Contacts of the helix formed by residues 160 - 169 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ARG* 3.3 43.0 + - - +
158I GLU 3.2 8.0 + - - -
159I ASN* 1.3 71.4 + - - +
161I MET* 1.3 65.0 + - - +
163I GLU* 3.3 5.6 + - - -
164I TYR* 3.1 19.6 + - - +
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Residues in contact with MET 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ARG 3.6 3.8 + - - -
154B LEU* 4.1 24.7 - - + +
159B ASN* 3.8 26.7 - - - +
161B MET* 3.6 30.1 - - + +
162B GLY* 4.5 4.3 - - - -
165B LEU* 4.0 24.2 - - + -
161H MET* 3.6 34.5 - - + +
159I ASN* 3.4 10.8 + - - +
160I GLY* 1.3 73.5 - - - +
162I GLY* 1.3 65.5 + - - +
164I TYR* 3.4 1.7 + - - +
165I LEU* 3.1 24.6 + - + +
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Residues in contact with GLY 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H MET* 4.4 3.4 - - - -
154I LEU* 3.3 35.7 - - - +
156I LEU* 3.9 5.4 - - - -
159I ASN* 3.3 24.0 + - - +
160I GLY 3.2 0.6 - - - -
161I MET* 1.3 79.0 - - - +
163I GLU* 1.3 60.4 + - - +
165I LEU* 3.5 1.9 + - - +
166I PHE 3.1 17.8 + - - -
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Residues in contact with GLU 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ARG* 3.4 21.6 + - - +
44I LEU* 3.9 18.7 - - + +
91I ASN* 3.5 13.1 - - - +
92I THR* 2.8 46.2 + - + +
156I LEU* 3.5 28.5 - - + +
159I ASN 3.3 10.1 + - - +
160I GLY* 3.3 10.8 + - - +
162I GLY* 1.3 74.2 - - - +
164I TYR* 1.3 64.7 + - - +
166I PHE* 3.3 6.6 + - - +
167I ASP* 3.2 20.8 + - - +
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Residues in contact with TYR 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ASN* 3.2 29.2 - - + -
153B ARG* 4.1 9.5 - - - +
154B LEU* 3.8 40.8 - - + -
165B LEU* 4.4 8.1 - - + -
166B PHE* 3.6 8.5 - + - -
169B HIS* 3.0 37.1 - + + +
170B SER* 3.0 29.7 + - - -
44I LEU* 4.6 2.2 - - - -
160I GLY 3.1 12.9 + - - +
161I MET 3.6 7.0 - - - +
163I GLU* 1.3 77.6 - - - +
165I LEU* 1.3 73.0 + - + +
167I ASP* 3.3 4.5 + - - +
168I LYS* 3.1 54.9 + - + +
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Residues in contact with LEU 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU* 4.0 31.0 - - + -
169B HIS* 4.7 7.4 - - - +
161H MET* 3.9 27.8 - - + -
164H TYR* 4.1 10.8 - - + -
165H LEU* 4.0 26.2 - - + -
154I LEU* 4.9 2.9 - - + -
161I MET* 3.1 25.3 + - + +
162I GLY* 3.8 5.6 - - - +
163I GLU 3.3 0.2 - - - -
164I TYR* 1.3 84.0 - - + +
166I PHE* 1.3 65.7 + - - +
168I LYS* 3.1 3.8 + - + +
169I HIS* 3.0 46.0 + - + +
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Residues in contact with PHE 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164H TYR* 3.5 10.1 - + - -
47I VAL* 4.3 6.7 - - + -
92I THR* 3.8 23.6 - - + -
96I MET* 4.3 6.3 - - + -
147I PHE* 3.6 45.8 - + + -
150I ASN* 4.6 2.7 - - + -
151I LEU* 3.5 35.0 - - + -
154I LEU* 3.8 14.1 - - + +
162I GLY 3.1 14.3 + - - +
163I GLU 3.5 9.2 - - - +
164I TYR 3.3 0.2 - - - -
165I LEU* 1.3 75.8 - - - +
167I ASP* 1.3 63.5 + - - +
170I SER* 3.0 47.7 + - - -
171I VAL* 3.8 19.9 + - + +
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Residues in contact with ASP 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ALA 5.5 0.2 - - - +
44I LEU* 3.3 29.2 - - + +
45I HIS* 4.4 2.3 + - - +
46I ASN* 3.0 66.6 + - - +
47I VAL* 3.1 22.7 + - + -
163I GLU 3.2 9.3 + - - +
164I TYR 3.4 10.5 - - - +
165I LEU 3.2 0.2 - - - -
166I PHE* 1.3 82.7 - - - +
168I LYS* 1.3 82.3 + - - +
169I HIS 3.6 0.2 + - - -
171I VAL* 4.4 8.0 + - - +
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Residues in contact with LYS 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ASN* 4.9 2.2 + - - -
169B HIS* 3.9 49.2 + - + +
170B SER* 4.5 3.8 - - - +
44I LEU* 5.0 0.8 - - - +
46I ASN* 4.4 8.5 - - - +
164I TYR* 3.1 60.8 + - + +
165I LEU* 3.1 8.2 + - - +
167I ASP* 1.3 104.3 + - - +
169I HIS* 1.3 67.5 + - + +
171I VAL 5.3 1.6 - - - -
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Residues in contact with HIS 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B HIS* 4.1 21.5 + + - -
164H TYR* 3.1 27.6 - + + +
165H LEU* 4.6 4.8 - - + +
168H LYS* 3.8 34.2 - - + +
169H HIS* 4.0 29.1 + + - -
165I LEU* 3.0 37.2 + - + +
166I PHE 3.4 0.2 + - - -
168I LYS* 1.3 85.2 + - + +
170I SER* 1.3 61.1 + - - +
171I VAL 3.5 3.4 - - - -
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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