Contacts of the helix formed by residues 154 - 163 (chain D) in PDB entry 2PPB
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 154 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LYS* 5.6 6.8 + - - +
132D TYR* 6.2 1.8 - - - +
133D ILE* 3.4 9.9 - - - +
153D LEU* 1.3 75.2 - - - +
155D ASP* 1.3 66.9 + - - +
156D GLU* 3.5 17.2 + - + +
157D GLU* 2.9 39.5 - - + +
158D TYR* 2.9 31.0 + - - +
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Residues in contact with ASP 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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133D ILE* 3.1 17.4 - - + +
154D THR* 1.3 79.6 + - - +
156D GLU* 1.3 58.7 + - + +
158D TYR* 3.7 16.7 - - - +
159D ARG* 2.6 53.9 + - - +
564D GLU* 2.7 54.6 - - + +
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Residues in contact with GLU 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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154D THR* 3.2 15.9 - - + +
155D ASP* 1.3 85.7 - - + +
157D GLU* 1.3 57.8 + - - +
159D ARG* 3.1 24.8 + - - +
160D GLU* 2.6 49.3 + - - +
564D GLU* 5.3 7.4 - - - +
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Residues in contact with GLU 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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143D ASN* 6.5 2.2 - - + -
153D LEU* 3.3 21.1 - - + +
154D THR* 2.9 27.0 + - + +
156D GLU* 1.3 81.5 - - - +
158D TYR* 1.3 58.0 + - - +
160D GLU* 3.5 16.1 - - + +
161D LEU* 3.5 23.2 + - - +
165D LYS* 6.0 3.4 - - - +
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Residues in contact with TYR 158 (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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133D ILE* 5.1 7.9 - - + -
153D LEU* 3.2 16.5 - - + +
154D THR 2.9 21.2 + - - +
155D ASP* 3.7 19.1 - - - +
157D GLU* 1.3 76.9 - - - +
159D ARG* 1.3 68.7 + - - +
161D LEU* 3.6 3.6 + - + +
162D ARG* 3.6 34.1 + - + +
452D ILE* 4.5 27.8 + - + -
454D ALA* 3.5 36.1 + - + +
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Residues in contact with ARG 159 (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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155D ASP* 2.6 41.6 + - - +
156D GLU* 3.1 22.3 + - - +
158D TYR* 1.3 79.1 - - - +
160D GLU* 1.3 73.1 + - - +
161D LEU 3.3 0.3 + - - -
162D ARG* 3.7 9.4 + - - +
163D TYR* 2.9 45.6 + - + +
564D GLU* 4.7 12.9 + - - +
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Residues in contact with GLU 160 (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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156D GLU* 2.6 40.4 + - - +
157D GLU* 3.4 17.4 + - + +
159D ARG* 1.3 92.9 - - - +
161D LEU* 1.3 55.6 + - - +
163D TYR* 3.2 18.5 + - - -
164D GLY 2.2 27.1 - - - +
165D LYS* 4.0 34.1 - - + +
166D GLN 3.7 3.5 + - - +
167D GLU* 4.5 20.6 - - + +
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Residues in contact with LEU 161 (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 ILE* 3.9 14.8 - - + +
142D LEU 3.8 22.0 - - - +
143D ASN* 5.5 4.7 - - + -
153D LEU* 5.0 8.1 - - + -
157D GLU 3.5 13.2 + - - +
158D TYR* 3.7 10.5 - - + +
159D ARG 3.3 0.4 - - - -
160D GLU* 1.3 76.4 - - - +
162D ARG* 1.3 51.5 + - + +
164D GLY 2.7 27.8 + - - +
449D SER* 2.6 49.2 + - - +
450D TYR 4.8 0.2 - - - +
452D ILE* 3.3 53.2 - - + -
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Residues in contact with ARG 162 (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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158D TYR* 3.6 29.2 + - + +
159D ARG* 3.7 9.1 + - - +
161D LEU* 1.3 78.6 - - - +
163D TYR* 1.3 64.2 + - + +
164D GLY 3.4 0.2 - - - -
412D GLY* 5.0 1.2 + - - -
414D ARG* 2.9 41.0 - - - +
434D ARG* 2.9 73.7 - - - +
449D SER* 4.2 5.8 - - - -
452D ILE* 5.3 4.7 - - + -
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Residues in contact with TYR 163 (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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159D ARG* 2.9 57.3 - - + +
160D GLU* 3.2 8.8 + - - -
162D ARG* 1.3 77.1 - - + +
164D GLY* 1.3 57.7 + - - +
166D GLN* 2.9 78.1 + - + +
167D GLU* 5.3 0.3 - - - -
168D THR* 5.7 4.3 - - - -
206D ARG* 6.0 0.4 - - - -
434D ARG* 3.0 24.5 - - - +
436D GLU* 2.7 20.0 - - - +
447D VAL* 3.0 8.9 - - - +
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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