VAL* 5.9 0.7 - - + -
129D LEU* 3.9 22.7 - - + -
143D LEU 3.0 13.6 + - - +
144D ALA 3.3 7.4 - - - +
146D GLU* 1.3 76.4 - - - +
148D GLU* 1.3 62.7 + - + +
150D MET* 3.2 11.7 + - - +
151D GLY 3.4 0.2 + - - -
152D ALA* 3.0 32.4 + - + +
153D VAL 3.9 1.8 - - - -
154D PHE* 3.3 49.6 - - + +
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Residues in contact with GLU 148 (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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144D ALA* 3.0 29.0 + - - +
145D LYS* 3.5 12.0 + - - +
146D GLU 3.2 0.2 - - - -
147D VAL* 1.3 74.8 - - + +
149D LYS* 1.3 57.6 + - - +
150D MET 3.0 2.0 - - - -
151D GLY* 2.8 23.9 + - - -
152D ALA 3.6 13.7 - - - +
153D VAL* 6.0 0.2 - - - -
178D VAL* 6.1 3.5 - - - +
202D VAL* 5.9 0.9 - - - +
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Residues in contact with LYS 149 (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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145D LYS* 3.2 20.0 + - - +
146D GLU* 3.4 31.0 - - - +
147D VAL 3.3 0.2 - - - -
148D GLU* 1.3 76.9 - - - +
150D MET* 1.3 68.5 + - + +
151D GLY 3.4 2.4 + - - -
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Residues in contact with MET 150 (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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120D LEU* 3.9 28.7 - - + +
123D VAL* 3.5 35.2 - - + +
124D LYS 4.8 1.7 - - - -
125D LYS* 4.1 17.8 + - - +
146D GLU* 3.6 23.0 + - - +
147D VAL* 3.2 12.4 + - - +
148D GLU 3.0 1.0 - - - -
149D LYS* 1.3 87.6 - - + +
151D GLY* 1.3 61.7 + - - +
152D ALA* 3.2 3.3 + - - +
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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