Contacts of the helix formed by residues 123 - 132 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7J ASN* 3.7 11.4 - - - +
121J VAL* 3.3 16.8 - - + +
122J ASP* 1.3 84.6 - - - +
124J HIS* 1.3 58.4 + - - +
126J CYS* 3.4 9.6 + - + +
127J ASP* 3.0 28.8 + - - +
111Q LEU* 3.7 18.8 - - + +
114Q HIS* 3.5 47.3 - - + +
115Q LYS 5.9 0.2 - - - +
130Q GLU* 4.3 6.0 - - - +
134Q LEU* 3.7 13.9 - - + -
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Residues in contact with HIS 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ASN* 6.3 0.2 - - - +
68J TYR* 2.8 40.1 + + - -
71J LYS* 5.4 0.9 - - + -
72J ARG* 3.6 13.6 + - - +
122J ASP* 3.3 8.0 + - - +
123J PRO* 1.3 79.6 - - + +
125J LEU* 1.3 60.7 + - - +
127J ASP* 3.5 8.8 + - + +
128J PHE* 3.1 24.6 + - + +
111Q LEU* 5.7 3.6 - - + -
134Q LEU* 3.5 39.8 - - + +
135Q GLU* 3.0 33.4 + - + +
138Q VAL* 3.3 27.8 - - + +
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Residues in contact with LEU 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J TYR* 4.4 6.7 - - + -
12J CYS* 4.0 28.5 - - + -
16J VAL* 4.3 13.9 - - + -
65J PHE* 5.3 0.4 - - + -
68J TYR* 3.2 33.4 + - + +
113J LEU* 4.4 12.6 - - + -
117J ALA* 3.9 20.0 - - + -
122J ASP* 2.9 23.4 + - - +
124J HIS* 1.3 74.8 - - - +
126J CYS* 1.3 65.3 + - - +
128J PHE* 3.5 12.9 + - + +
129J LEU* 3.1 36.4 + - + +
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Residues in contact with CYS 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J HIS* 3.6 22.0 - - + +
117J ALA* 3.6 18.2 - - - -
118J THR* 3.5 29.4 - - - -
122J ASP 3.4 15.3 + - - +
123J PRO* 3.5 12.1 - - + +
124J HIS 3.2 0.2 - - - -
125J LEU* 1.3 81.0 - - - +
127J ASP* 1.3 57.0 + - - +
129J LEU* 3.4 3.8 + - - +
130J GLU* 3.1 37.1 + - - +
130Q GLU* 5.7 3.6 - - - +
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Residues in contact with ASP 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J PRO 3.0 17.1 + - - +
124J HIS* 3.8 8.9 - - + +
126J CYS* 1.3 75.8 - - - +
128J PHE* 1.3 60.3 + - - +
130J GLU* 3.2 11.5 + - - +
131J SER* 2.9 50.5 + - - -
127N ASP* 5.6 1.0 - - - +
127Q ASP* 5.6 1.0 - - - +
130Q GLU* 3.7 47.5 + - + +
131Q SER* 5.0 4.0 + - - -
134Q LEU* 6.4 0.2 - - + -
135Q GLU* 5.1 7.4 - - - +
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Residues in contact with PHE 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64J LYS* 3.7 24.0 - - + -
65J PHE* 3.5 20.6 - + - -
68J TYR* 3.6 38.4 - + + -
71J LYS* 6.2 2.2 - - - -
124J HIS* 3.1 19.1 + - + +
125J LEU* 3.6 9.9 - - + +
127J ASP* 1.3 77.3 + - - +
129J LEU* 1.3 68.7 + - + +
131J SER* 4.7 2.7 - - - -
132J GLU* 3.0 51.5 + - + +
133J TYR* 3.5 31.0 - + - -
135Q GLU* 5.8 3.6 - - - -
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Residues in contact with LEU 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65J PHE* 4.0 33.2 - - + -
110J LEU* 4.3 16.6 - - + +
113J LEU* 3.9 19.1 - - + +
114J HIS* 3.8 41.5 - - + +
117J ALA* 5.1 0.2 - - + -
125J LEU* 3.1 27.3 + - + +
126J CYS* 3.6 4.7 - - - +
128J PHE* 1.3 88.4 - - + +
130J GLU* 1.3 58.1 + - - +
133J TYR* 3.0 15.6 + - + +
134J LEU* 2.9 33.8 + - + +
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Residues in contact with GLU 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J HIS* 2.9 28.7 + - - +
126J CYS* 3.1 24.6 + - - +
127J ASP* 3.7 8.2 - - - +
129J LEU* 1.3 76.8 - - - +
131J SER* 1.3 63.1 + - - +
134J LEU* 3.9 24.4 + - + +
135J GLU* 4.1 12.0 + - - +
123N PRO* 4.4 7.3 - - - +
126N CYS* 5.7 2.4 - - - +
127N ASP* 3.7 45.0 - - + +
130N GLU* 3.9 15.5 - - - +
130Q GLU* 3.9 12.2 - - - +
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Residues in contact with SER 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J ASP* 2.9 34.0 + - - -
128J PHE* 4.2 2.7 - - - -
130J GLU* 1.3 79.2 - - - +
132J GLU* 1.3 75.8 + - - +
135J GLU* 5.8 2.3 - - - +
127N ASP* 5.2 4.4 + - - -
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Residues in contact with GLU 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J HIS* 4.6 4.7 + - - -
64J LYS* 2.9 42.3 + - + +
128J PHE* 3.0 41.0 + - + +
131J SER* 1.3 89.5 - - - +
133J TYR* 1.3 78.3 + - + +
136J GLU* 4.2 11.7 - - - +
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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