Contacts of the strand formed by residues 226 - 231 (chain B) in PDB entry 4RN1
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 SER 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLU* 3.8 24.4 + - - +
190B SER* 4.6 4.5 - - - -
197B THR* 3.6 17.6 + - - -
216B ASP 3.6 4.6 - - - +
217B VAL* 3.2 41.4 + - - +
218B GLY* 3.7 13.0 - - - -
222B GLY 4.7 0.3 + - - -
224B TYR 3.3 2.7 - - - -
225B TYR* 1.3 81.9 + - - +
227B VAL* 1.3 63.2 + - - +
228B ASN 4.2 0.2 - - - -
403B K 3.8 7.6 - - - -
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU* 5.4 0.2 + - - -
196B MET* 4.4 7.9 - - - -
197B THR 2.8 10.1 + - - +
198B VAL* 3.3 24.3 - - + -
199B SER 2.9 25.5 + - - -
224B TYR 4.8 3.6 - - - +
226B SER* 1.3 77.2 - - - +
228B ASN* 1.3 66.7 + - - +
229B VAL* 4.4 2.2 - - + -
247B VAL* 4.1 16.8 - - + -
251B VAL* 4.3 3.8 - - + -
369B ILE* 3.8 35.9 - - + -
372B ASN* 6.3 2.2 - - + -
373B LEU* 4.0 27.8 - - + -
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Residues in contact with ASN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B HIS* 2.9 29.1 + - - -
186B GLU* 2.9 28.7 + - - +
199B SER* 3.7 5.6 - - - -
201B HIS* 3.4 2.6 - - + -
212B GLY* 3.4 16.8 - - - +
213B ASP 3.2 20.9 + - - +
214B VAL* 3.6 19.7 + - - +
216B ASP* 3.2 28.0 + - - +
226B SER* 4.1 1.4 + - - -
227B VAL* 1.3 78.3 - - - +
229B VAL* 1.3 64.6 + - - +
230B PRO* 3.3 8.9 - - - +
369B ILE* 3.9 3.5 - - - +
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Residues in contact with VAL 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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198B VAL* 5.1 0.9 - - + -
199B SER 2.8 17.7 + - - +
200B LEU* 4.0 17.7 - - + -
201B HIS* 3.3 25.5 + - - -
227B VAL* 4.4 4.0 - - + -
228B ASN* 1.3 77.6 - - - +
230B PRO* 1.3 64.6 - - - +
231B ILE* 3.4 12.9 + - + +
243B ILE* 3.7 29.2 - - + -
247B VAL* 4.0 18.6 - - + -
362B ILE* 6.5 0.7 - - + -
365B ILE* 4.3 16.4 - - + -
366B LEU* 5.5 0.2 - - + -
369B ILE* 3.7 18.8 - - + -
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Residues in contact with PRO 230 (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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201B HIS* 3.7 6.3 - - - +
203B PHE* 3.6 25.8 - - + -
212B GLY 4.0 4.0 - - - +
213B ASP* 3.7 11.2 - - - +
214B VAL* 3.4 35.0 - - + +
228B ASN 3.3 11.4 - - - +
229B VAL* 1.3 84.1 - - - +
231B ILE* 1.3 62.7 + - - +
232B GLN* 4.8 6.8 + - - +
361B ARG* 5.7 2.7 - - - +
362B ILE* 5.0 3.1 - - - +
365B ILE* 3.3 34.7 - - + +
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Residues in contact with ILE 231 (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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200B LEU* 4.0 37.7 - - + -
201B HIS 2.8 14.6 + - - +
202B LYS* 3.2 24.3 - - - +
203B PHE 3.3 6.3 + - - +
229B VAL* 3.4 16.8 - - + +
230B PRO* 1.3 80.3 - - - +
232B GLN* 1.3 77.7 + - - +
235B ILE* 3.7 23.8 - - + -
240B TYR* 4.1 15.7 - - + -
243B ILE* 4.6 11.4 - - + -
277B PHE* 3.7 14.8 - - + -
357B ASN* 3.3 13.5 - - - +
362B ILE* 5.5 1.3 - - + -
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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