Contacts of the helix formed by residues 153 - 160 (chain A) in PDB entry 1MF8
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 CYS 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ARG* 3.9 1.8 - - - +
150A ASN 3.1 26.5 - - - -
151A HIS 3.3 3.2 + - - -
152A GLU* 1.3 78.7 - - - +
154A ARG* 1.3 65.8 + - - +
155A HIS* 4.7 1.8 - - - -
156A LEU* 3.2 27.8 + - - +
157A THR* 2.9 25.6 + - - +
179A MET* 3.7 6.1 - - - -
182A PHE* 3.9 3.8 - - - -
220A GLU* 3.2 19.5 - - - +
221A PRO* 3.6 25.6 - - + -
232A TRP* 5.8 2.0 - - - -
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Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ARG* 4.7 0.8 - - - +
153A CYS* 1.3 69.7 - - - +
155A HIS* 1.3 63.9 + - - +
156A LEU 3.0 0.7 + - - -
157A THR* 3.0 3.4 + - - -
158A GLU* 3.0 34.3 + - - +
175A TYR* 3.6 6.4 + - + +
179A MET* 3.3 49.6 + - + +
180A ASP* 4.0 10.9 + - - -
183A ASP* 2.7 40.0 + - - -
220A GLU* 2.5 54.5 + - - +
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Residues in contact with HIS 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A CYS* 4.7 1.6 - - - -
154A ARG* 1.3 72.7 - - - +
156A LEU* 1.3 72.1 + - + +
158A GLU* 2.9 44.0 + - - +
159A TYR* 3.8 8.7 + - - +
220A GLU* 2.8 19.8 + - + +
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASP* 3.8 3.1 - - - +
150A ASN* 3.5 17.7 - - + +
151A HIS* 3.8 33.2 - - + +
153A CYS* 3.2 23.3 + - - +
155A HIS* 1.3 94.7 - - + +
157A THR* 1.3 58.0 + - - +
158A GLU 3.1 5.3 + - - -
159A TYR* 3.3 4.0 + - + +
160A PHE* 2.8 48.2 + - + -
232A TRP* 3.7 35.9 - - + -
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Residues in contact with THR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A VAL* 4.1 2.0 - - + -
121A ASP* 3.4 27.1 - - - +
151A HIS 3.6 17.0 - - - +
153A CYS 2.9 16.9 + - - +
154A ARG* 3.0 3.3 + - - -
156A LEU* 1.3 74.8 - - - +
158A GLU* 1.3 57.2 + - - +
160A PHE 3.1 13.2 - - - +
162A PHE* 3.7 21.1 - - + -
163A LYS* 3.1 22.9 + - - +
175A TYR* 2.8 32.6 + - - -
179A MET* 3.6 8.8 - - + -
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 3.0 15.0 + - - +
155A HIS* 2.9 58.7 + - - +
157A THR* 1.3 77.1 - - - +
159A TYR* 1.3 70.4 + - + +
160A PHE 3.5 4.7 - - - +
163A LYS* 4.3 26.6 + - + +
175A TYR* 4.7 1.3 - - - +
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Residues in contact with TYR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A HIS 3.9 11.2 - - - +
156A LEU* 3.6 8.7 - - + +
158A GLU* 1.3 85.4 - - + +
160A PHE* 1.3 83.6 + + - +
58C PRO* 3.4 32.1 - - - +
146C GLY 3.9 6.0 + - - -
147C SER* 3.4 22.6 - - - -
148C ARG* 3.6 38.1 + - + +
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Residues in contact with PHE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASP* 3.4 24.7 - - + -
122A ARG* 4.2 23.3 - - - +
151A HIS* 3.1 36.3 - + - -
156A LEU* 2.8 35.2 + - + +
157A THR 3.1 16.3 - - - +
158A GLU 3.5 4.5 - - - +
159A TYR* 1.3 98.4 - + - +
161A THR* 1.3 63.0 + - - +
162A PHE 3.4 1.6 - - - -
163A LYS* 4.3 1.6 + - - +
164A GLN* 4.9 1.7 + - - +
148C ARG* 3.2 44.0 - - + -
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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