Contacts of the strand formed by residues 243 - 246 (chain B) in PDB entry 4UT2
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 LEU 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LYS 3.2 3.8 + - - +
169B ILE* 3.4 28.3 - - + -
170B PHE* 3.0 26.5 + - - +
236B LEU* 3.8 5.0 - - - +
241B LEU* 3.8 1.0 - - - +
242B ASP* 1.3 81.9 - - + +
244B ILE* 1.3 76.8 + - - +
257B PHE* 4.5 7.6 - - + -
261B ARG 3.6 19.1 - - - +
262B GLN 3.5 18.4 - - - +
263B LEU 4.1 0.7 - - - -
264B VAL* 4.0 18.6 - - + +
283B MET* 4.2 20.9 - - + -
291B CSO 4.3 15.5 - - + +
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Residues in contact with ILE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B PHE* 3.5 19.1 - - + +
172B CYS* 5.5 4.7 - - - -
175B GLY* 5.7 2.7 - - - -
176B LEU* 3.8 38.4 - - + -
232B VAL* 3.9 23.1 - - + -
235B PHE* 4.1 15.9 - - + -
236B LEU* 4.0 11.7 - - + -
243B LEU* 1.3 77.7 - - - +
245B CYS* 1.3 61.5 + - - +
246B ARG* 4.2 13.0 - - + -
262B GLN 3.0 8.8 + - - +
263B LEU* 3.3 27.0 - - + -
264B VAL 2.8 28.2 + - - +
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Residues in contact with CYS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 3.9 14.1 - - - -
90B LEU* 4.1 4.7 - - - +
169B ILE* 3.8 22.2 - - + -
170B PHE 2.9 9.4 + - - +
171B CYS* 3.3 27.9 - - - +
172B CYS 3.3 5.5 + - - +
243B LEU* 4.0 1.2 + - + -
244B ILE* 1.3 72.1 - - - +
246B ARG* 1.3 62.6 + - - +
264B VAL* 3.6 9.9 - - + -
266B LEU* 3.5 35.0 - - - -
283B MET* 3.6 17.9 - - + -
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Residues in contact with ARG 246 (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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90B LEU* 3.9 5.2 - - - +
172B CYS* 3.2 20.0 - - - +
174B GLY 2.7 22.3 + - - +
175B GLY* 5.1 1.6 - - - -
207B SER 3.2 15.6 + - - -
208B ASP* 2.9 26.9 + - - -
209B PRO* 3.3 18.2 - - - +
227B PHE* 5.4 0.2 - - - -
244B ILE* 4.2 7.0 - - + -
245B CYS* 1.3 73.4 - - - +
247B ALA* 1.3 73.2 + - - +
248B HIS* 3.7 6.1 - - - +
249B GLN* 2.8 21.4 + - - -
263B LEU* 4.0 23.8 - - + -
264B VAL 2.9 12.7 + - - +
265B THR* 2.9 35.1 + - - +
266B LEU* 2.7 34.7 + - - +
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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