Contacts of the helix formed by residues 160 - 169 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158S GLU 3.2 8.0 + - - -
159S ASN* 1.3 71.3 + - - +
161S MET* 1.3 63.4 + - - +
163S GLU* 3.3 6.0 + - - -
164S TYR* 3.1 19.2 + - - +
153T ARG* 3.3 43.4 + - - +
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Residues in contact with MET 161 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161N MET* 3.5 34.1 - - + +
159S ASN* 3.4 10.1 + - - +
160S GLY* 1.3 73.9 - - - +
162S GLY* 1.3 65.1 + - - +
164S TYR* 3.4 2.1 + - - +
165S LEU* 3.1 24.6 + - + +
153T ARG 3.6 3.8 + - - -
154T LEU* 4.0 26.0 - - + +
159T ASN* 3.8 24.7 - - - +
161T MET* 3.6 31.2 - - + +
162T GLY* 4.4 4.3 - - - -
165T LEU* 3.9 25.4 - - + -
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Residues in contact with GLY 162 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161N MET* 4.4 3.1 - - - -
154S LEU* 3.3 36.3 - - - +
156S LEU* 3.9 6.3 - - - -
159S ASN* 3.3 22.9 + - - +
160S GLY 3.2 0.4 - - - -
161S MET* 1.3 80.2 - - - +
163S GLU* 1.3 62.0 + - - +
165S LEU* 3.5 1.8 + - - +
166S PHE 3.1 17.7 + - - -
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Residues in contact with GLU 163 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44S LEU* 3.9 19.2 - - + +
47S VAL* 5.8 0.2 - - - +
91S ASN* 3.5 12.8 - - - +
92S THR* 2.8 45.9 + - - +
156S LEU* 3.5 28.0 - - + +
159S ASN 3.3 9.6 + - - +
160S GLY* 3.3 11.1 + - - +
162S GLY* 1.3 74.0 - - - +
164S TYR* 1.3 65.5 + - - +
166S PHE* 3.3 7.3 + - - +
167S ASP* 3.2 19.9 + - - +
153T ARG* 3.5 21.5 + - - +
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Residues in contact with TYR 164 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44S LEU* 4.6 2.5 - - - -
160S GLY 3.1 13.0 + - - +
161S MET 3.6 7.2 - - - +
163S GLU* 1.3 77.9 - - - +
165S LEU* 1.3 71.0 + - + +
167S ASP* 3.3 4.3 + - - +
168S LYS* 3.1 54.6 + - + +
150T ASN* 3.2 28.5 - - + -
153T ARG* 4.1 8.5 - - - +
154T LEU* 3.8 41.1 - - + -
165T LEU* 4.3 7.9 - - + -
166T PHE* 3.5 8.7 - - - -
169T HIS* 3.1 37.6 - + + +
170T SER* 2.9 31.0 + - - -
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Residues in contact with LEU 165 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161N MET* 3.9 28.5 - - + -
164N TYR* 4.1 12.6 - - + -
165N LEU* 3.9 26.7 - - + -
154S LEU* 4.9 2.2 - - + -
161S MET* 3.1 25.9 + - + +
162S GLY* 3.8 4.7 - - - +
164S TYR* 1.3 81.1 - - + +
166S PHE* 1.3 66.0 + - - +
168S LYS* 3.1 3.8 + - + +
169S HIS* 3.0 46.9 + - + +
165T LEU* 4.0 30.7 - - + -
169T HIS* 4.6 7.6 - - + +
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Residues in contact with PHE 166 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164N TYR* 3.5 10.5 + + - -
47S VAL* 4.3 6.5 - - + -
92S THR* 3.8 24.7 - - + -
96S MET* 4.3 5.2 - - + -
147S PHE* 3.6 45.3 - + + -
150S ASN* 4.6 2.9 - - + -
151S LEU* 3.5 35.2 - - + -
154S LEU* 3.8 12.8 - - + +
162S GLY 3.1 13.8 + - - +
163S GLU 3.5 9.6 - - - +
164S TYR 3.3 0.2 - - - -
165S LEU* 1.3 76.9 - - - +
167S ASP* 1.3 64.4 + - - +
170S SER* 3.0 49.0 + - - -
171S VAL* 3.8 21.0 + - + -
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Residues in contact with ASP 167 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44S LEU* 3.3 27.7 - - + +
45S HIS* 4.4 2.3 + - - +
46S ASN* 3.0 67.2 + - - +
47S VAL* 3.1 22.7 + - + +
163S GLU 3.2 8.2 + - - +
164S TYR 3.4 10.3 - - - +
165S LEU 3.2 0.2 - - - -
166S PHE* 1.3 82.1 - - - +
168S LYS* 1.3 82.1 + - - +
169S HIS 3.6 0.3 + - - -
171S VAL* 4.4 7.8 + - - +
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Residues in contact with LYS 168 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44S LEU* 5.0 1.4 - - - +
46S ASN* 4.4 9.0 - - - +
164S TYR* 3.1 58.3 + - + +
165S LEU* 3.1 8.2 + - - +
167S ASP* 1.3 104.0 + - - +
169S HIS* 1.3 65.4 + - + +
171S VAL 5.3 1.8 - - - -
150T ASN* 4.9 2.2 + - - -
169T HIS* 3.8 49.8 + - + +
170T SER* 4.5 4.7 - - - +
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Residues in contact with HIS 169 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164N TYR* 3.1 24.2 - + - +
165N LEU* 4.5 4.4 - - + +
168N LYS* 3.8 37.1 - - + +
169N HIS* 4.0 29.1 + + - -
165S LEU* 3.0 34.5 + - + +
166S PHE 3.4 0.2 + - - -
167S ASP 3.4 0.2 - - - -
168S LYS* 1.3 84.0 + - + +
170S SER* 1.3 62.0 + - - +
171S VAL 3.5 3.3 - - - -
169T HIS* 4.0 25.2 + + - -
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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