Contacts of the helix formed by residues 235 - 242 (chain N) in PDB entry 1UCY
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 LYS 235 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1M THR* 3.0 63.7 + - - +
123N LEU* 3.7 26.8 - - + +
124N PRO* 3.0 28.9 - - + +
125N ASP* 4.8 0.7 - - - +
231N VAL* 2.9 12.0 + - + +
232N PHE* 3.3 28.5 + - + +
233N ARG 3.5 0.4 - - - -
234N LEU* 1.3 76.5 - - - +
236N LYS* 1.3 64.7 + - + +
238N ILE* 3.3 11.3 + - + +
239N GLN* 2.8 38.7 + - - +
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Residues in contact with LYS 236 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M THR 5.1 5.3 + - - +
126N LYS* 5.2 10.3 - - - +
232N PHE* 4.6 22.3 + - - +
233N ARG 5.1 2.1 + - - +
234N LEU 3.3 1.2 - - - -
235N LYS* 1.3 82.0 - - + +
237N TRP* 1.3 60.1 + - - +
239N GLN* 3.7 31.0 + - - +
240N LYS* 3.1 25.6 + - - +
246N GLY* 3.7 10.7 - - - +
247N SER* 4.7 11.0 - - - +
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Residues in contact with TRP 237 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89N TYR* 3.4 26.5 - - + -
90N ILE 3.8 4.5 - - - -
91N HIS* 3.5 55.4 - + + +
92N PRO* 3.4 17.8 - - + +
93N ARG* 5.4 0.7 - - - -
103N ILE* 4.1 27.1 - - + -
105N LEU* 3.8 28.0 - - + -
234N LEU* 2.9 16.6 + - + +
236N LYS* 1.3 75.7 - - - +
238N ILE* 1.3 84.8 + - + +
240N LYS* 3.3 32.4 + - - +
241N VAL* 3.1 47.0 + - + +
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Residues in contact with ILE 238 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N ILE* 4.5 6.5 - - + -
53N LEU* 4.2 10.1 - - + -
103N ILE* 3.9 21.5 - - + -
105N LEU* 3.7 20.6 - - + -
123N LEU* 4.1 23.8 - - + -
231N VAL* 4.1 23.1 - - + +
234N LEU 3.1 12.4 + - - +
235N LYS* 3.4 13.9 - - - +
237N TRP* 1.3 87.3 - - + +
239N GLN* 1.3 66.2 + - + +
241N VAL* 3.1 11.8 + - - +
242N ILE* 3.2 37.3 + - + +
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Residues in contact with GLN 239 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M THR* 3.1 47.8 + - - +
235N LYS* 2.8 41.9 + - + +
236N LYS* 3.7 22.1 - - - +
238N ILE* 1.3 75.5 - - + +
240N LYS* 1.3 52.6 + - - +
242N ILE* 2.8 8.8 + - - -
243N ASP* 2.6 46.7 + - - +
246N GLY 3.4 9.3 + - - +
247N SER* 3.1 31.9 + - - +
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Residues in contact with LYS 240 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92N PRO* 5.6 2.2 - - - +
93N ARG* 5.2 8.3 - - - +
236N LYS 3.1 12.1 + - - +
237N TRP* 3.5 36.1 - - - +
238N ILE 3.3 0.4 - - - -
239N GLN* 1.3 79.7 - - - +
241N VAL* 1.3 60.9 + - + +
242N ILE 3.6 0.3 + - - -
243N ASP* 3.8 1.9 - - - +
244N ARG 3.6 20.3 + - - +
245N LEU* 3.5 48.9 - - + +
246N GLY* 3.2 21.5 + - - +
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Residues in contact with VAL 241 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N TRP* 3.5 24.9 - - + -
89N TYR* 4.6 20.3 - - + -
105N LEU* 3.1 39.7 - - + -
237N TRP* 3.1 46.2 + - + +
238N ILE 3.1 1.5 + - - +
240N LYS* 1.3 80.9 - - + +
242N ILE* 1.3 61.1 + - + +
243N ASP 4.9 1.2 - - - +
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Residues in contact with ILE 242 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N ILE* 4.7 13.2 - - + -
48N SER* 6.5 0.9 - - - -
51N TRP* 3.9 40.3 - - + +
105N LEU* 4.7 1.6 - - + -
123N LEU* 5.8 1.6 - - + -
238N ILE* 3.2 35.0 - - + +
239N GLN* 2.8 8.4 + - - +
241N VAL* 1.3 83.9 - - + +
243N ASP* 1.3 69.5 + - - +
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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