Contacts of the helix formed by residues 128 - 135 (chain A) in PDB entry 1PTG
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 PHE 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A GLY 4.1 17.0 - - - -
71A ARG* 4.1 4.0 - - - -
72A LEU* 4.4 17.0 - - + -
78A ILE* 4.3 18.0 - - + +
114A LEU* 3.7 43.7 - - + -
115A LYS 4.3 0.4 - - - -
116A LYS* 4.0 33.0 - - + -
118A TYR 5.9 0.2 - - - -
120A ASP* 4.0 22.6 + - - +
127A SER* 1.3 72.4 - - - +
129A SER* 1.3 69.5 + - - +
131A THR* 3.4 2.8 + - - -
132A PHE* 3.0 22.5 + - + +
164A TYR* 3.8 30.5 - + + -
165A SER 5.9 0.4 - - - +
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A SER* 3.4 10.4 + - - -
128A PHE* 1.3 83.2 - - - +
130A SER* 1.3 58.2 + - - +
132A PHE* 2.9 5.5 + - - +
133A GLU* 2.8 41.5 + - - +
164A TYR* 4.0 16.6 - - - -
165A SER 3.8 12.0 + - - -
166A GLY* 2.8 35.9 + - - -
167A SER* 4.5 1.6 - - - -
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ASP* 3.0 28.7 + - - -
127A SER* 2.6 30.4 + - - -
129A SER* 1.3 78.9 + - - +
131A THR* 1.3 54.9 + - - +
133A GLU* 4.5 5.2 - - - +
134A LYS* 2.9 46.7 + - - +
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Residues in contact with THR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.5 26.3 - - + +
76A ASN* 3.6 26.5 + - + +
78A ILE* 4.4 9.9 - - + -
126A ASP* 3.3 18.0 + - - +
127A SER 2.7 24.6 + - - -
128A PHE 3.8 3.1 - - - -
130A SER* 1.3 75.3 + - - +
132A PHE* 1.3 63.4 + - - +
134A LYS* 5.2 1.3 - - - +
135A LYS* 3.0 42.1 + - + +
136A TYR* 4.0 1.1 - - + -
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Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 3.5 18.1 - - + +
91A LEU* 3.8 21.5 - - + -
95A ILE* 5.2 0.2 - - + -
112A MET* 4.0 25.1 - - + -
114A LEU* 3.8 22.4 - - + -
128A PHE* 3.0 13.8 + - + +
129A SER* 2.9 4.7 + - - +
131A THR* 1.3 77.7 - - - +
133A GLU* 1.3 64.1 + - + +
136A TYR* 3.0 25.3 + - + +
137A PHE* 2.8 59.8 + + + -
142A PHE* 4.4 6.3 - + - -
160A LEU* 4.2 5.4 - - + -
164A TYR* 3.4 35.9 - + - -
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A SER 2.8 27.8 + - - +
130A SER* 4.2 4.1 - - - +
132A PHE* 1.3 78.9 - - + +
134A LYS* 1.3 62.9 + - + +
137A PHE* 3.7 12.2 - - + +
138A VAL* 3.5 23.4 + - - +
162A LYS* 4.5 0.7 + - - -
164A TYR* 2.7 29.7 + - - +
166A GLY 4.9 0.5 - - - +
167A SER* 2.9 24.1 + - - -
168A ASN* 2.9 27.1 + - - +
169A GLU* 3.1 35.4 + - + +
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ASP* 3.0 30.0 + - - -
130A SER* 2.9 27.7 + - - +
131A THR* 4.6 1.3 - - - +
133A GLU* 1.3 80.2 - - + +
135A LYS* 1.3 63.9 + - + +
138A VAL* 3.5 17.0 - - - +
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Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ASP 5.5 0.4 - - - -
76A ASN* 3.5 39.5 + - - +
77A THR* 5.5 3.1 - - + -
92A HIS* 4.7 7.3 + - + -
125A GLU* 4.9 7.7 + - - -
126A ASP* 6.3 1.0 - - - +
131A THR* 3.0 25.9 + - + +
134A LYS* 1.3 84.4 - - + +
136A TYR* 1.3 76.3 + - + +
138A VAL* 4.6 4.3 - - - +
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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