Contacts of the helix formed by residues 160 - 169 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158O GLU 3.2 8.4 + - - -
159O ASN* 1.3 71.2 + - - +
161O MET* 1.3 64.3 + - - +
163O GLU* 3.3 6.3 + - - -
164O TYR* 3.1 19.4 + - - +
153R ARG* 3.3 41.5 + - - +
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Residues in contact with MET 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A MET* 3.6 29.4 - - + +
159O ASN* 3.4 10.4 + - - +
160O GLY* 1.3 72.6 - - - +
162O GLY* 1.3 65.9 + - - +
164O TYR* 3.4 1.6 + - - +
165O LEU* 3.1 24.6 + - + +
153R ARG 3.7 3.8 + - - -
154R LEU* 4.1 24.2 - - + -
159R ASN* 3.8 25.4 - - - +
161R MET* 3.6 35.2 - - + +
162R GLY* 4.5 3.8 - - - -
165R LEU* 4.0 25.4 - - + -
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Residues in contact with GLY 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A MET* 4.5 2.7 - - - -
154O LEU* 3.3 35.8 - - - +
156O LEU* 3.9 5.8 - - - -
159O ASN* 3.3 24.2 + - - +
160O GLY 3.2 0.6 - - - -
161O MET* 1.3 79.6 - - - +
163O GLU* 1.3 61.2 + - - +
165O LEU* 3.5 1.9 + - - +
166O PHE 3.1 17.3 + - - -
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Residues in contact with GLU 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O LEU* 3.9 19.1 - - + +
91O ASN* 3.5 12.0 - - - +
92O THR* 2.8 45.7 + - - +
156O LEU* 3.5 29.0 - - + +
159O ASN 3.3 9.4 + - - +
160O GLY* 3.5 10.1 - - - +
162O GLY* 1.3 75.4 - - - +
164O TYR* 1.3 65.9 + - - +
166O PHE* 3.3 6.5 + - - +
167O ASP* 3.2 19.9 + - - +
153R ARG* 3.5 20.5 + - - +
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Residues in contact with TYR 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O LEU* 4.6 2.5 - - - -
160O GLY 3.1 12.6 + - - +
161O MET 3.6 7.4 - - - +
162O GLY 3.3 0.2 - - - -
163O GLU* 1.3 78.3 - - - +
165O LEU* 1.3 73.3 + - + +
167O ASP* 3.3 3.8 + - - -
168O LYS* 3.1 55.3 + - + +
150R ASN* 3.2 28.7 - - + -
153R ARG* 4.1 9.1 - - - +
154R LEU* 3.8 42.0 - - + -
165R LEU* 4.4 7.9 - - + -
166R PHE* 3.5 9.1 - - - -
169R HIS* 3.1 36.5 - + + +
170R SER* 3.0 29.6 + - - -
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Residues in contact with LEU 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A MET* 4.0 27.4 - - + -
164A TYR* 4.1 11.9 - - + -
165A LEU* 4.0 26.5 - - + -
165J LEU* 6.5 0.2 - - + -
154O LEU* 4.9 2.9 - - + -
161O MET* 3.1 24.5 + - + +
162O GLY* 3.8 5.6 - - - +
163O GLU 3.3 0.2 - - - -
164O TYR* 1.3 82.1 - - + +
166O PHE* 1.3 66.0 + - - +
168O LYS* 3.1 3.4 + - + +
169O HIS* 3.0 45.5 + - + +
165R LEU* 4.0 31.0 - - + -
169R HIS* 4.6 7.6 - - + +
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Residues in contact with PHE 166 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A TYR* 3.5 9.2 - + - -
47O VAL* 4.3 6.7 - - + -
92O THR* 3.8 24.0 - - + -
96O MET* 4.3 6.7 - - + -
147O PHE* 3.6 44.9 - + + -
150O ASN* 4.6 2.7 - - + -
151O LEU* 3.5 33.4 - - + -
154O LEU* 3.8 14.8 - - + +
162O GLY 3.1 13.2 + - - +
163O GLU 3.5 9.9 - - - +
164O TYR 3.3 0.2 - - - -
165O LEU* 1.3 77.1 - - - +
167O ASP* 1.3 62.6 + - - +
170O SER* 3.0 48.7 + - - -
171O VAL* 3.8 20.3 + - + +
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Residues in contact with ASP 167 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O ALA 5.5 0.3 - - - +
44O LEU* 3.3 27.3 - - + +
45O HIS* 4.4 2.1 + - - +
46O ASN* 3.0 65.2 + - - +
47O VAL* 3.1 23.5 + - + +
163O GLU 3.2 8.9 + - - +
164O TYR 3.4 10.3 - - - +
165O LEU 3.2 0.4 - - - -
166O PHE* 1.3 82.7 - - - +
168O LYS* 1.3 81.7 + - - +
169O HIS 3.6 0.2 + - - -
171O VAL* 4.4 7.7 + - - +
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Residues in contact with LYS 168 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O LEU* 5.0 1.0 - - - +
46O ASN* 4.4 8.3 - - - +
164O TYR* 3.1 59.7 + - + +
165O LEU* 3.1 8.3 + - - +
167O ASP* 1.3 105.1 + - - +
169O HIS* 1.3 66.6 + - + +
171O VAL 5.3 1.6 - - - -
150R ASN* 4.9 2.2 + - - -
169R HIS* 3.8 49.6 + - + +
170R SER* 4.5 3.6 - - - +
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Residues in contact with HIS 169 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A TYR* 3.1 28.3 - + + +
165A LEU* 4.6 4.3 - - + +
168A LYS* 3.8 34.9 + - + +
169A HIS* 4.1 29.1 + + - -
165O LEU* 3.0 35.3 + - + +
166O PHE 3.4 0.4 + - - -
168O LYS* 1.3 83.6 + - + +
170O SER* 1.3 61.4 + - - +
171O VAL 3.5 2.9 - - - -
169R HIS* 4.1 24.9 + + - -
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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