Contacts of the helix formed by residues 128 - 132 (chain D) in PDB entry 4PE5
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 GLY 128 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ASP* 3.3 13.9 - - - -
102D ASP 5.3 0.2 - - - -
103D THR 3.5 11.2 - - - -
104D ASP* 5.2 1.6 - - - -
127D HIS* 1.3 80.6 - - - +
129D GLY* 1.3 61.1 + - - -
130D SER 3.1 1.3 - - - -
131D SER* 2.9 25.9 + - - -
132D MET* 3.2 5.9 + - - +
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Residues in contact with GLY 129 (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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101D ASP* 3.2 6.8 + - - -
103D THR 3.0 11.3 + - - -
104D ASP 4.1 2.2 - - - -
105D GLN 3.2 37.5 - - - -
106D GLU* 3.5 4.8 - - - -
109D ALA* 3.4 12.2 - - - +
128D GLY* 1.3 72.9 - - - -
130D SER* 1.3 60.4 + - - +
131D SER 3.0 0.4 - - - -
132D MET* 3.0 21.6 + - - +
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Residues in contact with SER 130 (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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99D PHE* 3.3 36.3 + - - -
101D ASP* 2.8 14.5 + - - -
108D ILE* 3.9 3.7 - - - +
109D ALA* 3.6 12.7 - - - +
112D LEU* 3.7 11.7 - - - -
125D GLY* 3.4 10.0 - - - -
127D HIS 3.0 19.6 + - - -
128D GLY 3.1 0.2 - - - -
129D GLY* 1.3 76.8 - - - +
131D SER* 1.3 51.5 + - - +
143D PHE* 3.5 13.2 - - - -
145D GLN* 2.6 23.5 + - - -
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Residues in contact with SER 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D GLY 3.4 21.5 - - - -
126D ILE 3.9 0.4 - - - -
127D HIS* 3.5 17.7 - - - -
128D GLY 2.9 19.9 + - - -
130D SER* 1.3 78.5 + - - +
132D MET* 1.3 62.8 + - - +
133D ILE* 3.2 5.2 + - - +
145D GLN* 3.3 11.2 + - - +
146D PHE 3.9 20.0 + - - +
147D GLY* 5.3 3.8 - - - -
282D TYR* 5.6 1.9 - - - +
292D ARG* 5.1 2.5 + - - -
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Residues in contact with MET 132 (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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104D ASP 5.8 1.1 - - - +
106D GLU* 3.7 24.6 - - + +
109D ALA* 3.6 8.5 - - - +
128D GLY 3.2 5.1 + - - +
129D GLY* 3.0 19.3 + - - +
131D SER* 1.3 75.1 - - - +
133D ILE* 1.3 67.0 + - - +
134D MET* 3.3 0.9 + - - -
145D GLN* 3.0 11.6 + - - -
260D SER* 6.1 1.3 - - - -
261D LEU* 4.1 24.5 - - + +
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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