Contacts of the helix formed by residues 155 - 163 (chain F) in PDB entry 6JBQ
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 SER 155 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149F ARG* 3.7 3.8 - - - +
153F GLY 4.0 0.2 + - - -
154F LEU* 1.3 78.3 - - - +
156F TYR* 1.3 66.8 + - - +
157F GLU* 3.2 33.1 + - - +
158F GLU* 3.7 13.1 + - - +
159F ILE* 3.3 21.9 + - - +
41G A 4.8 1.3 - - - -
42G A 3.4 17.5 - - - -
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Residues in contact with TYR 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F ARG* 4.0 15.0 - - - -
155F SER* 1.3 72.2 - - - +
157F GLU* 1.3 61.2 + - - +
159F ILE* 3.5 7.0 + - + +
160F ALA* 2.9 29.6 + - - +
167F VAL* 3.9 28.2 - - + +
170F VAL* 3.6 29.4 - - + +
171F ARG* 3.6 27.6 - - + +
174F ILE* 3.3 29.1 - - + +
41G A 5.0 6.7 - - + +
42G A 2.7 69.9 + + + +
43G G 3.7 11.8 + - - -
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Residues in contact with GLU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F SER* 3.2 28.5 + - - +
156F TYR* 1.3 76.5 + - - +
158F GLU* 1.3 71.7 + - + +
160F ALA* 3.4 6.9 + - - +
161F ALA* 2.9 30.5 + - - +
167F VAL* 6.0 1.3 - - - -
41G A 4.3 17.6 - - - +
42G A 4.2 2.9 + - - -
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Residues in contact with GLU 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F LEU* 4.8 20.6 - - + -
155F SER* 3.7 24.1 + - - +
156F TYR 3.3 0.4 - - - -
157F GLU* 1.3 82.9 - - + +
159F ILE* 1.3 60.8 - - + +
161F ALA* 3.4 6.0 + - - +
162F ILE* 2.9 45.9 + - + +
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Residues in contact with ILE 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F ALA* 4.4 12.6 - - + +
148F LEU* 4.4 17.0 - - + +
149F ARG* 4.0 41.1 - - + +
154F LEU* 4.7 7.9 - - + +
155F SER 3.3 18.8 - - - +
156F TYR* 3.5 10.0 + - + +
158F GLU* 1.3 77.2 - - + +
160F ALA* 1.3 61.5 + - - +
162F ILE* 4.8 3.6 - - - -
163F MET* 3.1 49.3 + - + +
170F VAL* 4.1 26.9 - - + +
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Residues in contact with ALA 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F TYR 2.9 18.8 + - - +
157F GLU* 3.4 7.8 + - - +
159F ILE* 1.3 77.7 - - - +
161F ALA* 1.3 59.5 + - - +
164F ASP* 3.7 2.6 + - - -
165F CYS 3.0 42.4 + - - +
166F PRO 4.5 11.0 - - - +
167F VAL* 4.5 12.1 - - + -
170F VAL* 4.8 5.1 - - + +
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Residues in contact with ALA 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F GLU 2.9 18.1 + - - +
158F GLU* 4.0 8.1 - - - +
160F ALA* 1.3 77.7 - - - +
162F ILE* 1.3 65.2 + - + +
164F ASP* 4.0 6.2 + - - +
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Residues in contact with ILE 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F MET* 5.9 3.4 - - - -
148F LEU* 4.8 23.6 - - + -
154F LEU* 5.7 4.0 - - + -
158F GLU* 2.9 34.0 + - + +
159F ILE* 4.4 2.9 - - - +
161F ALA* 1.3 83.4 - - + +
163F MET* 1.3 70.1 + - + +
164F ASP* 3.2 4.7 + - - +
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Residues in contact with MET 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F ASP* 3.4 42.2 - - + +
144F MET* 4.6 20.0 - - + -
145F ALA* 4.0 19.5 - - - -
148F LEU* 4.8 4.3 - - + -
159F ILE* 3.1 37.8 + - + +
162F ILE* 1.3 84.8 - - + +
164F ASP* 1.3 69.9 + - - +
165F CYS* 3.4 17.1 - - + -
170F VAL* 5.4 2.9 - - + -
173F ARG* 3.9 17.0 - - - +
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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