Contacts of the helix formed by residues 156 - 163 (chain B) in PDB entry 4MXR
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 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ASP 3.6 2.9 - - - -
144B ARG 3.1 24.7 - - - +
145B PRO 3.4 8.5 - - - +
146B PRO* 3.9 9.9 - - + -
152B VAL* 3.7 3.8 - - - +
153B HIS* 3.1 53.1 + - + +
155B GLY* 1.3 76.3 - - - +
157B PRO* 1.3 69.5 - - - +
158B PHE 3.0 3.2 + - - -
159B ARG* 3.1 4.6 + - - +
160B GLN* 2.9 39.8 + - - +
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Residues in contact with PRO 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 3.2 30.7 - - + +
115B ASP* 4.0 5.8 - - - -
117B SER* 4.0 4.3 - - - -
118B ALA* 4.0 19.1 - - + +
142B ASP* 3.5 15.9 - - + +
153B HIS 3.8 0.7 - - - +
154B SER 3.5 14.8 - - - +
155B GLY 3.2 7.2 - - - -
156B THR* 1.3 91.7 - - - +
158B PHE* 1.3 66.8 + - + +
160B GLN* 3.4 14.7 - - - +
161B LEU* 3.2 30.1 + - - +
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Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 4.3 8.1 - - - -
117B SER* 3.8 13.2 - - - -
134B VAL* 3.8 21.3 - - + -
136B ASN* 3.3 41.1 - - + -
141B LEU 4.2 0.7 - - - +
142B ASP* 3.2 23.5 + - + +
143B VAL* 3.8 8.1 - - + -
157B PRO* 1.3 84.5 - - + +
159B ARG* 1.3 62.0 + - - +
160B GLN 3.3 0.2 - - - -
161B LEU* 3.8 24.4 - - + +
162B LEU* 3.0 33.3 + - - +
172B PHE* 3.6 32.8 - + + -
224B PHE* 4.8 1.6 - + - -
226B SER* 3.6 23.1 - - - -
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Residues in contact with ARG 159 (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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142B ASP 3.7 4.0 + - - -
143B VAL* 2.7 45.6 + - - +
144B ARG 3.3 19.7 - - - +
145B PRO* 3.9 26.3 - - - +
146B PRO* 4.8 6.7 - - - +
156B THR* 3.1 9.8 + - - +
158B PHE* 1.3 76.4 - - - +
160B GLN* 1.3 60.6 + - + +
162B LEU 3.4 0.5 + - - -
163B GLU* 2.9 51.9 + - - +
186B HIS* 4.6 7.5 - - - -
189B TYR* 3.4 50.2 + - + +
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Residues in contact with GLN 160 (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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115B ASP* 6.0 1.4 - - - +
118B ALA* 3.6 20.2 - - + +
122B ARG* 3.3 29.2 - - - +
146B PRO* 6.3 2.2 - - + -
152B VAL* 3.4 29.9 - - + +
153B HIS 4.9 0.5 - - - +
156B THR* 2.9 35.0 + - - +
157B PRO* 3.4 7.8 - - - +
159B ARG* 1.3 77.9 - - + +
161B LEU* 1.3 63.0 + - + +
163B GLU* 3.1 26.6 + - - +
164B GLU* 3.4 13.1 + - - +
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Residues in contact with LEU 161 (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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117B SER 3.5 20.0 - - - +
118B ALA* 3.5 24.7 - - + +
121B GLY* 3.7 24.0 - - - -
122B ARG* 3.8 10.3 - - + +
125B LEU* 4.6 8.3 - - + -
134B VAL* 5.0 7.4 - - + -
157B PRO 3.2 16.3 + - - +
158B PHE* 3.9 28.3 - - + +
159B ARG 3.3 0.2 - - - -
160B GLN* 1.3 75.9 - - + +
162B LEU* 1.3 61.4 + - - +
164B GLU* 2.9 29.5 + - + +
167B PHE* 3.6 22.3 - - + +
172B PHE* 6.5 0.2 - - + -
224B PHE* 4.8 4.7 - - + -
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Residues in contact with LEU 162 (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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143B VAL* 4.1 7.9 - - + -
158B PHE 3.0 25.1 + - - +
159B ARG 3.9 3.4 - - - +
161B LEU* 1.3 75.8 - - + +
163B GLU* 1.3 60.0 + - - +
164B GLU 3.2 6.4 + - - +
167B PHE* 3.8 27.9 - - + +
169B GLY* 4.1 17.7 - - - -
172B PHE* 3.8 34.5 - - + -
189B TYR* 3.7 29.4 - - + +
190B VAL* 4.5 11.0 - - + -
193B HIS* 3.6 34.4 + - + -
195B GLY* 5.7 0.4 - - - -
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B PRO* 6.1 0.7 - - - +
159B ARG* 2.9 45.4 + - - +
160B GLN* 3.3 15.3 - - - +
161B LEU 3.0 0.4 - - - -
162B LEU* 1.3 76.0 - - - +
164B GLU* 1.3 61.8 + - - +
165B SER* 3.4 3.1 + - - -
189B TYR* 3.5 12.8 + - - +
193B HIS* 5.2 2.7 - - + +
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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