Contacts of the strand formed by residues 241 - 245 (chain B) in PDB entry 4IYM
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 ARG 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A TYR* 3.7 7.0 - - - -
457A GLY 3.6 30.9 + - - +
458A ASP* 3.6 28.5 + - + +
138B VAL* 3.6 11.9 - - - +
217B ALA* 3.2 8.4 + - + +
218B ALA* 3.4 26.2 - - + -
219B VAL* 3.1 22.0 + - - +
239B GLY 4.0 1.0 + - - -
240B LYS* 1.3 77.4 - - - +
242B ALA* 1.3 61.6 + - - +
468B LYS 3.4 7.5 + - - -
469B PHE* 2.9 33.6 + - + -
471B THR 2.8 29.0 + - - -
472B ARG* 4.0 16.4 - - - +
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Residues in contact with ALA 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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232A TYR* 4.4 4.1 + - - +
458A ASP* 4.3 5.4 + - - +
219B VAL* 3.2 10.8 - - + +
232B TYR* 3.9 35.9 - - + +
235B ALA* 3.9 22.9 - - + -
236B ALA* 5.2 1.8 - - + +
240B LYS 3.8 2.8 + - - +
241B ARG* 1.3 78.8 - - - +
243B GLN* 1.3 63.1 + - - +
244B CYS* 4.3 6.7 - - - -
457B GLY* 4.2 6.4 - - - -
458B ASP* 5.1 0.3 + - - +
469B PHE* 3.6 7.6 - - - -
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Residues in contact with GLN 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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157B MSE 5.4 0.3 - - - +
219B VAL 3.1 3.4 + - - -
220B SER* 2.8 31.7 + - - +
221B PHE 2.9 21.1 + - - +
242B ALA* 1.3 76.0 - - - +
244B CYS* 1.3 62.0 + - - +
245B PHE* 3.6 14.5 - - + -
456B PHE 3.6 7.2 - - - +
457B GLY* 5.5 0.2 - - - -
459B LEU* 3.0 30.4 + - - +
460B ASN 3.0 20.4 + - - +
461B GLN* 3.7 8.8 + - - +
466B SER* 5.7 2.3 - - - +
469B PHE* 3.7 34.7 - - + +
470B TRP* 4.6 5.4 + - - -
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Residues in contact with CYS 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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219B VAL 5.2 0.7 - - - -
221B PHE* 3.4 20.9 - - + -
228B ALA* 3.8 23.1 - - + +
231B VAL* 3.9 5.6 - - - -
232B TYR* 3.6 42.4 - - + -
242B ALA* 4.5 2.7 - - - -
243B GLN* 1.3 82.4 - - - +
245B PHE* 1.3 65.7 + - - +
455B SER* 3.2 4.0 - - - -
456B PHE* 2.7 42.9 + - + +
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Residues in contact with PHE 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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221B PHE* 2.9 21.8 + - - +
222B VAL* 3.5 13.0 - - + +
223B GLY 3.0 27.0 + - - +
228B ALA* 4.4 2.7 - - - -
243B GLN* 3.6 27.6 - - + -
244B CYS* 1.3 75.9 - - - +
246B GLY* 1.3 60.9 + - - +
409B ASN* 6.1 0.7 - - - +
448B PHE* 3.8 31.2 - + + -
449B GLY* 3.9 17.5 - - - -
450B GLY 4.6 0.2 - - - -
454B SER 3.6 4.9 - - - +
455B SER* 3.8 21.5 - - - -
456B PHE 5.2 2.0 - - - -
459B LEU 3.4 23.6 - - - -
460B ASN* 3.9 7.2 - - - -
461B GLN* 3.4 35.0 - - + -
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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