Contacts of the helix formed by residues 141 - 149 (chain E) in PDB entry 4PRH
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 SER 141 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138D TYR* 3.6 25.9 - - - +
139D GLN 3.4 27.1 + - - -
140D LEU* 4.2 6.2 - - - +
152D LEU* 6.2 0.2 - - - -
217D PRO* 5.4 0.2 - - - +
139E GLU 3.6 0.8 + - - -
140E PRO* 1.3 72.8 - - - +
142E GLU* 1.3 63.9 + - - +
143E ALA* 3.3 21.0 + - - +
144E GLU* 3.2 24.1 + - - +
145E ILE* 3.4 14.3 - - - +
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Residues in contact with GLU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PRO 3.7 5.9 + - - +
141E SER* 1.3 73.8 + - - +
143E ALA* 1.3 59.9 + - - +
144E GLU 3.3 0.2 - - - -
145E ILE* 3.4 32.1 + - - +
146E SER* 3.3 27.0 + - - +
211E TRP* 5.1 5.9 + - - -
212E GLN* 4.6 6.1 - - - +
253E ALA 5.5 0.5 - - - +
254E ASP* 3.0 35.6 - - + +
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Residues in contact with ALA 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D TYR* 3.9 4.8 - - + -
215D PHE* 4.7 3.7 - - + -
217D PRO* 3.7 35.9 - - + -
141E SER* 3.1 10.9 - - - +
142E GLU* 1.3 76.4 - - - +
144E GLU* 1.4 58.9 + - - +
146E SER* 3.7 7.1 + - - -
147E HIS* 3.1 31.4 + - - +
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Residues in contact with GLU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D TYR* 3.4 35.2 - - + -
152D LEU* 4.9 0.8 - - - +
140E PRO* 4.4 0.2 - - - +
141E SER* 3.2 28.2 + - - +
143E ALA* 1.4 77.0 - - - +
145E ILE* 1.3 59.3 + - - +
148E THR* 2.9 39.5 + - - +
150E LYS 3.3 14.9 - - - +
151E ALA* 3.5 2.9 - - - -
152E THR* 2.6 41.4 + - - +
205E ARG* 2.8 36.2 + - - +
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Residues in contact with ILE 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E PRO* 4.4 2.7 - - + -
141E SER 3.4 15.7 - - - +
142E GLU* 3.4 28.5 - - - +
143E ALA 3.3 0.2 - - - -
144E GLU* 1.3 76.1 - - - +
146E SER* 1.3 61.0 + - - +
149E GLN* 2.9 38.1 + - - +
150E LYS 3.8 5.4 - - - +
151E ALA* 3.4 33.7 - - + -
208E ALA* 3.8 18.8 - - + -
211E TRP* 3.9 19.1 - - + -
212E GLN* 3.4 24.2 - - - +
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Residues in contact with SER 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E GLU* 3.3 16.0 + - - +
143E ALA* 4.0 6.7 - - - -
144E GLU 3.5 0.2 - - - -
145E ILE* 1.3 78.3 - - - +
147E HIS* 1.3 59.7 + - - +
149E GLN* 4.7 10.2 + - - +
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Residues in contact with HIS 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D ASP* 2.9 45.3 + - - +
136D ALA* 4.7 2.5 - - + -
138D TYR* 3.2 24.0 - - - +
215D PHE* 4.3 42.5 - + + +
143E ALA 3.1 19.0 + - - +
146E SER* 1.3 78.1 - - - +
148E THR* 1.3 62.4 + - + +
149E GLN* 5.2 1.4 - - - +
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Residues in contact with THR 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D ASP* 4.3 6.1 - - - +
138D TYR* 3.7 21.8 - - + +
155D ASP* 4.1 15.9 - - + +
144E GLU* 2.9 21.9 + - + +
147E HIS* 1.3 80.3 - - + +
149E GLN* 1.4 69.5 + - - +
150E LYS* 3.1 37.2 + - - +
205E ARG* 3.6 21.4 + - - +
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Residues in contact with GLN 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E ILE* 2.9 31.4 + - - +
146E SER* 4.7 10.0 + - - +
147E HIS 5.2 1.1 - - - +
148E THR* 1.4 78.3 - - - +
150E LYS* 1.3 62.6 + - - +
207E SER* 3.8 6.2 - - - -
208E ALA* 3.0 32.1 + - + +
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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