Contacts of the helix formed by residues 160 - 169 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153C ARG* 3.3 43.2 + - - -
158M GLU 3.2 8.0 + - - -
159M ASN* 1.3 72.3 + - - +
161M MET* 1.3 64.0 + - - +
163M GLU* 3.3 6.1 + - - -
164M TYR* 3.1 18.9 + - - +
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Residues in contact with MET 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ARG 3.6 4.0 + - - -
154C LEU* 4.0 24.0 - - + -
159C ASN* 3.8 25.8 - - - +
161C MET* 3.6 34.1 - - + +
162C GLY* 4.4 4.3 - - - -
165C LEU* 3.9 25.6 - - + -
159M ASN* 3.4 9.7 + - - +
160M GLY* 1.3 72.8 - - - +
162M GLY* 1.3 65.3 + - - +
164M TYR* 3.4 1.9 + - - +
165M LEU* 3.1 25.0 + - + +
161V MET* 3.6 30.1 - - + +
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Residues in contact with GLY 162 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154M LEU* 3.3 37.1 - - - +
156M LEU* 3.9 5.2 - - - -
159M ASN* 3.3 23.7 + - - +
160M GLY 3.2 0.8 - - - -
161M MET* 1.3 79.6 - - - +
163M GLU* 1.3 60.4 + - - +
165M LEU* 3.5 1.9 + - - +
166M PHE* 3.1 17.3 + - - +
161V MET* 4.5 3.4 - - - -
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Residues in contact with GLU 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ARG* 3.4 21.5 + - - +
44M LEU* 3.9 19.6 - - + +
91M ASN* 3.5 12.5 - - - +
92M THR* 2.8 46.0 + - - +
156M LEU* 3.5 27.4 - - + +
159M ASN 3.3 10.3 + - - +
160M GLY* 3.3 10.1 + - - +
162M GLY* 1.3 75.0 - - - +
164M TYR* 1.3 64.9 + - - +
166M PHE* 3.3 6.3 + - - +
167M ASP* 3.2 20.4 + - - +
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Residues in contact with TYR 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ASN* 3.2 27.8 - - + -
153C ARG* 4.1 9.3 - - - +
154C LEU* 3.8 41.7 - - + -
165C LEU* 4.4 7.9 - - + -
166C PHE* 3.5 8.9 - - - -
169C HIS* 3.1 37.5 - + + +
170C SER* 2.9 31.1 + - - -
44M LEU* 4.6 2.7 - - - -
160M GLY 3.1 12.8 + - - +
161M MET 3.6 7.2 - - - +
163M GLU* 1.3 77.9 - - - +
165M LEU* 1.3 72.2 + - + +
167M ASP* 3.3 3.9 + - - -
168M LYS* 3.1 54.4 + - + +
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Residues in contact with LEU 165 (chain M).
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* 4.0 26.5 - - + -
169C HIS* 4.6 12.3 - - + +
154M LEU* 4.9 2.7 - - + -
161M MET* 3.1 25.7 + - + +
162M GLY* 3.8 5.2 - - - +
164M TYR* 1.3 81.2 - - + +
166M PHE* 1.3 67.2 + - - +
168M LYS* 3.1 3.5 + - + +
169M HIS* 3.0 46.6 + - + +
161V MET* 4.1 26.9 - - + -
164V TYR* 4.1 11.9 - - + -
165V LEU* 3.9 26.9 - - + -
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Residues in contact with PHE 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M VAL* 4.3 6.5 - - + -
92M THR* 3.8 23.6 - - + -
96M MET* 4.3 6.3 - - + -
147M PHE* 3.6 45.1 - + + -
150M ASN* 4.6 2.5 - - + -
151M LEU* 3.5 36.3 - - + -
154M LEU* 3.8 13.6 - - + +
162M GLY 3.1 14.5 + - - +
163M GLU 3.5 9.2 - - - +
165M LEU* 1.3 76.2 - - - +
167M ASP* 1.3 65.2 + - - +
170M SER* 3.0 48.4 + - - -
171M VAL* 3.8 20.5 + - + -
164V TYR* 3.5 11.2 - + - -
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Residues in contact with ASP 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44M LEU* 3.3 28.1 - - + +
45M HIS* 4.4 2.3 + - - +
46M ASN* 2.9 66.7 + - - +
47M VAL* 3.1 22.8 + - + +
163M GLU 3.2 8.9 + - - +
164M TYR 3.4 9.6 - - - +
166M PHE* 1.3 82.5 - - - +
168M LYS* 1.3 81.6 + - - +
171M VAL* 4.4 7.7 + - - +
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Residues in contact with LYS 168 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ASN* 4.9 2.6 + - - -
169C HIS* 3.8 48.3 + - + +
170C SER* 4.5 4.3 - - - +
44M LEU* 5.0 1.2 - - - +
46M ASN* 4.4 9.0 - - - +
164M TYR* 3.1 59.6 + - + +
165M LEU* 3.1 8.3 + - + +
167M ASP* 1.3 104.6 + - - +
169M HIS* 1.3 66.4 + - + +
171M VAL 5.3 1.3 - - - -
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Residues in contact with HIS 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C HIS* 4.0 25.3 + + - -
165M LEU* 3.0 34.1 + - + +
166M PHE 3.4 0.6 + - - -
167M ASP 3.4 0.2 - - - -
168M LYS* 1.3 84.7 + - + +
170M SER* 1.3 62.3 + - - +
171M VAL 3.5 3.3 - - - -
164V TYR* 3.2 23.3 - + - +
165V LEU* 4.7 4.4 - - + +
168V LYS* 3.8 36.6 + - + +
169V HIS* 4.0 29.5 + + - -
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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