Contacts of the helix formed by residues 139 - 151 (chain B) in PDB entry 5MR4
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 ARG 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ARG* 4.5 3.9 - - - +
170A TYR* 3.2 59.8 + - - -
188A GLU* 3.1 32.7 + - - +
137B ALA 3.5 5.1 + - - +
138B ALA* 1.3 76.6 - - - +
140B VAL* 1.3 60.4 + - + +
141B TYR* 3.9 8.3 - - - +
142B ASP* 3.2 26.1 + - - +
143B LEU* 3.0 28.5 + - - +
163B PRO* 5.9 4.2 - - + +
197B VAL 5.4 1.8 + - - -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 4.3 24.3 - - + +
119A TYR* 5.8 2.5 - - + +
186A VAL* 4.2 13.5 - - + -
187A HIS 3.4 25.1 - - - +
188A GLU* 3.6 10.1 - - + +
189A LEU* 3.9 15.3 - - + +
138B ALA 3.9 1.3 + - - +
139B ARG* 1.3 72.3 - - - +
141B TYR* 1.3 59.3 + - - +
143B LEU* 3.8 10.3 - - + +
144B GLY* 2.9 27.9 + - - -
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Residues in contact with TYR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 4.0 7.3 - + - -
128A ARG 3.6 19.7 - - - -
129A TYR* 3.5 12.4 - - + +
130A CYS* 3.0 28.2 + - - +
166A ARG* 3.9 7.2 - - - -
167A PRO* 3.6 22.4 - - + +
170A TYR* 3.8 21.3 - + + -
188A GLU 3.8 10.5 + - - +
189A LEU* 3.4 27.4 - - - +
190A SER 4.2 0.4 - - - -
191A ALA* 3.9 14.8 - - + -
139B ARG* 3.9 5.1 - - + +
140B VAL* 1.3 82.5 - - - +
142B ASP* 1.3 78.3 + - - +
144B GLY* 3.5 1.0 + - - -
145B LEU* 3.0 46.0 + - + +
160B ARG 4.9 1.2 + - - -
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Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ARG* 2.7 44.9 + - - -
138B ALA* 5.5 0.8 - - + -
139B ARG* 3.2 26.9 + - + +
141B TYR* 1.3 87.3 - - - +
143B LEU* 1.3 61.1 + - - +
145B LEU* 3.3 4.3 + - - +
146B ARG* 2.8 46.1 + - - +
161B ALA* 3.3 26.4 - - - +
162B GLN* 4.3 0.4 - - - -
163B PRO* 3.9 11.1 - - - +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU 4.2 3.6 - - - +
117A LEU* 3.8 18.8 - - + -
138B ALA* 3.9 25.4 - - + +
139B ARG 3.0 20.3 + - - +
140B VAL* 3.3 9.2 + - + +
142B ASP* 1.3 76.6 - - - +
144B GLY* 1.3 63.0 + - - +
146B ARG* 3.5 32.9 + - - +
147B ARG* 3.2 23.0 + - - +
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Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU* 4.1 26.6 - - - +
117A LEU* 4.5 4.5 - - - +
127A PHE* 4.5 7.9 - - - -
189A LEU* 5.3 0.4 - - - -
140B VAL 2.9 16.8 + - - -
141B TYR 3.8 1.3 - - - -
143B LEU* 1.3 77.2 - - - +
145B LEU* 1.3 55.6 + - - +
147B ARG* 3.3 3.5 + - - +
148B LEU* 3.0 35.4 + - - +
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PHE* 3.7 13.8 - - + -
129A TYR* 3.6 35.7 - - + -
141B TYR* 3.0 48.5 + - + +
142B ASP* 3.6 4.5 - - - +
144B GLY* 1.3 75.0 - - - +
146B ARG* 1.3 58.1 + - - +
148B LEU* 3.4 3.3 + - - +
149B ARG* 2.9 31.6 + - - +
154B LEU* 3.9 17.2 - - + +
159B VAL* 3.8 22.4 - - + -
160B ARG 3.9 11.9 - - - +
161B ALA* 4.0 13.0 - - + -
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ALA* 4.2 12.1 - - - +
142B ASP* 2.8 32.9 + - - +
143B LEU* 3.6 30.2 - - - +
144B GLY 3.3 0.2 - - - -
145B LEU* 1.3 76.8 - - - +
147B ARG* 1.3 56.5 + - - +
149B ARG* 3.5 18.1 + - - +
150B GLN* 3.0 27.4 + - - +
161B ALA* 2.9 37.8 + - + +
162B GLN* 4.0 17.6 - - - +
163B PRO* 4.8 3.8 - - - +
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A SER 4.5 3.8 + - - -
114A GLU 3.1 40.4 + - - +
115A LEU* 3.5 19.7 - - - +
116A GLY* 3.5 25.4 + - - +
143B LEU 3.2 7.5 + - - +
144B GLY 3.6 5.4 - - - +
146B ARG* 1.3 77.1 - - - +
148B LEU* 1.3 67.8 + - + +
150B GLN* 3.3 8.4 + - - +
151B ARG* 3.0 57.9 + - - +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 3.9 12.8 - - + -
110A VAL* 4.0 15.0 - - + -
114A GLU* 3.8 29.2 - - + +
115A LEU* 4.1 15.9 - - + -
127A PHE* 3.6 38.1 - - + -
144B GLY 3.0 18.8 + - - +
145B LEU 3.9 3.4 - - - +
147B ARG* 1.3 77.3 - - + +
149B ARG* 1.3 59.8 + - - +
151B ARG* 3.4 5.4 + - + +
152B ARG 3.3 3.1 + - - -
153B ARG* 2.9 45.6 + - + +
154B LEU* 3.9 14.9 + - + -
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LEU 2.9 18.1 + - - +
146B ARG* 3.7 17.3 + - - +
147B ARG 3.2 0.2 - - - -
148B LEU* 1.3 73.4 - - - +
150B GLN* 1.3 66.6 + - - +
152B ARG* 3.0 17.2 + - - +
153B ARG 4.9 0.2 - - - +
154B LEU* 4.0 18.9 - - + +
157B GLU 6.1 0.2 - - - -
159B VAL* 3.3 41.3 + - + +
161B ALA* 3.9 24.2 - - - +
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Residues in contact with GLN 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ARG 3.0 17.8 + - - +
147B ARG* 3.3 8.9 + - - +
149B ARG* 1.3 77.0 - - - +
151B ARG* 1.3 77.9 + - - +
152B ARG* 3.2 12.8 + - - +
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A SER 5.7 0.4 + - - -
114A GLU* 3.3 40.8 + - - +
147B ARG* 3.0 41.9 + - - +
148B LEU* 3.9 7.5 - - + +
149B ARG 3.1 0.6 - - - -
150B GLN* 1.3 89.3 + - - +
152B ARG* 1.3 69.9 + - - +
153B ARG* 3.2 21.6 + - + +
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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