Contacts of the helix formed by residues 129 - 137 (chain A) in PDB entry 2P1Q
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A GLY 5.7 0.7 - - - +
128A LYS* 1.3 76.7 - - - +
130A PRO* 1.4 76.9 - - + +
131A GLU* 3.6 8.3 + - - +
132A GLU* 2.8 44.2 + - - +
133A ILE* 2.9 22.2 + - - +
29B SER* 4.6 1.1 - - - -
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Residues in contact with PRO 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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129A THR* 1.4 87.4 - - + +
131A GLU* 1.3 55.4 + - - +
133A ILE* 3.3 7.9 + - + +
134A ARG* 3.0 43.2 + - - +
152A ARG* 4.1 18.6 - - - +
29B SER* 3.6 34.0 - - - +
32B LEU* 3.6 38.1 - - + +
33B VAL* 4.3 3.1 - - + +
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Residues in contact with GLU 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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129A THR* 3.1 7.8 - - - +
130A PRO* 1.3 79.7 - - + +
132A GLU* 1.3 61.0 + - + +
134A ARG* 3.4 34.5 + - - +
135A THR* 3.1 38.0 + - - +
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Residues in contact with GLU 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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127A GLY 4.5 1.7 - - - +
128A LYS* 3.4 26.0 - - + +
129A THR* 2.8 46.1 + - - +
131A GLU* 1.3 74.0 - - + +
133A ILE* 1.3 56.4 + - - +
135A THR* 3.5 6.8 + - - +
136A THR* 2.6 34.6 + - - +
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Residues in contact with ILE 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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125A ILE* 3.7 48.2 - - + +
128A LYS* 3.6 29.8 - - + +
129A THR 2.9 21.5 + - - +
130A PRO* 3.5 7.2 - - + +
132A GLU* 1.3 77.0 - - - +
134A ARG* 1.3 60.0 + - - +
136A THR* 2.7 18.9 + - - -
137A PHE* 2.9 19.7 + - + +
29B SER* 4.2 11.7 - - - -
33B VAL* 3.6 32.3 - - + -
37B TRP* 3.8 9.6 - - + -
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Residues in contact with ARG 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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130A PRO* 3.0 23.9 + - - +
131A GLU* 3.4 40.7 + - - +
133A ILE* 1.3 75.5 - - - +
135A THR* 1.3 60.7 + - - +
137A PHE 4.4 0.4 - - - +
138A ASN* 2.9 9.2 + - - -
139A ILE* 2.8 65.4 + - + +
141A ASN* 3.5 40.3 - - - +
148A GLU* 3.9 10.9 + - - -
152A ARG* 5.6 0.6 - - - +
32B LEU 3.1 17.8 + - - -
33B VAL* 2.8 43.4 + - + +
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Residues in contact with THR 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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131A GLU* 3.1 29.6 + - - +
132A GLU* 3.7 8.1 - - - +
133A ILE 3.2 0.2 - - - -
134A ARG* 1.3 75.4 - - - +
136A THR* 1.3 69.6 - - + +
137A PHE 3.4 0.2 + - - -
138A ASN* 3.5 18.8 + - - +
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Residues in contact with THR 136 (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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95A GLN* 2.5 37.7 + - - +
124A MET* 4.6 11.2 + - + +
128A LYS* 4.0 24.6 - - - +
132A GLU 2.6 24.4 + - - +
133A ILE* 2.7 14.0 + - - -
135A THR* 1.3 78.6 - - + +
137A PHE* 1.3 67.0 + - - +
138A ASN* 4.1 2.8 + - - -
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Residues in contact with PHE 137 (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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95A GLN* 3.9 4.6 - - - +
99A PHE* 4.3 20.9 - + - -
121A VAL* 3.5 36.1 - - + -
124A MET* 3.6 33.0 - - + -
125A ILE* 3.6 25.1 - - + -
133A ILE 2.9 18.5 + - - +
136A THR* 1.3 87.7 - - - +
138A ASN* 1.3 72.7 + - - +
139A ILE* 3.5 22.5 + - + +
9B PHE* 4.3 14.8 - + - -
14B LEU* 5.9 0.7 - - + -
37B TRP* 4.1 21.8 - + - -
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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