Contacts of the strand formed by residues 213 - 218 (chain B) in PDB entry 5N4D
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 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B TRP* 3.2 18.0 - - - -
208B THR* 3.0 22.9 + - - -
211B SER 3.4 2.0 + - - -
212B LYS* 1.3 77.9 - - - +
214B PHE* 1.3 62.4 + - - -
238B TYR* 3.2 17.3 + - - -
239B HIS 3.0 15.7 - - - -
241B VAL* 4.1 2.7 - - - -
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Residues in contact with PHE 214 (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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158B ALA* 4.0 6.3 - - + -
171B ILE* 3.7 34.1 - - + -
173B VAL* 3.7 26.0 - - + -
197B VAL* 4.4 5.4 - - + -
205B ILE* 3.8 19.3 - - + -
206B ILE 3.2 19.5 - - - +
207B TRP* 3.9 26.0 - + + -
213B GLY* 1.3 75.7 - - - +
215B LEU* 1.3 64.8 + - - +
216B TYR* 3.9 14.3 - + + -
238B TYR* 3.4 9.1 - - - -
239B HIS* 2.8 64.7 + + + -
241B VAL* 4.7 1.1 - - + -
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B THR 3.7 2.0 - - - +
205B ILE* 3.7 5.2 - - - -
206B ILE* 2.8 47.9 + - + +
208B THR* 4.4 12.1 - - + -
214B PHE* 1.3 75.7 - - - +
216B TYR* 1.3 65.2 + - - +
236B MET* 4.1 16.8 - - + -
237B CYS 3.0 8.5 - - - +
238B TYR* 3.9 8.1 - - + -
251B VAL* 3.7 39.7 - - + -
264B ALA* 4.4 6.3 - - + -
266B THR* 4.0 13.5 - - + -
273B LEU* 3.7 31.9 - - + -
297B VAL* 5.0 1.8 - - + -
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Residues in contact with TYR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ILE* 3.8 21.1 - - + -
197B VAL* 3.3 20.4 - - + -
198B LYS 4.6 1.1 - - - -
200B PHE* 4.0 12.8 - + + -
203B SER* 3.9 7.0 - - - -
204B THR 4.1 1.6 - - - +
205B ILE* 5.0 0.9 - - + -
214B PHE* 3.9 17.0 - + + -
215B LEU* 1.3 78.6 - - - +
217B GLN* 1.3 68.8 + - - +
218B ARG* 3.6 27.7 - - + -
236B MET* 3.7 7.1 - - - -
237B CYS* 2.9 52.9 + - + +
239B HIS* 3.8 14.4 - - + -
245B GLN* 3.1 15.2 + - - +
248B ASP* 2.5 33.8 + - - +
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Residues in contact with GLN 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PHE* 3.2 26.5 - - - -
201B LYS 3.1 19.0 + - - +
202B PHE* 3.1 34.8 + - - +
203B SER* 3.0 21.6 + - - +
216B TYR* 1.3 73.9 - - - +
218B ARG* 1.3 65.1 + - - +
219B TYR* 3.9 7.2 + - + -
234B ALA* 3.3 27.5 - - + +
235B MET 3.2 11.4 - - - +
236B MET* 4.1 8.5 - - + +
261B ILE* 3.5 7.7 - - - +
262B TYR* 2.8 33.7 + - - +
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Residues in contact with ARG 218 (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 LYS 4.1 0.4 - - - +
199B TRP* 3.2 41.6 - - - +
216B TYR* 3.6 19.0 + - + -
217B GLN* 1.3 75.9 - - - +
219B TYR* 1.3 88.1 + - - +
220B PRO* 3.9 2.4 - - - +
221B ALA* 3.4 15.2 - - - +
234B ALA* 3.5 3.5 - - - +
235B MET* 2.8 47.1 + - + +
237B CYS* 3.7 25.5 - - - -
245B GLN* 3.7 31.2 + - - +
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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
------------------------------------------------------------
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