Contacts of the helix formed by residues 222 - 229 (chain B) in PDB entry 1UJN
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B ASP* 2.5 20.2 + - - -
221B LYS* 1.3 74.7 - - - +
223B LYS* 1.3 61.2 + - - -
224B ARG 2.9 1.2 + - - -
225B ARG* 2.7 43.9 - - - +
226B LEU* 4.2 1.0 + - - +
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Residues in contact with LYS 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B ILE* 5.7 3.5 + - + -
213B VAL* 3.0 33.6 - - + +
216B GLU* 4.8 12.6 - - + +
217B ASP* 3.4 9.5 + - + +
222B GLY* 1.3 69.8 - - - -
224B ARG* 1.3 62.9 + - - +
226B LEU* 3.0 47.7 + - + +
318B GLY 4.6 13.9 + - - -
320B LEU 5.5 6.3 + - - +
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Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLY* 4.5 23.0 + - - -
131B LYS* 6.0 3.8 - - - +
146B PHE* 5.4 7.3 - - - -
148B PHE* 6.2 1.6 - - - -
213B VAL* 3.2 14.5 - - + +
214B THR* 4.1 27.1 + - - +
217B ASP* 3.0 35.3 + - + +
218B PRO* 2.8 37.0 + - - +
220B GLU* 3.7 29.4 + - + +
222B GLY 2.9 4.9 + - - -
223B LYS* 1.3 75.7 - - - +
225B ARG* 1.3 57.7 + - - +
226B LEU 3.2 0.7 + - - -
227B LEU* 3.3 31.3 + - + +
228B ASN* 5.8 0.2 - - - -
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Residues in contact with ARG 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B GLU* 3.8 27.9 + - + +
221B LYS* 3.6 14.8 + - - +
222B GLY* 2.7 49.9 + - - +
224B ARG* 1.3 73.6 - - - +
226B LEU* 1.3 62.3 + - - +
227B LEU 3.0 6.9 + - - -
228B ASN* 3.2 20.8 + - - +
310B HIS* 5.7 2.6 - - - -
312B VAL* 3.5 13.0 - - - +
322B VAL* 3.6 52.1 + - + +
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B ILE* 3.4 33.3 - - + +
222B GLY 4.5 1.6 - - - +
223B LYS* 3.0 54.8 + - + +
225B ARG* 1.3 73.7 - - + +
227B LEU* 1.3 56.3 + - - +
228B ASN 3.0 5.8 - - - -
229B LEU* 3.0 29.2 + - - +
312B VAL* 4.1 9.0 - - + -
320B LEU* 3.8 40.8 - - + +
322B VAL* 3.8 24.7 - - + -
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LYS* 2.7 33.2 + - - +
177B HIS* 4.3 19.3 - - + +
180B ILE* 4.0 18.4 - - + -
209B VAL* 5.9 1.3 - - + -
210B LYS* 4.2 33.0 - - + -
213B VAL* 4.4 18.2 - - + -
214B THR* 4.3 17.5 - - + -
224B ARG* 3.3 26.7 - - + +
225B ARG 3.0 0.4 - - - -
226B LEU* 1.3 77.4 - - - +
228B ASN* 1.3 60.1 + - - +
229B LEU 3.2 2.4 + - - -
231B HIS* 3.8 3.3 + - - -
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Residues in contact with ASN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B GLU* 4.2 15.6 + - - -
224B ARG 5.6 0.2 + - - -
225B ARG* 3.2 16.9 + - - +
226B LEU 3.0 2.0 - - - -
227B LEU* 1.3 81.0 - - - +
229B LEU* 1.3 66.0 + - - +
230B GLY 3.1 1.0 + - - -
231B HIS* 2.9 32.8 + - + +
232B THR* 4.2 7.7 + - - +
312B VAL* 4.0 11.6 - - + +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LYS* 3.4 26.5 - - + +
179B LEU* 3.9 32.1 - - + -
180B ILE* 4.2 1.8 - - + -
226B LEU 3.0 15.8 + - - +
227B LEU 3.2 2.0 - - - -
228B ASN* 1.3 75.5 - - - +
230B GLY* 1.3 60.7 + - - +
231B HIS* 3.0 15.9 + - - -
251B VAL* 4.5 0.3 - - - +
255B LEU* 3.7 20.2 - - + +
258B ALA* 3.8 17.0 - - + -
312B VAL* 3.6 37.6 - - + +
314B PRO* 3.8 12.8 - - + -
320B LEU* 3.9 15.5 - - + -
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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