Contacts of the helix formed by residues 142 - 155 (chain D) in PDB entry 2GRA
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 GLN 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D ARG* 3.2 36.2 + - - +
137D THR* 4.1 9.5 + - - -
140D HIS 4.2 7.9 - - - +
141D ALA* 1.3 81.1 - - - +
143D VAL* 1.3 68.4 + - - +
144D GLU* 4.5 10.9 - - - +
145D ASP* 2.5 21.9 + - - +
146D GLY* 4.3 1.4 + - - -
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Residues in contact with VAL 143 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D GLN* 1.3 82.7 - - - +
144D GLU* 1.3 58.4 + - - +
145D ASP 2.6 14.4 + - - -
146D GLY* 2.8 14.2 + - - -
147D ARG* 2.9 29.7 + - + +
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Residues in contact with GLU 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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142D GLN* 4.5 10.4 - - - +
143D VAL* 1.3 80.6 - - - +
145D ASP* 1.3 59.4 + - - +
147D ARG* 3.1 29.2 - - + +
148D LEU* 2.9 31.8 + - - +
151D GLN* 4.5 8.2 + - - -
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Residues in contact with ASP 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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91D ILE* 3.9 22.1 - - + +
116D ARG* 2.6 41.0 + - - +
118D ILE* 4.6 14.4 - - + -
141D ALA* 3.5 5.4 - - - -
142D GLN* 2.5 46.6 + - - +
143D VAL 2.6 0.8 + - - -
144D GLU* 1.3 76.6 - - - +
146D GLY* 1.3 67.4 + - - +
148D LEU* 2.8 17.5 + - - +
149D MET* 2.8 12.7 + - - +
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Residues in contact with GLY 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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118D ILE* 5.0 5.7 - - - +
135D TYR* 4.5 19.5 - - - -
137D THR* 5.0 8.3 + - - -
142D GLN 4.3 3.4 + - - -
143D VAL 2.8 10.9 + - - -
145D ASP* 1.3 75.4 - - - +
147D ARG* 1.3 53.5 + - - -
149D MET* 2.6 31.9 + - - +
150D GLU* 3.0 13.5 + - - +
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Residues in contact with ARG 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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143D VAL* 2.9 29.9 + - + +
144D GLU* 3.1 26.5 - - - +
146D GLY* 1.3 74.7 - - - +
148D LEU* 1.3 59.0 + - - +
150D GLU* 3.6 7.8 + - - +
151D GLN* 3.3 30.6 + - - +
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Residues in contact with LEU 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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1D MET* 4.3 31.2 - - + -
65D VAL* 5.9 3.4 - - + -
91D ILE* 4.1 22.9 - - + -
144D GLU* 2.9 30.5 + - - +
145D ASP 2.8 9.8 + - - +
147D ARG* 1.3 70.9 - - - +
149D MET* 1.3 68.8 + - - +
151D GLN* 3.8 15.9 + - + +
152D LEU* 3.2 23.5 + - + +
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Residues in contact with MET 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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67D PHE* 5.1 5.6 - - + -
93D VAL* 3.3 39.5 - - + -
118D ILE* 4.4 12.3 - - + -
120D CYS* 3.9 20.6 - - + -
135D TYR* 3.7 35.9 - - + -
145D ASP 2.8 9.7 + - - +
146D GLY* 2.6 21.6 + - - +
148D LEU* 1.3 72.5 - - - +
150D GLU* 1.3 64.6 + - - +
152D LEU* 2.9 10.9 + - - +
153D LEU* 2.9 45.9 + - + +
159D CYS* 5.3 0.2 - - - -
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Residues in contact with GLU 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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135D TYR* 3.3 37.9 + - + +
146D GLY 3.0 5.7 + - - +
147D ARG* 3.8 9.9 - - - +
149D MET* 1.3 76.1 - - - +
151D GLN* 1.3 61.4 + - + +
152D LEU 2.9 0.3 + - - -
154D SER* 2.5 53.9 + - - +
159D CYS* 3.3 25.8 - - - +
160D THR* 4.0 7.6 + - - -
161D GLU* 4.1 2.6 + - - +
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Residues in contact with GLN 151 (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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24D VAL* 5.9 0.4 - - - +
144D GLU* 4.5 10.1 + - - -
147D ARG* 3.3 22.9 + - - +
148D LEU* 4.0 16.8 - - + +
150D GLU* 1.3 78.7 - - + +
152D LEU* 1.3 63.2 + - + +
154D SER* 3.9 4.5 - - - -
155D SER* 3.2 23.0 + - - -
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Residues in contact with LEU 152 (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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1D MET* 3.7 35.2 - - + -
3D VAL* 5.5 4.9 - - + -
19D PHE* 3.2 55.2 - - + -
24D VAL* 4.0 18.8 - - + -
25D LEU* 5.7 1.3 - - + -
65D VAL* 5.9 3.6 - - + -
67D PHE* 4.2 14.6 - - + -
148D LEU* 3.2 17.6 + - + +
149D MET* 2.9 17.5 + - - +
150D GLU 2.9 0.6 + - - -
151D GLN* 1.3 79.1 - - + +
153D LEU* 1.3 60.8 + - + +
155D SER* 2.4 27.1 + - - -
156D VAL 4.3 0.2 + - - -
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Residues in contact with LEU 153 (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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15D LEU* 4.1 10.5 - - + -
19D PHE* 3.3 34.1 - - + -
67D PHE* 4.8 4.5 - - + -
120D CYS* 4.7 8.7 - - - -
122D THR* 3.9 11.0 - - + -
126D VAL* 6.2 2.5 - - + -
133D THR* 3.1 31.4 - - + +
135D TYR* 6.1 0.4 - - + -
149D MET* 2.9 40.4 + - + +
152D LEU* 1.3 75.5 - - + +
154D SER* 1.3 61.2 + - - +
155D SER 2.9 5.5 + - - -
156D VAL* 3.2 16.8 + - + +
157D GLY 3.1 11.3 - - - +
158D PHE 3.7 3.3 - - - +
159D CYS* 3.2 21.8 - - - -
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Residues in contact with SER 154 (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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150D GLU* 2.5 44.1 + - - -
151D GLN* 3.9 4.7 - - - -
153D LEU* 1.3 72.5 - - - +
155D SER* 1.3 47.9 - - - +
156D VAL 3.2 1.1 - - - -
157D GLY 3.2 9.7 - - - +
159D CYS* 3.0 21.5 + - - +
4300D NAP 1.8 42.7 + - - -
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Residues in contact with SER 155 (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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19D PHE* 4.3 0.5 - - - -
22D ALA* 3.4 12.5 - - - +
24D VAL* 3.5 28.8 - - - +
129D ARG* 3.5 12.6 + - - -
151D GLN 3.2 14.0 + - - -
152D LEU* 2.4 24.3 + - - -
153D LEU 2.9 0.8 - - - -
154D SER* 1.3 80.0 - - - +
156D VAL* 1.3 66.4 + - - +
4300D NAP 3.6 9.2 + - - -
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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