Contacts of the strand formed by residues 241 - 246 (chain B) in PDB entry 5D9I
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 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B PRO* 4.3 12.8 - - + -
141B GLU* 4.3 13.5 - - + -
142B LEU* 3.8 39.5 - - + -
187B HIS* 5.1 0.2 - - + -
188B ASN 3.4 17.0 - - - +
189B SER* 3.4 27.8 - - - -
190B TYR* 4.7 3.1 - + - -
194B ILE* 4.2 0.9 - - + -
235B ALA* 3.3 21.5 - - + -
236B LEU* 3.3 31.6 - - + +
237B THR 3.9 0.7 - - - +
238B ARG* 2.8 30.8 + - - +
239B ASP* 3.4 6.6 + - - +
240B PRO* 1.3 99.8 - - + +
242B SER* 1.3 66.4 + - - +
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B HIS* 3.0 6.4 - - - +
188B ASN* 2.9 45.9 + - - +
236B LEU 3.5 8.5 - - - -
237B THR 4.5 7.2 - - - -
239B ASP* 5.9 0.4 - - - -
240B PRO 5.3 0.5 + - - -
241B PHE* 1.3 78.6 - - - +
243B VAL* 1.3 65.4 + - - +
244B ILE* 5.3 1.0 - - - +
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ARG 3.8 4.3 - - - +
187B HIS* 3.7 24.0 - - + -
233B TYR* 4.6 0.4 - - - +
237B THR* 3.8 24.1 + - + +
242B SER* 1.3 77.9 + - - +
244B ILE* 1.3 66.1 + - - +
245B GLU* 3.7 20.4 - - - +
246B GLU* 3.8 34.3 - - + +
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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
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165B LYS* 4.0 14.4 - - - +
186B ARG* 2.7 46.4 + - + +
187B HIS 3.7 3.6 - - - -
188B ASN* 3.4 36.6 - - + +
193B ASN* 3.5 30.3 - - - +
242B SER* 5.2 1.3 - - - +
243B VAL* 1.3 78.9 - - - +
245B GLU* 1.3 61.0 + - + +
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Residues in contact with GLU 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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169B ALA 4.8 2.6 - - - +
172B TYR* 3.7 39.0 - - + +
173B LYS* 3.9 10.3 + - - -
185B SER* 3.4 0.9 - - - -
186B ARG* 2.8 71.1 + - + +
243B VAL* 3.9 4.2 - - - +
244B ILE* 1.3 83.3 - - + +
246B GLU* 1.3 63.6 + - - +
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Residues in contact with GLU 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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172B TYR* 3.1 7.2 + - - -
183B PHE* 3.5 7.1 - - + -
184B ILE 3.3 11.7 - - - +
185B SER* 3.6 9.0 - - - -
233B TYR* 2.6 35.7 + - - -
243B VAL* 3.8 22.0 - - + +
245B GLU* 1.3 77.8 - - - +
247B SER* 1.3 65.2 - - - +
248B LEU 3.5 14.8 + - - +
249B PRO* 5.7 0.4 - - + +
250B GLY* 3.9 5.8 + - - +
251B GLY* 3.3 23.2 + - - -
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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