Contacts of the helix formed by residues 131 - 140 (chain D) in PDB entry 3P1M
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 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D LEU* 4.7 2.9 - - - +
129D ALA 3.5 7.2 + - - +
130D ILE* 1.3 80.0 - - - +
132D ASP* 1.3 66.4 + - - +
133D GLU* 3.5 10.8 + - - +
134D GLU* 3.1 23.8 + - - +
135D ASN* 2.9 21.9 + - - +
153D GLN* 5.5 2.1 + - - +
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Residues in contact with ASP 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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130D ILE 4.0 0.4 + - - +
131D THR* 1.3 74.5 - - - +
133D GLU* 1.3 64.7 + - - +
135D ASN* 3.1 9.5 + - - +
136D ASP* 3.0 32.2 + - - +
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Residues in contact with GLU 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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109D THR 4.8 2.8 - - - +
110D LEU* 3.7 32.6 - - + +
131D THR* 3.5 9.8 + - - +
132D ASP* 1.3 80.9 - - - +
134D GLU* 1.3 64.0 + - - +
136D ASP* 3.3 20.7 + - - +
137D MET* 3.5 10.7 + - - +
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Residues in contact with GLU 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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110D LEU* 3.7 19.2 - - + +
130D ILE* 3.8 12.9 - - + +
131D THR* 3.1 18.8 + - - +
133D GLU* 1.3 78.9 - - - +
135D ASN* 1.3 59.5 - - - +
137D MET* 3.1 4.7 + - - +
138D LEU* 2.8 26.7 + - + +
149D ARG* 2.7 48.5 + - - +
150D LEU* 3.1 36.2 + - + +
153D GLN* 3.4 23.7 - - + +
154D ILE* 4.8 0.2 - - - +
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Residues in contact with ASN 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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130D ILE* 3.5 27.6 - - + +
131D THR 2.9 18.1 + - - +
132D ASP* 3.1 9.4 + - - +
134D GLU* 1.3 78.3 - - - +
136D ASP* 1.3 65.2 + - - +
138D LEU* 3.7 6.8 - - - +
139D ASP* 2.9 39.0 + - - +
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Residues in contact with ASP 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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132D ASP* 3.0 21.8 + - - +
133D GLU* 3.5 11.8 - - - +
134D GLU 3.2 0.2 - - - -
135D ASN* 1.3 80.4 + - - +
137D MET* 1.3 76.9 + - + +
139D ASP* 3.5 18.7 + - - +
140D LEU* 3.9 10.6 + - - +
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Residues in contact with MET 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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110D LEU* 3.2 34.5 - - + +
111D ALA* 3.9 19.3 - - - +
112D CYS* 3.5 17.3 - - - +
113D SER* 2.9 23.4 + - - -
133D GLU 3.5 8.9 + - - +
134D GLU 3.1 3.4 + - - +
136D ASP* 1.3 91.1 - - + +
138D LEU* 1.3 66.0 + - - +
140D LEU* 3.0 25.0 + - + +
141D ALA 3.5 0.7 + - - -
150D LEU* 3.6 14.8 - - + -
102E GLY* 5.8 4.0 - - - +
105E ALA* 4.0 20.9 - - + -
114E THR* 5.7 0.9 - - - -
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Residues in contact with LEU 138 (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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116D HIS* 4.5 1.3 - - + -
130D ILE* 3.5 26.7 - - + -
134D GLU* 2.8 19.3 + - + +
135D ASN* 3.8 9.9 - - - +
137D MET* 1.3 75.5 - - - +
139D ASP* 1.3 64.3 + - - +
141D ALA* 3.0 23.6 + - + +
144D LEU* 3.5 30.6 - - + +
148D SER* 3.8 22.4 - - - +
149D ARG* 4.1 18.6 - - - -
150D LEU* 3.8 28.2 - - + +
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Residues in contact with ASP 139 (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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135D ASN* 2.9 30.4 + - - +
136D ASP* 3.6 15.1 - - - +
137D MET 3.2 0.2 - - - -
138D LEU* 1.3 76.0 - - - +
140D LEU* 1.3 59.7 + - + +
141D ALA 3.3 0.4 - - - -
144D LEU* 4.4 11.2 - - - +
171E VAL* 3.8 2.6 - - - +
172E ALA* 3.9 15.2 - - + +
175E ARG* 2.7 38.5 + - - +
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Residues in contact with LEU 140 (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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113D SER* 3.5 14.3 + - - +
136D ASP 3.9 14.1 - - - +
137D MET* 3.0 25.6 + - + +
139D ASP* 1.3 80.7 - - + +
141D ALA* 1.3 62.4 + - - +
142D TYR* 3.4 2.6 + - - +
102E GLY* 5.4 6.3 - - - +
114E THR* 4.0 26.2 - - + -
170E THR* 3.9 34.3 - - + +
171E VAL* 3.4 15.9 - - + +
172E ALA* 4.4 7.6 - - + -
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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