Contacts of the helix formed by residues 123 - 132 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7P ASN* 3.7 11.4 - - - +
121P VAL* 3.3 17.2 - - + +
122P ASP* 1.3 84.4 - - - +
124P HIS* 1.3 59.0 + - - +
126P CYS* 3.4 8.6 + - + +
127P ASP* 3.0 28.2 + - - +
111U LEU* 3.7 19.3 - - + +
114U HIS* 3.5 43.7 - - + +
115U LYS 5.9 0.2 - - - +
130U GLU* 4.4 6.1 - - - +
134U LEU* 3.7 16.8 - - + -
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Residues in contact with HIS 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P TYR* 2.8 39.8 + + - -
71P LYS* 5.4 0.7 - - + -
72P ARG* 3.6 12.7 + - - +
122P ASP* 3.3 8.2 + - - +
123P PRO* 1.3 79.4 - - + +
125P LEU* 1.3 60.2 + - - +
127P ASP* 3.5 9.1 + - + +
128P PHE* 3.1 24.7 + - + +
111U LEU* 5.7 3.1 - - + -
134U LEU* 3.4 39.8 - - + +
135U GLU* 3.0 33.8 + - + +
138U VAL* 3.3 30.2 - - + +
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Residues in contact with LEU 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P TYR* 4.4 7.4 - - + -
12P CYS* 4.0 28.0 - - + -
16P VAL* 4.3 13.2 - - + -
65P PHE* 5.3 0.2 - - + -
68P TYR* 3.2 32.9 + - + +
113P LEU* 4.4 12.6 - - + -
117P ALA* 3.9 20.4 - - + -
122P ASP* 2.9 24.3 + - - +
124P HIS* 1.3 74.8 - - - +
126P CYS* 1.3 65.8 + - - +
128P PHE* 3.5 12.7 + - + -
129P LEU* 3.1 36.2 + - + +
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Residues in contact with CYS 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114P HIS* 3.6 21.9 - - + +
117P ALA* 3.6 18.2 - - - -
118P THR* 3.5 28.9 - - - -
122P ASP 3.4 15.8 + - - +
123P PRO* 3.5 11.4 - - + +
124P HIS 3.2 0.2 - - - -
125P LEU* 1.3 80.2 - - - +
127P ASP* 1.3 58.0 + - - +
129P LEU* 3.4 3.5 + - - +
130P GLU* 3.1 37.7 + - - +
130U GLU* 5.7 3.1 - - - +
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Residues in contact with ASP 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K ASP* 5.7 0.7 - - - +
123P PRO 3.0 17.1 + - - +
124P HIS* 3.8 8.9 - - + +
126P CYS* 1.3 73.7 - - - +
128P PHE* 1.3 61.6 + - - +
130P GLU* 4.2 12.0 - - - +
131P SER* 2.9 50.2 + - - -
127U ASP* 5.6 0.9 - - - +
130U GLU* 3.6 47.8 + - + +
131U SER* 5.0 4.2 + - - -
134U LEU* 6.1 0.6 - - + +
135U GLU* 5.0 8.7 + - - +
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Residues in contact with PHE 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64P LYS* 3.7 24.7 - - + -
65P PHE* 3.5 20.4 - + - -
68P TYR* 3.6 38.4 - + + -
71P LYS* 6.2 2.5 - - - -
124P HIS* 3.1 19.2 + - + +
125P LEU* 3.6 9.4 - - + +
126P CYS 3.3 0.2 - - - -
127P ASP* 1.3 77.2 + - - +
129P LEU* 1.3 68.3 + - + +
131P SER* 4.7 2.7 - - - -
132P GLU* 3.0 52.4 + - + +
133P TYR* 3.5 30.9 - + - -
135U GLU* 5.7 3.8 - - - -
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Residues in contact with LEU 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65P PHE* 4.0 32.5 - - + -
110P LEU* 4.3 15.9 - - + +
113P LEU* 3.9 18.2 - - + +
114P HIS* 3.8 40.4 - - + +
125P LEU* 3.1 26.7 + - + +
126P CYS* 3.6 4.5 - - - +
128P PHE* 1.3 89.6 - - + +
130P GLU* 1.3 59.0 + - - +
133P TYR* 3.0 15.8 + - + +
134P LEU* 2.9 33.1 + - + +
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Residues in contact with GLU 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K PRO* 4.4 7.6 - - - +
126K CYS* 5.8 2.5 - - - +
127K ASP* 3.7 45.7 - - + +
130K GLU* 4.0 10.1 - - - +
114P HIS* 2.9 29.3 + - - +
126P CYS* 3.1 23.9 + - - +
127P ASP* 3.7 8.6 - - - +
129P LEU* 1.3 77.5 - - - +
131P SER* 1.3 62.3 + - - +
134P LEU* 3.9 17.3 - - + +
135P GLU* 4.1 19.1 + - - +
130U GLU* 3.9 18.2 - - - +
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Residues in contact with SER 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K ASP* 5.3 3.6 + - - -
127P ASP* 2.9 35.2 + - - -
128P PHE* 4.2 2.2 - - - -
130P GLU* 1.3 79.2 - - - +
132P GLU* 1.3 74.7 + - - +
135P GLU* 5.8 2.8 - - - +
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Residues in contact with GLU 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P HIS* 4.6 4.2 + - - -
64P LYS* 2.9 42.0 + - + +
128P PHE* 3.0 40.7 + - + +
131P SER* 1.3 89.3 - - - +
133P TYR* 1.3 78.0 + - + +
136P GLU* 4.2 12.8 - - - +
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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