Contacts of the helix formed by residues 123 - 132 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111K LEU* 3.8 18.6 - - + +
114K HIS* 3.5 45.5 - - + +
115K LYS 5.9 0.2 - - - +
130K GLU* 4.4 6.5 - - - +
134K LEU* 3.8 14.1 - - + -
7U ASN* 3.7 11.7 - - - +
121U VAL* 3.3 17.0 - - + +
122U ASP* 1.3 83.6 - - - +
124U HIS* 1.3 60.1 + - + +
125U LEU 3.4 0.2 - - - -
126U CYS* 3.4 7.9 + - + +
127U ASP* 3.0 28.2 + - - +
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Residues in contact with HIS 124 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K LEU* 5.7 3.1 - - + -
134K LEU* 3.5 40.5 - - + +
135K GLU* 3.0 33.1 + - + +
138K VAL* 3.4 28.1 - - + +
7U ASN* 6.3 0.2 - - - +
68U TYR* 2.8 40.5 + + - -
71U LYS* 5.4 0.7 - - + -
72U ARG* 3.6 13.3 + - - +
122U ASP* 3.3 7.7 + - - +
123U PRO* 1.3 79.6 - - + +
125U LEU* 1.3 59.6 + - - +
127U ASP* 3.5 8.5 + - + +
128U PHE* 3.1 25.1 + - + +
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Residues in contact with LEU 125 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8U TYR* 4.4 7.2 - - + -
12U CYS* 4.0 28.9 - - + -
16U VAL* 4.3 13.0 - - + -
65U PHE* 5.3 0.2 - - + -
68U TYR* 3.2 33.4 + - + +
113U LEU* 4.4 13.0 - - + -
117U ALA* 3.9 19.1 - - + -
122U ASP* 2.9 24.3 + - - +
124U HIS* 1.3 73.5 - - - +
126U CYS* 1.3 65.6 + - - +
128U PHE* 3.5 13.1 + - + +
129U LEU* 3.1 35.6 + - + +
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Residues in contact with CYS 126 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K GLU* 5.7 2.9 - - - +
114U HIS* 3.6 20.7 - - - +
117U ALA* 3.6 18.8 - - - -
118U THR* 3.5 29.4 - - - -
122U ASP 3.4 14.5 + - - +
123U PRO* 3.5 11.9 - - + +
124U HIS 3.2 0.4 - - - -
125U LEU* 1.3 80.8 - - - +
127U ASP* 1.3 58.0 + - - +
129U LEU* 3.4 4.0 + - - +
130U GLU* 3.1 37.0 + - - +
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Residues in contact with ASP 127 (chain U).
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* 5.6 1.2 - - - +
130K GLU* 3.7 47.1 + - + +
131K SER* 5.0 3.2 + - - -
134K LEU* 6.2 0.9 - - + -
135K GLU* 5.1 7.4 - - - +
127P ASP* 5.6 0.7 - - - +
123U PRO 3.0 16.8 + - - +
124U HIS* 3.8 9.0 - - + +
125U LEU 3.3 0.2 - - - -
126U CYS* 1.3 74.5 - - - +
128U PHE* 1.3 60.6 + - - +
130U GLU* 4.2 11.8 - - - +
131U SER* 2.9 50.1 + - - -
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Residues in contact with PHE 128 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135K GLU* 5.8 3.1 - - - -
64U LYS* 3.7 25.4 - - + -
65U PHE* 3.5 20.4 - + - -
68U TYR* 3.6 38.6 - + + -
71U LYS* 6.2 3.1 - - - -
124U HIS* 3.1 19.2 + - + +
125U LEU* 3.6 9.6 - - + +
127U ASP* 1.3 78.3 + - - +
129U LEU* 1.3 68.2 + - + +
131U SER* 4.7 2.9 - - - -
132U GLU* 3.0 53.2 + - + +
133U TYR* 3.5 31.2 - + - -
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Residues in contact with LEU 129 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65U PHE* 4.0 24.0 - - + -
110U LEU* 4.2 17.3 - - + +
113U LEU* 3.9 18.4 - - + +
114U HIS* 3.8 40.6 - - + +
117U ALA* 5.1 0.2 - - + -
125U LEU* 3.1 26.9 + - + +
126U CYS* 3.6 4.9 - - - +
127U ASP 3.2 0.2 - - - -
128U PHE* 1.3 98.6 - - + +
130U GLU* 1.3 57.2 + - - +
133U TYR* 3.0 14.9 + - + +
134U LEU* 2.9 33.3 + - + +
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Residues in contact with GLU 130 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K GLU* 4.0 12.3 - - - +
123P PRO* 4.4 7.1 - - - +
126P CYS* 5.7 2.6 - - - +
127P ASP* 3.6 44.7 - - + +
130P GLU* 3.9 14.7 - - - +
114U HIS* 2.9 29.0 + - - +
126U CYS* 3.1 24.3 + - - +
127U ASP* 3.7 9.4 - - - +
129U LEU* 1.3 77.9 - - - +
131U SER* 1.3 62.1 + - - +
134U LEU* 3.9 17.6 - - + +
135U GLU* 4.1 18.4 + - - +
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Residues in contact with SER 131 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127P ASP* 5.2 4.2 + - - -
127U ASP* 2.9 35.6 + - - -
128U PHE* 4.2 2.2 - - - -
130U GLU* 1.3 79.8 - - - +
132U GLU* 1.3 75.0 + - - +
135U GLU* 5.8 2.5 - - - +
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Residues in contact with GLU 132 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61U HIS* 4.6 4.2 + - - -
64U LYS* 2.9 42.0 + - + +
128U PHE* 3.0 40.3 + - + +
131U SER* 1.3 89.7 - - - +
133U TYR* 1.3 78.6 + - + +
136U 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