Contacts of the helix formed by residues 160 - 169 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158T GLU 3.2 7.9 + - - -
159T ASN* 1.3 70.8 + - - +
161T MET* 1.3 64.6 + - - +
163T GLU* 3.3 6.4 + - - -
164T TYR* 3.1 18.5 + - - +
153U ARG* 3.3 43.1 - - - +
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Residues in contact with MET 161 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161S MET* 3.6 29.8 - - + +
159T ASN* 3.4 10.1 + - - +
160T GLY* 1.3 73.0 - - - +
162T GLY* 1.3 65.6 + - - +
164T TYR* 3.4 2.4 + - - +
165T LEU* 3.1 24.5 + - + +
153U ARG 3.6 3.6 + - - -
154U LEU* 4.0 25.8 - - + -
159U ASN* 3.8 25.6 - - - +
161U MET* 3.6 34.5 - - + +
162U GLY* 4.4 4.0 - - - -
165U LEU* 3.9 24.9 - - + -
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Residues in contact with GLY 162 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161S MET* 4.5 3.4 - - - -
154T LEU* 3.3 35.7 - - - +
156T LEU* 3.9 5.6 - - - -
159T ASN* 3.3 24.1 + - - +
160T GLY 3.2 0.8 - - - -
161T MET* 1.3 78.9 - - - +
163T GLU* 1.3 61.3 + - - +
165T LEU* 3.5 2.1 + - - +
166T PHE* 3.1 17.5 + - - +
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Residues in contact with GLU 163 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T LEU* 3.9 18.7 - - + +
47T VAL* 5.8 0.2 - - - +
91T ASN* 3.5 12.2 - - - +
92T THR* 2.8 46.9 + - - +
156T LEU* 3.5 28.0 - - + +
159T ASN 3.3 9.6 + - - +
160T GLY* 3.3 10.3 + - - +
162T GLY* 1.3 73.8 - - - +
164T TYR* 1.3 64.8 + - - +
166T PHE* 3.3 6.8 + - - +
167T ASP* 3.2 19.9 + - - +
153U ARG* 3.4 21.3 + - - +
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Residues in contact with TYR 164 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T LEU* 4.6 3.1 - - - -
160T GLY 3.1 12.6 + - - +
161T MET 3.6 7.0 - - - +
163T GLU* 1.3 76.8 - - - +
165T LEU* 1.3 72.4 + - + +
167T ASP* 3.3 3.9 + - - -
168T LYS* 3.1 52.7 + - + +
150U ASN* 3.2 28.9 - - + -
153U ARG* 4.1 9.5 - - - +
154U LEU* 3.8 42.2 - - + -
165U LEU* 4.3 8.1 - - + -
166U PHE* 3.5 8.8 - - - -
169U HIS* 3.1 38.0 - + + +
170U SER* 2.9 30.8 + - - -
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Residues in contact with LEU 165 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161S MET* 3.9 27.8 - - + -
164S TYR* 4.2 11.7 - - + -
165S LEU* 4.0 25.8 - - + -
154T LEU* 4.9 2.7 - - + -
161T MET* 3.1 21.0 + - + +
162T GLY* 3.8 5.2 - - - +
164T TYR* 1.3 81.7 - - + +
166T PHE* 1.3 66.6 + - - +
168T LYS* 3.1 3.6 + - + +
169T HIS* 3.0 46.5 + - + +
165U LEU* 3.9 36.1 - - + -
169U HIS* 4.6 7.2 - - + +
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Residues in contact with PHE 166 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164S TYR* 3.5 9.6 - + - -
47T VAL* 4.3 7.0 - - + -
92T THR* 3.8 23.3 - - + -
96T MET* 4.3 5.8 - - + -
147T PHE* 3.6 45.8 - + + -
150T ASN* 4.6 2.7 - - + -
151T LEU* 3.5 34.3 - - + -
154T LEU* 3.8 13.9 - - + +
162T GLY 3.1 13.6 + - - +
163T GLU 3.5 10.3 - - - +
164T TYR 3.3 0.4 - - - -
165T LEU* 1.3 76.0 - - - +
167T ASP* 1.3 63.6 + - - +
170T SER* 3.0 47.6 + - - -
171T VAL* 3.8 20.4 + - + -
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Residues in contact with ASP 167 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T LEU* 3.3 28.0 - - + +
45T HIS* 4.4 2.1 + - - +
46T ASN* 2.9 67.1 + - - +
47T VAL* 3.1 22.8 + - + -
163T GLU 3.2 8.4 + - - +
164T TYR 3.4 10.5 - - - +
165T LEU 3.2 0.4 - - - -
166T PHE* 1.3 82.1 - - - +
168T LYS* 1.3 80.4 + - - +
169T HIS 3.6 0.2 + - - -
171T VAL* 4.4 7.9 + - - +
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Residues in contact with LYS 168 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T LEU* 5.0 1.0 - - - +
46T ASN* 4.4 8.3 - - - +
164T TYR* 3.1 60.0 + - + +
165T LEU* 3.1 8.0 + - - +
167T ASP* 1.3 104.9 + - - +
169T HIS* 1.3 65.0 + - + +
171T VAL 5.3 1.8 - - - -
150U ASN* 4.9 2.4 + - - -
169U HIS* 3.8 51.1 + - + +
170U SER* 4.5 4.0 - - - +
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Residues in contact with HIS 169 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164S TYR* 3.1 27.1 - + + +
165S LEU* 4.6 4.4 - - + +
168S LYS* 3.8 34.0 + - + +
169S HIS* 4.0 27.8 + + - -
165T LEU* 3.0 35.1 + - + +
166T PHE 3.4 0.4 + - - -
167T ASP 3.4 0.4 - - - -
168T LYS* 1.3 84.9 + - + +
170T SER* 1.3 61.5 + - - +
171T VAL 3.5 2.9 - - - -
169U HIS* 4.0 25.3 + + - -
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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