Contacts of the helix formed by residues 147 - 153 (chain X) in PDB entry 1Y1F
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 THR 147 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136X PHE* 3.8 23.8 - - + -
145X TYR* 3.7 6.3 - - + +
146X LEU* 1.3 75.7 - - - +
148X GLU* 1.3 65.2 + - - +
149X ALA* 3.9 6.4 + - - +
150X GLU* 2.6 49.3 + - - +
151X LYS* 3.1 11.5 + - - +
187X ASN* 4.8 0.7 - - - +
188X TRP* 3.8 21.6 - - + +
208X HIS 4.7 4.2 + - - +
209X VAL* 4.8 4.0 - - + -
213X ASP* 3.4 23.1 - - - +
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Residues in contact with GLU 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145X TYR* 4.4 5.4 - - - +
147X THR* 1.3 74.5 - - - +
149X ALA* 1.3 51.6 + - - +
151X LYS* 3.2 21.3 + - - +
152X PHE* 2.7 58.2 + - + -
210X SER* 2.5 33.1 + - - +
212X ASN* 3.0 31.3 + - - +
213X ASP* 3.1 14.8 + - - +
355X ASP* 3.5 19.6 - - - +
357X SER* 6.4 0.4 - - - -
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Residues in contact with ALA 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147X THR* 3.3 3.2 + - - +
148X GLU* 1.3 77.7 - - - +
150X GLU* 1.3 57.9 + - - +
152X PHE* 4.5 4.3 - - - -
153X GLY* 2.9 24.8 + - - -
154X ASP 3.4 23.0 + - - +
155X SER* 4.0 9.0 - - - -
186X ALA 4.1 8.1 - - - +
187X ASN* 4.2 9.8 + - + +
208X HIS 3.9 15.0 - - - +
213X ASP* 4.8 1.4 + - - -
357X SER* 3.6 24.4 + - - +
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Residues in contact with GLU 150 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145X TYR 4.6 1.6 - - - +
146X LEU* 3.2 30.5 - - + +
147X THR* 2.6 44.4 + - - +
149X ALA* 1.3 78.6 - - - +
151X LYS* 1.3 62.1 + - - +
153X GLY* 3.6 9.9 + - - -
187X ASN* 3.9 29.1 - - + +
188X TRP* 3.5 18.2 + - - -
189X ARG* 5.3 6.8 + - - +
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Residues in contact with LYS 151 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145X TYR* 5.3 5.1 + - - -
146X LEU* 3.5 47.4 + - + +
147X THR 3.1 9.1 + - - +
148X GLU* 3.7 22.0 + - - +
150X GLU* 1.3 76.3 - - - +
152X PHE* 1.3 66.8 + - + +
153X GLY* 3.4 0.7 + - - -
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Residues in contact with PHE 152 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148X GLU* 2.7 46.8 + - + +
149X ALA* 4.0 5.4 - - - +
151X LYS* 1.3 74.2 - - + +
153X GLY* 1.3 61.2 + - - +
154X ASP* 3.4 22.6 + - - +
355X ASP* 3.8 46.0 - - + -
357X SER* 6.0 0.4 - - - -
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Residues in contact with GLY 153 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149X ALA 2.9 11.9 + - - -
150X GLU* 3.6 8.7 + - - -
151X LYS 3.3 3.2 - - - -
152X PHE* 1.3 76.6 - - - +
154X ASP* 1.3 62.4 + - - +
184X LYS* 3.3 9.1 - - - +
185X GLY* 2.9 25.4 + - - -
186X ALA 5.4 0.2 - - - -
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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