Contacts of the helix formed by residues 160 - 169 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158C GLU 3.2 7.9 + - - -
159C ASN* 1.3 71.5 + - - +
161C MET* 1.3 64.8 + - - +
163C GLU* 3.3 5.6 + - - -
164C TYR* 3.1 18.9 + - - +
153F ARG* 3.3 42.3 + - - -
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Residues in contact with MET 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ASN* 3.4 10.5 + - - +
160C GLY* 1.3 72.6 - - - +
162C GLY* 1.3 65.6 + - - +
164C TYR* 3.4 1.9 + - - +
165C LEU* 3.1 25.0 + - + +
153F ARG 3.6 3.6 + - - -
154F LEU* 4.1 25.8 - - + -
159F ASN* 3.8 26.2 - - - +
161F MET* 3.6 35.4 - - + +
162F GLY* 4.4 4.0 - - - -
165F LEU* 4.0 24.7 - - + -
161M MET* 3.6 29.2 - - + +
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Residues in contact with GLY 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C LEU* 3.3 36.9 - - - +
156C LEU* 3.9 6.1 - - - -
159C ASN* 3.3 23.7 + - - +
160C GLY 3.2 0.6 - - - -
161C MET* 1.3 79.1 - - - +
163C GLU* 1.3 60.4 + - - +
165C LEU* 3.5 1.9 + - - +
166C PHE* 3.1 17.7 + - - +
161M MET* 4.5 3.1 - - - -
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Residues in contact with GLU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU* 3.9 19.4 - - + +
47C VAL* 5.8 0.2 - - - +
91C ASN* 3.5 12.3 - - - +
92C THR* 2.8 47.0 + - - +
156C LEU* 3.5 28.0 - - + +
159C ASN 3.3 9.9 + - - +
160C GLY* 3.3 10.3 + - - +
162C GLY* 1.3 74.4 - - - +
164C TYR* 1.3 65.1 + - - +
166C PHE* 3.3 6.6 + - - +
167C ASP* 3.2 20.3 + - - +
153F ARG* 3.4 22.0 + - - +
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Residues in contact with TYR 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU* 4.6 2.5 - - - -
160C GLY 3.1 13.4 + - - +
161C MET 3.6 7.0 - - - +
162C GLY 3.3 0.2 - - - -
163C GLU* 1.3 77.4 - - - +
165C LEU* 1.3 72.4 + - + +
167C ASP* 3.3 3.9 + - - +
168C LYS* 3.1 59.4 + - + +
150F ASN* 3.2 29.2 - - + -
153F ARG* 4.1 8.9 - - - +
154F LEU* 3.7 42.6 - - + -
165F LEU* 4.3 8.1 - - + -
166F PHE* 3.5 9.4 - - - -
169F HIS* 3.1 30.9 - + + +
170F SER* 2.9 30.3 + - - -
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C LEU* 4.9 2.9 - - + -
161C MET* 3.1 21.7 + - + +
162C GLY* 3.8 5.6 - - - +
163C GLU 3.3 0.2 - - - -
164C TYR* 1.3 82.7 - - + +
166C PHE* 1.3 66.0 + - - +
168C LYS* 3.1 3.5 + - + +
169C HIS* 3.0 49.2 + - + +
165F LEU* 4.0 36.6 - - + -
169F HIS* 4.6 7.6 - - + +
161M MET* 3.9 27.6 - - + -
164M TYR* 4.2 8.5 - - + -
165M LEU* 4.0 25.1 - - + -
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Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 4.3 7.2 - - + -
92C THR* 3.8 23.3 - - + -
96C MET* 4.3 5.2 - - + -
147C PHE* 3.6 44.2 - + + -
150C ASN* 4.6 4.3 - - + -
151C LEU* 3.5 35.2 - - + -
154C LEU* 3.8 15.1 - - + +
162C GLY 3.1 13.9 + - - +
163C GLU* 3.5 9.0 - - - +
164C TYR 3.3 0.2 - - - -
165C LEU* 1.3 77.4 - - - +
167C ASP* 1.3 64.4 + - - +
170C SER* 3.0 49.1 + - - -
171C VAL* 3.8 20.1 + - + -
164M TYR* 3.5 7.9 - - - -
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Residues in contact with ASP 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU* 3.3 27.7 - - + +
45C HIS* 4.4 2.3 + - - +
46C ASN* 2.9 68.4 + - - +
47C VAL* 3.1 23.2 + - + +
163C GLU 3.2 8.9 + - - +
164C TYR 3.4 10.1 - - - +
165C LEU 3.2 0.4 - - - -
166C PHE* 1.3 82.1 - - - +
168C LYS* 1.3 81.8 + - - +
169C HIS 3.6 0.2 + - - -
171C VAL* 4.4 7.5 + - - +
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Residues in contact with LYS 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU* 5.0 1.4 - - - +
46C ASN* 4.4 8.3 - - - +
164C TYR* 3.1 59.1 + - + +
165C LEU* 3.1 7.6 + - - +
167C ASP* 1.3 104.2 + - - +
169C HIS* 1.3 66.6 + - + +
171C VAL 5.3 1.6 - - - -
150F ASN* 4.8 2.2 + - - -
169F HIS* 3.8 50.5 + - + +
170F SER* 4.4 4.3 - - - +
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Residues in contact with HIS 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C LEU* 3.0 35.1 + - + +
166C PHE 3.4 0.2 + - - -
167C ASP 3.4 0.2 - - - -
168C LYS* 1.3 84.2 + - + +
170C SER* 1.3 62.7 + - - +
171C VAL 3.5 2.9 - - - -
169F HIS* 4.0 25.5 + + - -
164M TYR* 3.1 26.2 - + + +
165M LEU* 4.6 4.4 - - + +
168M LYS* 3.8 36.0 + - + +
169M HIS* 4.0 27.8 + + - -
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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