Contacts of the strand formed by residues 224 - 229 (chain B) in PDB entry 4RMA
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 GLY 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLY 3.9 0.2 - - - +
220B VAL* 3.9 1.9 - - - -
221B ASP* 3.0 34.2 + - - +
223B LEU* 1.3 81.4 - - - +
225B LEU* 1.3 63.8 + - - +
226B ASN* 4.7 1.8 - - - -
240B PHE 3.5 9.4 - - - -
241B PRO* 4.2 0.7 - - - -
242B TRP* 3.1 25.5 - - - +
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 4.1 15.3 - - + -
219B GLY 3.3 4.5 - - - +
220B VAL* 3.6 33.9 - - + -
224B GLY* 1.3 78.4 - - - +
226B ASN* 1.3 66.9 + - - +
240B PHE* 2.7 52.7 + - + +
242B TRP* 4.1 5.2 - - + -
245B ILE* 3.9 18.6 - - + -
248B ILE* 4.1 16.6 - - + -
257B ILE* 3.7 27.4 - - + -
269B PHE* 5.2 3.6 - - + -
284B CYS* 3.8 13.9 - - - -
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Residues in contact with ASN 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP 3.7 0.3 - - - +
218B LEU* 3.4 6.8 - - - +
219B GLY* 2.8 37.0 + - - +
221B ASP* 3.3 26.5 + - - -
224B GLY 4.5 1.2 + - - -
225B LEU* 1.3 83.6 - - - +
227B ILE* 1.3 65.8 + - - +
228B TYR* 3.6 26.6 + - + +
236B PRO* 3.5 21.9 - - + +
238B ILE 3.4 4.3 - - - +
239B GLY* 3.4 16.8 - - - -
240B PHE* 5.4 0.2 - - - -
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Residues in contact with ILE 227 (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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208B ILE* 3.8 18.2 - - + -
216B LEU* 3.8 32.8 - - + -
217B TRP 3.4 4.5 - - - +
218B LEU* 3.9 13.0 - - + -
226B ASN* 1.3 79.7 - - - +
228B TYR* 1.3 64.6 + - - +
236B PRO* 3.7 1.6 - - - +
237B LYS* 2.8 30.8 + - + +
238B ILE* 2.9 28.1 + - + +
240B PHE* 4.0 20.0 - - + -
257B ILE* 5.4 0.9 - - + -
267B PHE* 3.5 37.7 - - + -
269B PHE* 4.9 0.7 - - + -
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Residues in contact with TYR 228 (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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203B ILE* 3.3 26.2 - - - +
205B TYR* 3.7 22.7 - + - -
216B LEU* 3.4 12.3 - - - +
217B TRP* 2.8 51.7 + - + +
219B GLY* 3.8 13.0 - - - -
226B ASN* 3.6 31.9 + - + +
227B ILE* 1.3 75.5 - - - +
229B GLU* 1.3 63.2 + - - +
232B ASP 3.5 22.0 - - - +
233B LYS* 3.3 22.2 - - - -
234B LEU 4.1 1.1 - - - -
235B THR 4.8 0.4 - - - -
236B PRO* 3.5 38.1 - - + +
237B LYS* 4.5 3.6 - - - +
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Residues in contact with GLU 229 (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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216B LEU* 4.0 11.0 - - + -
217B TRP* 3.6 4.7 - - - -
228B TYR* 1.3 76.1 - - - +
230B LYS* 1.3 66.5 + - - +
231B ASP* 3.1 16.8 - - - +
232B ASP* 3.0 26.1 + - + +
235B THR 5.2 1.8 + - - -
237B LYS* 3.3 39.7 + - + +
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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