Contacts of the helix formed by residues 233 - 239 (chain A) in PDB entry 1ULH
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 PHE 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A THR* 3.7 9.9 - - + -
151A ASP* 3.3 28.3 - - - -
152A GLU* 3.3 41.3 - - + -
155A LEU* 4.3 13.7 - - + -
156A TRP* 4.1 19.1 - + + -
190A ASP* 3.6 15.3 - - - -
229A GLY 2.9 13.5 + - - +
230A LYS 2.9 14.1 + - - +
232A SER* 1.3 76.8 - - - +
234A PRO* 1.4 55.4 - - + +
236A ILE* 2.7 46.1 + - + +
237A GLN* 3.3 40.0 + - + -
201B TYR* 5.4 0.4 - - - -
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Residues in contact with PRO 234 (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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216A VAL* 4.7 6.3 - - + -
220A PHE* 3.7 39.7 - - + -
222A PHE* 3.7 18.6 - - + -
230A LYS 3.3 13.0 - - - +
231A ILE 3.6 7.6 - - - +
232A SER 3.4 4.0 - - - -
233A PHE* 1.4 89.8 - - + +
235A ALA* 1.3 59.8 + - - +
237A GLN* 3.6 13.1 + - + +
238A ALA* 3.3 22.3 + - - +
272A MET* 3.7 20.0 - - - +
273A THR* 5.1 0.2 + - - -
228B ILE* 5.2 2.5 - - + -
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Residues in contact with ALA 235 (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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204A VAL* 3.8 13.2 - - + +
207A ILE* 3.7 32.6 - - + +
208A GLN* 3.7 24.9 - - + -
232A SER 3.2 13.0 + - - +
233A PHE 2.8 3.4 + - - -
234A PRO* 1.3 76.8 - - - +
236A ILE* 1.3 59.9 + - - +
239A ALA* 3.1 28.9 + - - +
228B ILE* 3.9 6.7 - - + +
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Residues in contact with ILE 236 (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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147A GLN* 3.6 4.3 - - - +
151A ASP* 3.6 3.8 - - - +
190A ASP* 3.4 36.1 - - - +
194A MET* 3.4 22.4 - - + -
200A PHE* 3.7 11.5 - - + -
204A VAL* 4.2 17.7 - - + -
208A GLN* 6.0 0.2 - - - +
232A SER 4.9 2.5 - - - +
233A PHE* 2.7 35.9 + - + +
235A ALA* 1.3 70.5 - - - +
237A GLN* 1.3 58.4 + - - +
240A PRO* 3.0 23.7 - - - +
201B TYR* 3.0 31.2 - - + +
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Residues in contact with GLN 237 (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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112A TYR* 3.8 23.5 + - - +
147A GLN* 3.9 14.9 + - - +
149A THR* 5.4 1.4 - - - +
152A GLU* 4.2 9.0 + - - -
220A PHE* 5.1 13.4 - - - -
233A PHE* 3.3 43.6 + - + +
234A PRO* 3.9 10.7 - - + +
235A ALA 3.4 0.4 - - - -
236A ILE* 1.3 76.7 - - - +
238A ALA* 1.3 62.4 + - - +
240A PRO* 3.3 9.0 - - - +
241A SER* 4.6 1.9 + - - -
270A PHE* 5.5 11.7 - - + -
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Residues in contact with ALA 238 (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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207A ILE* 3.9 18.2 - - + -
234A PRO 3.3 15.8 + - - +
235A ALA 3.9 0.9 - - - +
236A ILE 3.2 0.6 - - - -
237A GLN* 1.3 77.2 - - - +
239A ALA* 1.3 59.8 + - - +
240A PRO 3.2 2.9 - - - -
241A SER* 2.8 32.3 + - - -
242A PHE* 3.5 4.7 - - - -
272A MET* 4.0 9.9 - - + -
273A THR* 3.1 35.9 + - + +
276A VAL* 6.5 0.2 - - + -
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Residues in contact with ALA 239 (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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200A PHE* 3.5 26.0 - - + +
203A ASN* 4.4 1.1 - - + -
204A VAL* 3.7 23.8 - - + +
207A ILE* 3.7 10.9 - - + +
235A ALA 3.1 16.8 + - - +
236A ILE 4.0 0.2 - - - +
238A ALA* 1.3 75.6 - - - +
240A PRO* 1.4 64.6 - - + +
241A SER 3.0 1.4 + - - -
242A PHE* 3.1 13.7 + - - -
245A SER* 2.8 24.9 + - - +
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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