Contacts of the helix formed by residues 216 - 221 (chain Q) in PDB entry 1U8F
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 ALA 216 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124Q PRO* 6.2 2.9 - - + -
130Q MET* 4.2 20.9 - - + +
154Q THR* 3.8 15.7 - - - +
212Q GLY 2.8 19.1 + - - +
213Q ALA* 3.6 9.4 - - - +
214Q ALA 3.1 0.4 - - - -
215Q LYS* 1.3 73.3 - - - +
217Q VAL* 1.3 65.0 + - - +
218Q GLY 2.9 2.9 - - - -
219Q LYS* 2.9 30.5 + - + +
220Q VAL* 3.9 2.3 + - - +
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Residues in contact with VAL 217 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154Q THR* 4.4 6.1 - - + -
157Q LEU* 3.6 31.9 - - + -
158Q ALA* 4.1 14.1 - - + +
161Q ALA* 4.3 6.5 - - + -
213Q ALA 3.6 8.5 + - - +
214Q ALA 3.3 15.7 - - - +
215Q LYS 3.1 0.6 - - - -
216Q ALA* 1.3 77.8 - - - +
218Q GLY* 1.3 57.7 + - - +
220Q VAL* 3.1 10.5 + - - +
221Q ILE* 2.8 50.1 + - + +
224Q LEU* 4.1 6.5 - - + -
228Q LEU* 3.7 19.3 - - + -
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Residues in contact with GLY 218 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214Q ALA 4.4 0.2 + - - -
215Q LYS 3.0 10.7 + - - -
216Q ALA 2.9 1.6 - - - -
217Q VAL* 1.3 80.7 - - - +
219Q LYS* 1.3 60.6 + - - +
221Q ILE 3.5 11.2 - - - -
222Q PRO* 3.2 25.3 - - - +
224Q LEU* 4.4 4.5 + - - +
225Q ASN* 3.3 33.3 + - - +
228Q LEU* 5.4 0.6 - - - +
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Residues in contact with LYS 219 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125Q SER 5.8 2.2 - - - -
126Q ALA 5.3 6.7 + - - -
130Q MET* 4.5 31.7 - - + +
136Q ASN* 4.4 5.0 + - - -
215Q LYS 4.4 0.8 + - - +
216Q ALA* 2.9 25.1 + - + +
218Q GLY* 1.3 78.1 - - - +
220Q VAL* 1.3 65.6 + - + +
222Q PRO* 4.4 7.8 - - - +
225Q ASN* 5.0 0.7 - - - +
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Residues in contact with VAL 220 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130Q MET* 3.8 17.5 - - + +
131Q PHE 4.3 0.2 - - - -
132Q VAL* 3.8 21.1 - - + +
135Q VAL* 3.7 20.8 - - + +
136Q ASN* 3.6 49.1 - - - +
154Q THR* 5.0 1.3 - - + -
158Q ALA* 4.0 16.4 - - + -
216Q ALA 4.5 2.2 - - - +
217Q VAL* 3.2 18.8 - - - +
219Q LYS* 1.3 85.0 - - + +
221Q ILE* 1.3 62.6 + - + +
222Q PRO* 3.6 7.8 - - - +
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Residues in contact with ILE 221 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135Q VAL* 3.5 17.9 - - + -
158Q ALA* 3.6 24.5 - - - +
161Q ALA* 4.3 0.2 - - + -
162Q LYS* 3.9 20.6 - - + +
165Q HIS* 4.8 7.9 - - + -
217Q VAL* 2.8 26.9 + - + +
218Q GLY* 3.3 9.4 - - - +
220Q VAL* 1.3 84.1 - - + +
222Q PRO* 1.3 59.5 - - + +
223Q GLU* 4.3 8.3 - - + +
224Q LEU* 2.8 50.3 + - + +
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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