Contacts of the helix formed by residues 222 - 227 (chain A) in PDB entry 5UFL
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 GLY 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A THR* 3.4 36.8 + - - -
217A LEU 5.0 1.3 - - - +
219A GLU 3.8 2.6 + - - -
220A GLU 3.5 0.6 - - - -
221A VAL* 1.3 76.7 - - - +
223A GLU* 1.3 58.1 + - - +
224A LYS* 3.1 3.8 - - - -
225A LEU* 3.3 7.7 + - - -
226A PHE* 3.1 34.9 + - - +
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLU 4.7 1.2 + - - +
220A GLU* 2.9 25.4 + - - +
221A VAL* 2.9 11.2 - - - +
222A GLY* 1.3 69.2 - - - +
224A LYS* 1.3 84.2 + - - +
225A LEU 3.1 1.6 - - - -
226A PHE* 3.8 5.6 - - - +
227A HIS* 3.1 32.8 + - + +
230A ASN* 3.0 27.0 + - - +
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ILE* 4.6 21.3 - - + -
221A VAL* 4.2 17.7 - - + +
222A GLY* 4.9 1.8 - - - -
223A GLU* 1.3 94.9 + - - +
225A LEU* 1.3 61.6 + - + +
230A ASN* 3.2 27.4 + - - +
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ILE* 5.5 4.9 - - + -
197A LEU* 4.1 16.4 - - + -
209A LEU* 3.7 22.4 - - + -
212A LEU* 3.8 37.9 - - + -
216A THR* 4.4 6.3 - - - +
222A GLY* 3.3 5.4 + - - +
224A LYS* 1.3 85.6 - - + +
226A PHE* 1.3 87.7 + - + +
227A HIS 3.7 1.1 - - - -
230A ASN* 3.8 1.1 - - - -
231A ILE* 3.5 18.2 + - - +
234A THR* 2.8 34.5 + - + +
237A LEU* 5.9 2.0 - - + -
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Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 5.1 3.6 - - + -
213A SER* 3.9 33.9 - - - -
216A THR* 3.8 18.6 - - - -
217A LEU* 4.2 18.2 - - + +
222A GLY 3.1 23.9 + - - +
223A GLU* 4.1 5.3 - - - -
225A LEU* 1.3 107.0 - - + +
227A HIS* 1.3 58.8 + - - +
231A ILE* 3.8 21.1 - - + -
234A THR* 4.1 16.2 - - + -
257A LEU* 6.1 0.2 - - + -
261A LEU* 4.1 19.1 - - + -
266A LYS* 4.7 8.7 + - - -
267A ILE* 4.1 23.3 - - + +
270A TYR* 4.3 12.2 + - - -
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Residues in contact with HIS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLU* 3.1 36.5 + - + +
226A PHE* 1.3 78.6 - - - +
228A ALA* 1.3 68.7 + - + +
229A ARG* 2.6 53.0 + - + +
230A ASN* 3.1 12.7 + - - +
231A ILE* 3.0 22.4 + - - +
270A TYR* 4.6 2.0 - - - -
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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