Contacts of the helix formed by residues 160 - 169 (chain D) in PDB entry 1MFR
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 GLY 160 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158D GLU 3.2 8.0 + - - -
159D ASN* 1.3 71.2 + - - +
161D MET* 1.3 64.0 + - - +
163D GLU* 3.3 6.4 + - - -
164D TYR* 3.1 18.5 + - - +
153X ARG* 3.3 42.5 - - - +
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Residues in contact with MET 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* 3.4 11.2 + - - +
160D GLY* 1.3 72.6 - - - +
162D GLY* 1.3 65.4 + - - +
164D TYR* 3.4 1.7 + - - +
165D LEU* 3.1 24.2 + - + +
161K MET* 3.6 34.3 - - + +
153X ARG 3.6 3.8 + - - +
154X LEU* 4.1 26.5 - - + -
159X ASN* 3.7 26.5 - - - +
161X MET* 3.6 30.1 - - + +
162X GLY* 4.4 4.0 - - - -
165X LEU* 4.0 24.2 - - + -
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Residues in contact with GLY 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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154D LEU* 3.3 35.7 - - - +
156D LEU* 3.9 5.8 - - - -
159D ASN* 3.3 24.4 + - - +
160D GLY 3.2 0.4 - - - -
161D MET* 1.3 79.4 - - - +
163D GLU* 1.3 61.1 + - - +
165D LEU* 3.5 2.3 + - - +
166D PHE* 3.1 17.8 + - - +
161K MET* 4.4 2.9 - - - -
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Residues in contact with GLU 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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44D LEU* 3.9 20.2 - - + +
91D ASN* 3.5 12.4 - - - +
92D THR* 2.8 46.8 + - - +
156D LEU* 3.5 28.8 - - + +
159D ASN 3.3 9.6 + - - +
160D GLY* 3.3 10.7 + - - +
162D GLY* 1.3 73.9 - - - +
164D TYR* 1.3 64.5 + - - +
166D PHE* 3.3 6.7 + - - +
167D ASP* 3.2 20.6 + - - +
153X ARG* 3.5 21.2 + - - +
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Residues in contact with TYR 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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44D LEU* 4.6 2.5 - - - -
160D GLY 3.1 12.8 + - - +
161D MET 3.6 7.6 - - - +
163D GLU* 1.3 78.1 - - - +
165D LEU* 1.3 70.8 + - + +
167D ASP* 3.3 3.7 + - - -
168D LYS* 3.1 60.9 + - + +
150X ASN* 3.2 28.3 - - + -
153X ARG* 4.1 9.1 - - - +
154X LEU* 3.7 43.3 - - + -
165X LEU* 4.4 8.1 - - + -
166X PHE* 3.5 8.8 - - - -
169X HIS* 3.1 31.0 - + + +
170X SER* 2.9 29.6 + - - -
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Residues in contact with LEU 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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154D LEU* 4.9 3.1 - - + -
161D MET* 3.1 25.7 + - + +
162D GLY* 3.8 5.2 - - - +
164D TYR* 1.3 82.3 - - + +
166D PHE* 1.3 64.7 + - - +
168D LYS* 3.1 3.9 + - + +
169D HIS* 3.0 46.2 + - + +
161K MET* 4.0 27.4 - - + -
164K TYR* 4.2 11.9 - - + -
165K LEU* 4.0 26.5 - - + -
165X LEU* 4.0 31.4 - - + -
169X HIS* 4.6 7.4 - - + +
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Residues in contact with PHE 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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47D VAL* 4.3 7.4 - - + -
92D THR* 3.8 23.3 - - + -
96D MET* 4.3 5.6 - - + -
147D PHE* 3.6 45.1 - + + -
150D ASN* 4.6 2.5 - - + -
151D LEU* 3.5 35.9 - - + -
154D LEU* 3.8 14.3 - - + +
162D GLY 3.1 14.0 + - - +
163D GLU 3.5 9.6 - - - +
164D TYR 3.3 0.2 - - - -
165D LEU* 1.3 75.9 - - - +
167D ASP* 1.3 64.3 + - - +
170D SER* 3.0 48.0 + - - -
171D VAL* 3.8 20.1 + - + +
164K TYR* 3.5 10.5 + + - -
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Residues in contact with ASP 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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44D LEU* 3.3 28.0 - - + +
45D HIS* 4.4 2.1 + - - +
46D ASN* 3.0 67.7 + - - +
47D VAL* 3.1 24.2 + - + -
163D GLU 3.2 9.3 + - - +
164D TYR 3.4 10.8 - - - +
166D PHE* 1.3 82.0 - - - +
168D LYS* 1.3 80.5 + - - +
169D HIS 3.6 0.3 + - - -
171D VAL* 4.4 7.6 + - - +
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Residues in contact with LYS 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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44D LEU* 5.0 1.4 - - - +
46D ASN* 4.4 9.0 - - - +
164D TYR* 3.1 59.0 + - + +
165D LEU* 3.1 9.1 + - + +
167D ASP* 1.3 104.2 + - - +
169D HIS* 1.3 65.1 + - + +
171D VAL 5.3 1.8 - - - -
150X ASN* 4.8 2.4 + - - -
169X HIS* 3.8 49.2 + - + +
170X SER* 4.5 3.8 - - - +
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Residues in contact with HIS 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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165D LEU* 3.0 34.7 + - + +
166D PHE 3.4 0.2 + - - -
168D LYS* 1.3 84.8 + - + +
170D SER* 1.3 62.9 + - - +
171D VAL 3.5 3.3 - - - -
164K TYR* 3.1 27.1 - + + +
165K LEU* 4.6 4.0 - - + +
168K LYS* 3.8 34.1 + - + +
169K HIS* 4.0 28.8 + + - -
169X HIS* 4.1 25.1 + + - -
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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