Contacts of the helix formed by residues 160 - 170 (chain D) in PDB entry 5MR5
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 HIS 160 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159D ASN* 1.3 75.8 - - - +
161D CYS* 1.3 56.9 + - - +
163D ASP* 3.5 17.0 + - - +
164D ALA* 3.0 26.2 + - - +
218D ARG* 4.9 3.5 + - - +
222D CYS* 3.8 12.6 - - + +
223D SER* 3.4 42.7 + - - +
225D GLN* 5.8 5.5 + - - -
356D GLY 4.2 11.1 + - - +
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Residues in contact with CYS 161 (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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159D ASN* 2.8 7.9 + - - +
160D HIS* 1.3 75.4 - - - +
162D LEU* 1.3 64.0 + - - +
164D ALA* 3.3 4.2 + - - +
165D ALA* 3.1 19.9 + - - +
219D MET* 5.4 0.9 - - - +
222D CYS* 2.0 49.8 - - - -
224D CYS* 3.4 10.5 - - - -
229D CYS* 3.3 27.8 - - - +
232D ARG* 3.6 27.1 - - + -
233D ARG* 3.9 6.1 - - - +
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Residues in contact with LEU 162 (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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111B ARG* 4.9 6.7 - - - +
122B ASP* 3.9 41.1 - - + +
123B GLU* 4.0 14.9 - - + +
124B THR* 6.3 1.3 - - + -
159D ASN* 2.7 39.0 + - - +
161D CYS* 1.3 70.3 - - - +
163D ASP* 1.3 64.8 + - - +
165D ALA* 3.3 4.6 + - - +
166D LYS* 3.0 22.6 + - + +
232D ARG* 3.6 34.4 - - - +
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Residues in contact with ASP 163 (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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159D ASN 3.1 24.2 + - - +
160D HIS* 3.5 24.5 + - - +
162D LEU* 1.3 77.4 - - - +
164D ALA* 1.3 58.0 + - - +
166D LYS* 3.3 13.3 + - - +
167D ALA* 3.0 23.9 + - - +
218D ARG* 3.5 24.2 + - - +
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Residues in contact with ALA 164 (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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160D HIS 3.0 12.8 + - - +
161D CYS 3.5 9.9 - - - +
163D ASP* 1.3 74.3 - - - +
165D ALA* 1.3 64.2 + - - +
167D ALA* 3.5 3.4 + - - +
168D CYS* 3.1 22.5 + - - +
215D TYR* 5.0 2.1 - - - +
218D ARG* 3.5 51.8 - - + +
219D MET* 3.7 15.8 - - + +
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Residues in contact with ALA 165 (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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123B GLU* 3.7 28.0 - - + +
161D CYS 3.1 12.9 + - - +
162D LEU* 3.3 8.5 + - - +
164D ALA* 1.3 75.7 - - - +
166D LYS* 1.3 56.7 + - - +
168D CYS* 3.2 7.3 + - - +
169D ASN* 2.9 33.4 + - - +
178D ARG* 3.8 17.9 - - - +
219D MET* 4.2 6.8 - - + +
232D ARG* 4.0 7.9 - - - +
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Residues in contact with LYS 166 (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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109B GLU* 3.7 23.6 + - - -
123B GLU* 6.3 0.2 - - - +
124B THR* 3.6 43.1 - - + +
162D LEU* 3.0 13.8 + - + +
163D ASP* 3.4 16.4 - - - +
165D ALA* 1.3 73.6 - - - +
167D ALA* 1.3 66.5 + - - +
169D ASN* 3.2 1.7 + - - +
170D LEU* 3.0 43.0 + - + +
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Residues in contact with ALA 167 (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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163D ASP 3.0 5.9 + - - +
164D ALA 3.8 6.7 - - - +
166D LYS* 1.3 79.3 - - - +
168D CYS* 1.3 64.1 + - - +
170D LEU* 3.5 7.6 + - - +
171D ASN* 3.3 20.3 + - - +
215D TYR* 3.7 22.0 - - + -
218D ARG* 3.5 29.6 - - - +
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Residues in contact with CYS 168 (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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164D ALA 3.1 14.0 + - - +
165D ALA* 3.5 8.5 - - - +
166D LYS 3.1 0.2 - - - -
167D ALA* 1.3 75.7 - - - +
169D ASN* 1.3 59.4 + - - +
171D ASN 2.9 27.9 + - - +
174D CYS* 2.1 63.4 - - - +
175D LYS 3.3 4.9 + - - -
178D ARG* 3.8 23.1 - - - -
207D PHE* 4.3 0.2 - - - -
215D TYR* 4.3 5.1 - - + -
219D MET* 3.8 15.5 - - - -
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Residues in contact with ASN 169 (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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123B GLU* 3.4 7.1 + - - -
124B THR 3.3 27.9 + - - +
125B VAL* 4.0 15.3 - - - +
126B LEU* 4.5 8.3 + - - +
174B VAL* 4.1 2.5 - - + +
175B SER 3.3 23.0 + - - +
176B PHE* 4.8 0.2 - - - +
165D ALA 2.9 15.2 + - - +
166D LYS 3.2 1.8 + - - +
168D CYS* 1.3 73.7 - - - +
170D LEU* 1.3 61.0 + - - +
171D ASN 3.2 1.1 - - - +
172D ASP* 5.4 0.2 - - - -
175D LYS* 3.4 41.7 - - + +
178D ARG* 3.1 33.2 + - - +
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Residues in contact with LEU 170 (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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109B GLU* 3.5 43.1 - - + +
124B THR* 4.2 4.7 - - - +
125B VAL* 4.2 4.9 - - - -
126B LEU* 3.7 43.5 - - + +
166D LYS* 3.0 42.0 + - + +
167D ALA* 3.8 6.7 - - - +
168D CYS 3.2 0.2 + - - -
169D ASN* 1.3 76.7 - - + +
171D ASN* 1.3 57.5 + - - +
172D ASP 4.1 0.2 - - - -
401D SO4 3.6 10.6 + - - -
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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