Contacts of the helix formed by residues 240 - 245 (chain B) 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 PRO 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B TYR* 2.7 32.9 + - - -
112B TYR* 3.3 35.1 - - + +
147B GLN* 3.5 25.1 - - - +
188B PHE* 3.9 9.0 - - + -
200B PHE* 3.9 4.3 - - + -
236B ILE 3.5 8.1 - - - +
237B GLN 3.2 18.4 - - - +
239B ALA* 1.4 87.8 - - + +
241B SER* 1.3 49.0 + - - -
242B PHE 3.0 2.5 - - - -
245B SER* 4.6 0.2 - - - +
246B PHE* 3.7 26.9 - - + -
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Residues in contact with SER 241 (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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110B TYR* 3.1 9.3 + - - -
112B TYR* 3.6 15.5 - - - -
238B ALA 2.8 18.8 + - - -
239B ALA 2.9 1.2 - - - -
240B PRO* 1.3 75.4 - - - +
242B PHE* 1.3 68.1 + - - +
256B ILE 5.4 0.7 - - - +
258B CYS* 3.5 24.6 - - - +
260B ILE* 3.7 8.9 - - - +
270B PHE* 4.2 4.0 - - - -
273B THR* 3.9 15.6 - - - +
283B PRO 4.8 2.1 - - - +
285B PRO* 4.0 18.3 - - - +
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Residues in contact with PHE 242 (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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110B TYR* 2.9 7.2 + - - -
203B ASN* 4.2 9.2 - - - +
207B ILE* 3.6 32.8 - - + -
238B ALA 3.7 9.6 - - - -
239B ALA 3.2 14.1 + - - +
240B PRO 3.0 0.9 - - - +
241B SER* 1.3 88.8 - - - +
243B SER* 1.3 66.7 + - - +
244B ASN* 2.9 3.7 + - - +
245B SER* 3.1 17.5 + - - -
246B PHE* 4.1 3.3 - - - -
254B THR 5.8 1.6 - - - +
273B THR* 3.5 23.1 - - + -
276B VAL* 5.6 0.4 - - + -
277B ALA* 3.7 33.4 - - + -
280B ILE* 4.3 4.5 - - + -
282B TYR* 3.5 45.3 - + + -
283B PRO* 3.7 13.9 - - + -
285B PRO* 4.5 2.9 - - + -
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Residues in contact with SER 243 (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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110B TYR* 3.2 12.7 + - - -
242B PHE* 1.3 70.3 - - - +
244B ASN* 1.3 55.1 + - - +
246B PHE* 2.9 22.2 + - - +
247B PRO* 5.0 0.2 - - - +
250B PHE* 3.5 27.5 - - - +
253B ARG 6.0 0.7 - - - -
254B THR 3.2 25.3 + - - -
255B ASP 3.7 0.2 - - - -
256B ILE* 3.0 52.5 + - - -
283B PRO* 5.7 0.5 - - - +
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Residues in contact with ASN 244 (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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199B GLY* 3.7 8.1 - - - +
203B ASN* 3.2 19.1 - - - +
206B LYS* 5.0 0.7 + - - -
242B PHE* 2.9 2.3 + - + +
243B SER* 1.3 69.9 + - - +
245B SER* 1.3 58.5 + - - +
246B PHE 2.9 10.1 + - - -
247B PRO* 3.2 21.8 - - - +
252B ASP* 4.5 12.3 + - - +
254B THR* 3.1 39.5 + - - +
282B TYR* 2.6 34.4 + - + +
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Residues in contact with SER 245 (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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193B TYR* 2.5 31.7 + - - -
197B SER* 3.8 3.8 + - - -
199B GLY 3.9 8.1 - - - -
200B PHE* 3.8 26.1 - - - -
203B ASN* 2.7 23.8 + - - +
239B ALA 3.0 21.5 + - - -
242B PHE 3.1 7.4 + - - -
244B ASN* 1.3 75.6 - - - +
246B PHE* 1.3 61.8 + - - +
247B PRO* 3.4 5.3 - - - +
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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