Contacts of the helix formed by residues 147 - 157 (chain D) in PDB entry 2IYL
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 147 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148D GLN* 1.3 86.0 + - + +
149D LEU* 3.4 4.0 + - - +
150D SER* 3.8 13.3 + - - +
151D GLU* 3.4 31.1 + - - +
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Residues in contact with GLN 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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116D THR* 3.7 18.8 - - + +
117D THR* 5.6 1.3 + - - +
147D THR* 1.3 86.1 - - + +
149D LEU* 1.3 63.9 + - - +
151D GLU* 3.0 27.2 + - - +
152D TRP* 3.1 48.9 + - + +
1001D GDP 5.3 7.8 + - - +
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Residues in contact with LEU 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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116D THR* 3.7 28.4 - - + +
119D ILE* 3.8 26.2 - - + -
120D ALA 4.7 0.2 - - - +
135D PHE* 3.8 32.8 - - + -
136D CYS 3.8 22.0 - - - +
137D ALA* 3.8 21.8 - - + +
147D THR 3.4 2.7 - - - +
148D GLN* 1.3 76.5 - - - +
150D SER* 1.3 64.0 + - - +
152D TRP* 3.1 11.0 + - + +
153D GLY* 2.9 20.3 + - - -
160D VAL* 3.9 4.0 - - + +
191D ASP* 3.9 18.6 - - + +
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Residues in contact with SER 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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147D THR 3.8 16.6 + - - +
149D LEU* 1.3 77.9 - - - +
151D GLU* 1.3 58.0 + - - +
153D GLY* 3.3 2.6 + - - -
154D LYS* 3.1 41.5 + - - +
160D VAL* 4.3 15.9 - - - +
162D GLN* 3.3 35.3 + - - -
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Residues in contact with GLU 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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147D THR* 3.4 28.2 + - - +
148D GLN* 3.0 18.8 + - - +
150D SER* 1.3 73.7 - - - +
152D TRP* 1.3 66.8 + - + +
154D LYS* 3.5 20.0 + - - +
155D ARG* 3.1 23.4 + - - +
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Residues in contact with TRP 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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116D THR* 4.2 9.0 - - + -
117D THR* 4.2 27.8 + - + +
120D ALA* 3.3 32.9 - - + +
135D PHE* 4.7 2.2 - - + -
148D GLN* 3.1 58.1 + - + +
149D LEU* 3.1 12.0 + - + +
151D GLU* 1.3 76.6 - - - +
153D GLY* 1.3 56.5 + - - +
155D ARG* 3.3 45.9 + - - +
156D LEU* 2.8 46.9 + - + +
284D GLU 4.8 6.7 - - - -
286D PRO* 4.1 27.6 - - + -
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Residues in contact with GLY 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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135D PHE* 4.5 3.4 - - - -
149D LEU 2.9 10.7 + - - -
150D SER 3.3 4.5 + - - -
152D TRP* 1.3 75.9 - - - +
154D LYS* 1.3 55.6 + - - +
157D SER* 2.9 10.4 + - - -
158D ILE* 2.8 52.5 + - - +
160D VAL* 3.7 12.3 - - - -
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Residues in contact with LYS 154 (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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150D SER* 3.1 35.0 + - - +
151D GLU* 3.7 18.8 - - - +
153D GLY* 1.3 74.1 - - - +
155D ARG* 1.3 64.0 + - - +
157D SER* 3.2 16.2 + - - +
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Residues in contact with ARG 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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124D ARG* 5.3 3.8 - - - +
151D GLU 3.1 14.9 + - - +
152D TRP* 3.5 39.9 - - - +
154D LYS* 1.3 80.5 - - - +
156D LEU* 1.3 68.8 + - + +
157D SER* 3.5 1.9 + - - -
286D PRO* 3.5 31.7 - - - +
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Residues in contact with LEU 156 (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 ALA* 3.3 41.1 - - + +
124D ARG* 3.5 38.1 - - + +
127D GLN* 3.2 36.6 + - - +
135D PHE* 4.5 2.5 - - + -
152D TRP* 2.8 31.9 + - + +
153D GLY 4.3 0.4 - - - +
155D ARG* 1.3 83.6 - - + +
157D SER* 1.3 66.7 + - - +
158D ILE* 4.0 20.9 - - + -
286D PRO* 4.7 6.7 - - + -
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Residues in contact with SER 157 (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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127D GLN* 4.5 3.8 + - - -
153D GLY 2.9 6.4 + - - -
154D LYS* 3.2 12.6 + - - +
155D ARG 3.3 2.1 + - - -
156D LEU* 1.3 79.2 - - - +
158D ILE* 1.3 59.6 + - - +
159D PRO* 4.1 5.6 - - - +
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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