Contacts of the helix formed by residues 129 - 137 (chain D) in PDB entry 2P1N
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D GLY 4.3 0.4 + - - -
128D LYS 1.3 67.7 - - - -
130D PRO* 1.3 65.5 - - + +
131D GLU* 3.4 16.7 + - - +
132D GLU* 2.1 74.7 + - - +
133D ILE* 2.9 18.4 + - - +
29E SER* 4.2 0.7 - - - -
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Residues in contact with PRO 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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129D THR* 1.3 93.2 - - + +
131D GLU* 1.3 57.1 + - - +
133D ILE* 3.8 2.8 - - + +
134D ARG* 2.7 48.4 + - - +
148D GLU* 5.4 0.2 - - - +
152D ARG* 4.8 7.4 - - - +
29E SER* 3.9 26.9 - - - +
32E LEU* 3.7 39.5 - - + +
33E VAL* 4.0 14.5 - - + +
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Residues in contact with GLU 131 (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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129D THR* 3.2 19.5 + - - +
130D PRO* 1.3 83.8 - - - +
132D GLU* 1.3 61.3 + - + +
134D ARG* 2.7 38.3 + - - +
135D THR* 2.8 30.5 + - - -
148D GLU* 4.0 8.5 - - - +
152D ARG* 4.7 5.4 + - - -
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Residues in contact with GLU 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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127D GLY 4.1 2.7 - - - +
128D LYS* 2.8 26.2 - - + -
129D THR* 2.1 58.4 + - - +
131D GLU* 1.3 74.9 - - + +
133D ILE* 1.3 55.8 + - - +
135D THR* 3.5 8.5 - - - +
136D THR* 2.1 43.0 + - - +
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Residues in contact with ILE 133 (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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124D MET 5.4 0.2 - - - +
125D ILE* 3.6 37.7 - - + +
128D LYS* 3.5 27.4 - - + +
129D THR 3.2 16.4 - - - +
130D PRO* 3.8 4.5 - - + +
132D GLU* 1.3 71.3 - - - +
134D ARG* 1.3 53.3 - - - +
135D THR 2.3 18.7 + - - -
136D THR* 3.3 12.5 + - - -
137D PHE* 3.3 22.8 + - + +
139D ILE* 5.9 0.2 - - + -
29E SER* 4.5 9.6 - - - -
30E VAL* 4.8 0.9 - - + +
33E VAL* 3.9 20.0 - - + -
37E TRP* 3.8 29.8 - - + -
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Residues in contact with ARG 134 (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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130D PRO* 2.7 27.6 + - - +
131D GLU* 2.7 56.7 + - - +
133D ILE* 1.3 70.6 - - - +
135D THR* 1.3 57.0 + - - +
137D PHE 3.7 2.7 - - - +
138D ASN* 3.8 3.8 + - - -
139D ILE* 2.7 51.4 + - + +
140D LYS* 4.7 0.2 - - - +
141D ASN* 3.0 53.7 - - - +
148D GLU* 3.8 11.1 + - - -
32E LEU 3.5 13.5 + - - -
33E VAL* 3.3 26.2 + - + +
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Residues in contact with THR 135 (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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131D GLU 2.8 20.2 + - - +
132D GLU* 3.5 9.4 - - - +
133D ILE 2.3 19.0 + - - -
134D ARG* 1.3 69.5 + - - +
136D THR* 1.3 60.1 + - + +
137D PHE 2.3 17.7 - - - +
138D ASN* 4.5 4.0 + - - +
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Residues in contact with THR 136 (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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95D GLN* 2.6 38.8 + - - +
124D MET* 4.8 11.2 - - + +
128D LYS* 3.9 23.4 - - - +
132D GLU 2.1 36.9 + - - -
133D ILE* 3.6 2.9 - - - -
135D THR* 1.3 73.2 - - + +
137D PHE* 1.3 70.0 + - - +
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Residues in contact with PHE 137 (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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95D GLN* 4.3 5.2 - - - +
99D PHE* 4.1 18.2 - + + -
121D VAL* 3.6 25.8 - - + -
124D MET* 3.8 24.0 - - + -
125D ILE* 3.7 27.4 - - + -
133D ILE* 3.3 19.7 + - + +
135D THR* 2.3 39.3 - - - +
136D THR* 1.3 79.8 - - - +
138D ASN* 1.3 61.3 + - - +
139D ILE* 3.7 17.9 - - + -
9E PHE* 3.8 28.5 - + - -
37E TRP* 4.0 22.9 - + - -
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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