Contacts of the strand formed by residues 153 - 159 (chain F) in PDB entry 3X0X
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 TYR 153 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145F ALA* 4.2 20.0 - - + -
146F THR 3.2 10.3 - - - +
147F PRO* 3.6 26.2 - - + -
148F THR* 3.7 2.8 + - - -
151F GLY 3.9 12.6 - - - -
152F GLY* 1.3 87.3 - - - -
154F VAL* 1.3 62.2 + - - +
155F LEU* 4.1 2.7 - - + -
177F VAL* 4.1 2.0 - - + -
183F GLN* 2.7 38.8 + - - -
188F ILE* 3.6 44.2 - - + +
224F LYS* 3.4 7.4 - - - +
225F VAL* 2.7 48.6 + - + -
230F VAL* 4.0 20.4 - - + +
234F PRO* 3.7 6.4 - - - +
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Residues in contact with VAL 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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144F ARG 3.7 0.7 - - - +
145F ALA* 3.7 0.5 - - - -
146F THR* 2.8 44.1 + - + +
148F THR* 3.9 14.1 - - + -
153F TYR* 1.3 78.8 - - - +
155F LEU* 1.3 63.8 + - - +
156F ASN* 3.6 13.5 + - - +
222F ASN* 3.6 36.8 - - + +
223F VAL 3.0 4.0 - - - +
224F LYS* 3.8 20.4 - - + -
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Residues in contact with LEU 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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143F VAL* 3.9 15.7 - - + -
144F ARG 3.3 3.1 - - - +
145F ALA* 3.7 28.0 - - + -
153F TYR* 4.7 3.6 - - + -
154F VAL* 1.3 74.6 - - - +
156F ASN* 1.3 69.2 + - - +
173F VAL* 3.7 39.0 - - + -
175F GLY* 4.5 6.7 - - - +
188F ILE* 6.0 2.5 - - + -
192F ILE* 5.0 0.2 - - + -
220F PHE* 3.8 22.7 - - + +
222F ASN 3.3 2.3 + - - -
223F VAL* 2.6 39.1 + - + +
225F VAL* 4.0 24.9 - - + -
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Residues in contact with ASN 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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142F LYS 3.4 2.3 - - - +
143F VAL* 4.5 1.8 - - - -
144F ARG* 3.0 43.9 + - + +
146F THR* 5.5 3.8 + - - -
154F VAL* 3.6 12.7 + - - +
155F LEU* 1.3 84.6 + - - +
157F GLY* 1.3 58.3 - - - +
220F PHE* 3.4 8.5 - - - +
221F HIS* 3.6 9.2 - - - -
222F ASN* 2.8 43.9 + - - +
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Residues in contact with GLY 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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142F LYS 3.5 12.8 - - - -
143F VAL* 4.8 1.1 - - - -
156F ASN* 1.3 75.1 - - - +
158F THR* 1.3 64.6 + - - -
159F LYS 4.0 0.4 - - - -
219F ASP* 4.1 2.5 - - - -
220F PHE* 2.8 41.0 + - - +
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Residues in contact with THR 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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142F LYS* 3.0 28.6 + - - +
143F VAL* 4.8 0.2 - - - -
157F GLY* 1.3 72.0 - - - -
159F LYS* 1.3 62.6 + - - +
160F HIS* 3.4 5.3 + - + +
202F ASN* 5.2 2.5 - - - +
217F SER* 4.1 23.8 - - - +
218F THR 3.5 13.2 - - - +
219F ASP* 2.8 25.8 + - + +
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Residues in contact with LYS 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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130F ALA* 3.6 9.2 - - + +
131F SER 3.4 42.2 - - - +
132F SER 3.1 19.6 + - - -
133F GLU* 3.8 22.1 - - + +
142F LYS* 4.6 3.6 - - - -
143F VAL* 4.0 23.9 - - + +
157F GLY 4.0 1.8 + - - -
158F THR* 1.3 67.8 - - - +
160F HIS* 1.3 64.2 + - - +
161F PHE* 2.9 27.2 + - - +
162F CYS* 3.4 23.9 - - - -
174F PHE 5.6 0.4 - - - +
217F SER* 3.1 3.2 - - - -
218F THR 2.8 35.5 + - - +
220F PHE* 4.4 6.1 - - + -
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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