Contacts of the helix formed by residues 123 - 132 (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 PRO 123 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111L LEU* 3.7 19.7 - - + +
114L HIS* 3.5 43.1 - - + +
130L GLU* 4.4 5.6 - - - +
134L LEU* 3.8 17.5 - - + -
7T ASN* 3.7 11.4 - - - +
121T VAL* 3.3 16.8 - - + +
122T ASP* 1.3 83.8 - - - +
124T HIS* 1.3 58.7 + - + +
126T CYS* 3.4 8.2 + - + +
127T ASP* 3.0 29.1 + - - +
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Residues in contact with HIS 124 (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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111L LEU* 5.7 3.6 - - + -
134L LEU* 3.5 39.4 - - + +
135L GLU* 3.0 32.8 + - + +
138L VAL* 3.3 28.9 - - + +
7T ASN* 6.3 0.2 - - - +
68T TYR* 2.8 39.4 + + - -
71T LYS* 5.4 0.4 - - + -
72T ARG* 3.6 13.8 + - - +
122T ASP* 3.3 7.7 - - - +
123T PRO* 1.3 80.0 - - + +
125T LEU* 1.3 60.5 + - - +
127T ASP* 3.5 8.3 + - + +
128T PHE* 3.1 25.0 + - + +
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Residues in contact with LEU 125 (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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8T TYR* 4.4 7.4 - - + -
12T CYS* 4.0 28.0 - - + -
16T VAL* 4.3 14.4 - - + -
65T PHE* 5.3 0.2 - - + -
68T TYR* 3.2 33.6 + - + +
113T LEU* 4.4 12.3 - - + -
117T ALA* 3.9 20.9 - - + -
122T ASP* 2.9 23.2 + - - +
124T HIS* 1.3 75.4 - - - +
126T CYS* 1.3 66.0 + - - +
128T PHE* 3.6 13.2 - - + +
129T LEU* 3.1 35.7 + - + +
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Residues in contact with CYS 126 (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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130L GLU* 5.7 3.1 - - - +
114T HIS* 3.6 21.1 - - + +
117T ALA* 3.6 18.6 - - - -
118T THR* 3.5 29.4 - - - -
122T ASP 3.4 14.9 + - - -
123T PRO* 3.5 12.8 - - + +
125T LEU* 1.3 80.5 - - - +
127T ASP* 1.3 58.2 + - - +
129T LEU* 3.4 3.8 + - - +
130T GLU* 3.1 37.0 + - - +
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Residues in contact with ASP 127 (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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127L ASP* 5.6 1.0 - - - +
130L GLU* 3.7 48.1 - - + +
131L SER* 5.3 2.9 + - - -
134L LEU* 6.1 0.6 - - + +
135L GLU* 5.1 7.8 - - - +
127M ASP* 5.6 1.0 - - - +
123T PRO 3.0 17.1 + - - +
124T HIS* 3.8 9.0 - - + +
125T LEU 3.3 0.2 - - - -
126T CYS* 1.3 74.7 - - - +
128T PHE* 1.3 60.8 + - - +
130T GLU* 4.2 11.9 - - - +
131T SER* 2.9 49.6 + - - -
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Residues in contact with PHE 128 (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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135L GLU* 5.7 4.0 - - - -
64T LYS* 3.7 24.2 - - + -
65T PHE* 3.5 20.4 - + - -
68T TYR* 3.6 38.1 - + + -
71T LYS* 6.2 2.9 - - - -
124T HIS* 3.1 19.6 + - + +
125T LEU* 3.6 9.6 - - + +
126T CYS 3.3 0.2 - - - -
127T ASP* 1.3 77.5 + - - +
129T LEU* 1.3 68.8 + - + +
131T SER* 4.7 2.9 - - - -
132T GLU* 3.0 53.0 + - + +
133T TYR* 3.5 30.7 - + - -
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Residues in contact with LEU 129 (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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65T PHE* 4.0 33.7 - - + -
110T LEU* 4.2 17.0 - - + +
113T LEU* 3.9 19.1 - - + +
114T HIS* 3.8 40.8 - - + +
117T ALA* 5.1 0.2 - - + -
125T LEU* 3.1 26.7 + - + +
126T CYS* 3.6 4.3 - - - +
127T ASP 3.2 0.2 - - - -
128T PHE* 1.3 89.8 - - + +
130T GLU* 1.3 57.8 + - - +
133T TYR* 3.0 15.3 + - + +
134T LEU* 2.9 33.0 + - + +
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Residues in contact with GLU 130 (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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130L GLU* 3.9 18.1 - - - +
123M PRO* 4.4 7.2 - - - +
126M CYS* 5.7 2.2 - - - +
127M ASP* 3.7 45.5 - - + +
130M GLU* 4.0 9.5 - - - +
114T HIS* 2.9 29.1 + - - +
126T CYS* 3.1 23.5 + - - +
127T ASP* 3.7 8.8 - - - +
129T LEU* 1.3 77.4 - - - +
131T SER* 1.3 62.5 + - - +
134T LEU* 3.9 25.6 + - + +
135T GLU* 4.1 11.6 + - - +
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Residues in contact with SER 131 (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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127M ASP* 5.3 3.8 + - - -
127T ASP* 2.9 34.6 + - - -
128T PHE* 4.2 2.5 - - - -
130T GLU* 1.3 78.6 - - - +
132T GLU* 1.3 75.7 + - - +
135T GLU* 5.8 3.0 - - - +
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Residues in contact with GLU 132 (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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61T HIS* 4.6 4.2 + - - -
64T LYS* 2.9 41.5 + - + +
128T PHE* 3.0 39.9 + - + +
131T SER* 1.3 91.1 - - - +
133T TYR* 1.3 79.3 + - + +
136T GLU* 4.2 12.2 - - - +
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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