Contacts of the helix formed by residues 160 - 169 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158N GLU 3.2 8.6 + - - -
159N ASN* 1.3 71.0 + - - +
161N MET* 1.3 64.7 + - - +
163N GLU* 3.3 5.6 + - - -
164N TYR* 3.1 19.1 + - - +
153S ARG* 3.2 42.9 + - - +
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Residues in contact with MET 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159N ASN* 3.4 10.3 + - - +
160N GLY* 1.3 73.1 - - - +
162N GLY* 1.3 66.4 + - - +
164N TYR* 3.4 1.9 + - - +
165N LEU* 3.1 25.0 + - + +
153S ARG 3.6 3.8 + - - -
154S LEU* 4.0 25.4 - - + +
159S ASN* 3.7 26.0 - - - +
161S MET* 3.5 35.4 - - + +
162S GLY* 4.3 4.5 - - - -
165S LEU* 3.9 25.1 - - + -
161U MET* 3.6 29.6 - - + +
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Residues in contact with GLY 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154N LEU* 3.3 35.7 - - - +
156N LEU* 3.9 5.8 - - - -
159N ASN* 3.3 24.2 + - - +
160N GLY 3.2 0.8 - - - -
161N MET* 1.3 78.9 - - - +
163N GLU* 1.3 60.2 + - - +
165N LEU* 3.5 2.1 + - - +
166N PHE 3.1 17.3 + - - -
161U MET* 4.5 3.4 - - - -
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Residues in contact with GLU 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N LEU* 3.9 18.3 - - + +
91N ASN* 3.5 12.7 - - - +
92N THR* 2.8 46.4 + - - +
151N LEU* 5.6 0.2 - - + -
156N LEU* 3.5 26.9 - - + +
159N ASN 3.3 10.3 + - - +
160N GLY* 3.3 10.1 + - - +
162N GLY* 1.3 74.3 - - - +
164N TYR* 1.3 64.5 + - - +
166N PHE* 3.3 7.2 + - - +
167N ASP* 3.2 20.3 + - - +
153S ARG* 3.4 21.9 + - - +
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Residues in contact with TYR 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N LEU* 4.6 2.5 - - - -
160N GLY 3.1 12.7 + - - +
161N MET 3.6 7.4 - - - +
163N GLU* 1.3 76.8 - - - +
165N LEU* 1.3 71.3 + - + +
167N ASP* 3.3 4.3 + - - -
168N LYS* 3.1 53.1 + - + +
150S ASN* 3.1 28.9 - - + -
153S ARG* 4.0 9.3 - - - +
154S LEU* 3.8 43.1 - - + -
165S LEU* 4.3 8.7 - - + -
166S PHE* 3.5 9.3 - + - -
169S HIS* 3.1 37.1 - + + +
170S SER* 2.9 30.3 + - - -
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Residues in contact with LEU 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154N LEU* 4.9 2.9 - - + -
161N MET* 3.1 20.8 + - + +
162N GLY* 3.8 5.6 - - - +
164N TYR* 1.3 82.5 - - + +
166N PHE* 1.3 66.6 + - - +
168N LYS* 3.1 3.3 + - + +
169N HIS* 3.0 49.8 + - + +
165S LEU* 3.9 36.6 - - + -
169S HIS* 4.5 7.6 - - + +
161U MET* 4.0 27.1 - - + -
164U TYR* 4.2 9.2 - - + -
165U LEU* 4.0 25.1 - - + -
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Residues in contact with PHE 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N VAL* 4.3 6.7 - - + -
92N THR* 3.8 24.9 - - + -
96N MET* 4.3 5.6 - - + -
147N PHE* 3.6 44.9 - + + -
150N ASN* 4.6 4.0 - - + -
151N LEU* 3.5 35.4 - - + -
154N LEU* 3.8 13.6 - - + +
162N GLY 3.1 14.1 + - - +
163N GLU* 3.5 9.4 - - - +
164N TYR 3.3 0.2 - - - -
165N LEU* 1.3 77.3 - - - +
167N ASP* 1.3 64.5 + - - +
170N SER* 3.0 48.6 + - - -
171N VAL* 3.8 20.4 + - + -
164U TYR* 3.5 8.5 + - - -
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Residues in contact with ASP 167 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N LEU* 3.3 28.4 - - + +
45N HIS* 4.4 2.1 + - - +
46N ASN* 3.0 67.1 + - - +
47N VAL* 3.1 23.1 + - + +
163N GLU 3.2 9.2 + - - +
164N TYR 3.4 9.9 - - - +
165N LEU 3.2 0.2 - - - -
166N PHE* 1.3 82.2 - - - +
168N LYS* 1.3 81.7 + - - +
171N VAL* 4.4 7.0 + - - +
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Residues in contact with LYS 168 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N LEU* 5.0 1.0 - - - +
46N ASN* 4.4 9.2 - - - +
164N TYR* 3.1 59.2 + - + +
165N LEU* 3.1 8.5 + - - +
167N ASP* 1.3 105.3 + - - +
169N HIS* 1.3 64.9 + - + +
171N VAL 5.3 1.8 - - - -
150S ASN* 4.8 2.8 + - - -
169S HIS* 3.8 50.7 + - + +
170S SER* 4.4 4.5 - - - +
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Residues in contact with HIS 169 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165N LEU* 3.0 34.7 + - + +
166N PHE 3.4 0.2 + - - -
167N ASP 3.4 0.4 - - - -
168N LYS* 1.3 85.3 + - + +
170N SER* 1.3 61.5 + - - +
171N VAL 3.5 3.2 - - - -
169S HIS* 4.0 25.7 + + - -
169T HIS* 6.1 0.2 - + - -
164U TYR* 3.1 27.1 - + + +
165U LEU* 4.7 4.6 - - + +
168U LYS* 3.9 34.6 - - + +
169U HIS* 4.1 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