Contacts of the helix formed by residues 139 - 149 (chain D) in PDB entry 2RHM
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 SER 139 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D ASP* 3.4 4.2 - - - -
138D ARG* 1.3 82.8 - - - +
140D PRO* 1.3 78.2 - - - +
141D ALA* 3.7 7.3 + - - +
142D ASP* 2.4 43.7 + - - -
143D LEU* 3.1 9.4 + - - +
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Residues in contact with PRO 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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138D ARG 4.6 1.1 - - - +
139D SER* 1.3 88.8 - - - +
141D ALA* 1.3 55.9 + - - +
143D LEU* 3.4 9.5 + - + +
144D GLU* 2.9 29.5 + - - +
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Residues in contact with ALA 141 (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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139D SER* 3.2 7.4 + - - +
140D PRO* 1.3 79.2 - - - +
142D ASP* 1.3 59.8 + - - +
144D GLU* 3.4 7.1 + - - +
145D LEU* 2.9 29.3 + - - +
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Residues in contact with ASP 142 (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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137D ASP* 3.1 47.4 - - - +
138D ARG* 4.5 0.7 - - - -
139D SER* 2.4 28.9 + - - +
141D ALA* 1.3 79.1 - - - +
143D LEU* 1.3 57.5 + - + +
145D LEU* 3.4 12.7 + - - +
146D VAL* 3.0 33.6 + - + +
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Residues in contact with LEU 143 (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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118D VAL* 3.6 24.6 - - + +
121D ILE* 4.7 13.9 - - + -
122D LEU* 4.1 37.9 - - + -
137D ASP 5.2 0.9 - - - +
138D ARG* 3.8 26.7 - - + +
139D SER 3.1 12.1 + - - +
140D PRO* 3.9 9.2 - - + +
142D ASP* 1.3 73.7 - - + +
144D GLU* 1.3 60.4 + - - +
146D VAL* 3.3 10.8 + - + +
147D ARG* 2.8 39.6 + - - +
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Residues in contact with GLU 144 (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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140D PRO 2.9 18.3 + - - +
141D ALA* 3.7 7.4 - - - +
142D ASP 3.3 0.2 - - - -
143D LEU* 1.3 75.2 - - - +
145D LEU* 1.3 61.3 + - - +
147D ARG* 3.3 20.2 + - - +
148D SER* 2.8 52.9 + - - +
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Residues in contact with LEU 145 (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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141D ALA 2.9 17.4 + - - +
142D ASP* 3.5 12.1 - - - +
143D LEU 3.2 0.2 - - - -
144D GLU* 1.3 77.0 - - - +
146D VAL* 1.3 63.7 + - + +
148D SER* 4.0 4.7 - - - +
149D ARG* 2.9 66.4 + - + +
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Residues in contact with VAL 146 (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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13D PRO 5.6 0.7 - - - +
114D GLY* 4.1 6.2 - - - -
117D LEU* 3.7 36.4 - - + +
118D VAL* 4.0 11.4 - - + -
121D ILE* 3.8 28.0 - - + -
142D ASP* 3.0 19.2 + - + +
143D LEU* 3.5 13.5 - - + +
145D LEU* 1.3 77.1 - - + +
147D ARG* 1.3 63.0 + - - +
148D SER 3.4 0.7 + - - -
149D ARG* 4.0 34.9 + - - +
150D GLY 5.1 1.2 + - - -
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Residues in contact with ARG 147 (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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114D GLY* 3.4 28.3 + - - -
115D ASP* 2.9 39.0 + - - +
118D VAL* 3.7 34.4 - - + +
143D LEU* 2.8 29.0 + - - +
144D GLU* 3.3 21.2 + - - +
146D VAL* 1.3 74.4 - - - +
148D SER* 1.3 57.2 + - - +
150D GLY 5.3 0.7 + - - -
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Residues in contact with SER 148 (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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144D GLU* 2.8 39.5 + - - +
145D LEU* 3.7 6.1 + - - +
147D ARG* 1.3 79.1 - - - +
149D ARG* 1.3 65.2 + - - +
150D GLY* 3.2 5.0 + - - -
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Residues in contact with ARG 149 (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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12D HIS* 3.7 35.4 + - + +
13D PRO* 3.8 28.7 + - - +
117D LEU* 6.3 0.6 - - - +
121D ILE* 5.7 0.6 - - - +
145D LEU* 2.9 49.2 + - + +
146D VAL* 4.0 37.9 + - - +
147D ARG 3.9 0.8 - - - -
148D SER* 1.3 77.2 + - - +
150D GLY* 1.3 71.2 + - - +
151D ASP 4.7 2.1 - - - +
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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