Contacts of the helix formed by residues 149 - 164 (chain F) in PDB entry 3J8B
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 ASP 149 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137F VAL* 6.1 1.2 - - + +
138F PRO* 3.9 25.3 + - + +
147F ALA 4.4 0.2 + - - -
148F VAL* 1.3 71.2 - - - +
150F MET* 1.3 63.6 + - - +
151F GLU* 3.3 2.2 - - + +
152F PHE* 3.1 28.6 + - + +
153F ALA* 3.2 12.1 + - - +
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Residues in contact with MET 150 (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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148F VAL* 3.2 9.7 + - - +
149F ASP* 1.3 68.9 - - - +
151F GLU* 1.3 66.0 + - - +
153F ALA* 3.3 9.8 + - - +
154F LYS* 3.2 21.7 + - - +
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Residues in contact with GLU 151 (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 ASP* 3.3 1.1 - - + -
150F MET* 1.3 76.3 - - - +
152F PHE* 1.3 60.4 + - - +
154F LYS* 3.9 5.4 - - - +
155F ASN* 2.9 32.6 + - - +
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Residues in contact with PHE 152 (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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137F VAL* 6.0 4.3 - - + -
138F PRO* 5.5 9.4 - - + -
149F ASP* 3.1 27.6 + - + +
151F GLU* 1.3 78.9 - - - +
153F ALA* 1.3 62.8 + - - +
155F ASN* 4.7 3.6 - - - -
156F MET* 2.9 29.6 + - - +
106H SER* 5.6 11.7 - - - +
109H HIS* 5.9 4.3 - - + -
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Residues in contact with ALA 153 (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 ASP 3.2 8.8 + - - +
150F MET* 3.3 12.5 + - - +
152F PHE* 1.3 78.9 - - - +
154F LYS* 1.3 56.7 + - - +
156F MET* 4.2 2.1 - - - +
157F TYR* 2.9 34.0 + - - +
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Residues in contact with LYS 154 (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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150F MET 3.2 13.5 + - - +
151F GLU* 3.9 6.3 - - - +
153F ALA* 1.3 79.2 - - - +
155F ASN* 1.3 58.2 + - - +
157F TYR* 3.9 4.5 - - - +
158F GLU* 3.0 30.5 + - - +
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Residues in contact with ASN 155 (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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151F GLU 2.9 19.1 + - - +
152F PHE* 4.0 3.4 - - - +
154F LYS* 1.3 75.2 - - - +
156F MET* 1.3 65.3 + - - +
158F GLU* 3.5 6.8 + - - +
159F LEU* 3.4 18.7 + - - +
102H GLU* 6.5 1.1 - - + -
106H SER* 6.2 3.4 - - - -
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Residues in contact with MET 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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135F PHE* 5.5 11.7 - - + -
136F SER 6.0 2.0 - - - +
152F PHE 2.9 18.1 + - - +
153F ALA* 4.3 2.0 - - - +
155F ASN* 1.3 73.0 - - - +
157F TYR* 1.3 68.2 + - - +
159F LEU* 3.0 10.0 + - - +
160F HIS* 2.8 21.2 + - - +
106H SER* 5.1 14.9 - - - -
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Residues in contact with TYR 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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153F ALA 2.9 21.7 + - - +
154F LYS* 3.9 4.3 - - - +
156F MET* 1.3 75.9 - - - +
158F GLU* 1.3 58.1 + - - +
160F HIS* 3.0 10.7 + - - +
161F LYS* 2.8 30.0 + - - +
169F ILE* 5.4 11.7 - - + -
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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 LYS 3.0 19.0 + - - +
155F ASN* 3.7 8.1 - - - +
156F MET 3.2 0.2 - - - -
157F TYR* 1.3 77.3 - - - +
159F LEU* 1.3 59.2 + - - +
161F LYS* 3.6 8.3 + - - +
162F LYS* 3.4 19.1 + - - +
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Residues in contact with LEU 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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155F ASN 3.4 9.4 + - - +
156F MET* 3.0 11.0 + - - +
158F GLU* 1.3 77.0 - - - +
160F HIS* 1.3 65.8 + - - +
162F LYS* 3.1 17.3 + - - +
163F VAL* 3.2 11.6 + - - +
103H MET* 6.3 3.8 - - + -
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Residues in contact with HIS 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 MET 2.8 12.4 + - - +
157F TYR* 3.4 13.5 - - - +
159F LEU* 1.3 75.5 - - - +
161F LYS* 1.3 57.0 + - - +
163F VAL* 3.0 9.0 + - - +
164F SER* 2.9 30.7 + - - +
167F GLU 5.5 6.7 - - - +
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Residues in contact with LYS 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 TYR 2.8 15.4 + - - +
158F GLU* 3.7 9.9 - - - +
159F LEU 3.2 0.2 - - - -
160F HIS* 1.3 75.8 - - - +
162F LYS* 1.3 60.5 + - - +
163F VAL 3.4 0.5 + - - -
164F SER 4.4 5.8 - - - -
165F PRO* 3.5 29.4 - - + +
167F GLU 5.9 1.1 - - - -
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Residues in contact with LYS 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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158F GLU 3.4 10.4 + - - +
159F LEU* 3.1 13.2 + - - +
161F LYS* 1.3 77.3 - - - +
163F VAL* 1.3 61.4 + - - +
85H PRO* 5.5 13.3 - - + +
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Residues in contact with VAL 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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159F LEU 3.2 9.4 + - - +
160F HIS* 3.0 10.8 + - - +
161F LYS 4.2 0.2 - - - -
162F LYS* 1.3 80.2 - - - +
164F SER* 1.3 65.3 + - - +
83H PRO* 5.4 11.9 - - + -
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Residues in contact with SER 164 (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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160F HIS 2.9 16.6 + - - +
161F LYS* 3.6 1.9 + - - -
163F VAL* 1.3 82.7 - - - +
165F PRO* 1.3 61.8 - - - +
166F ASN* 3.1 10.9 + - - -
167F GLU* 3.4 25.0 + - - +
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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