Contacts of the strand formed by residues 211 - 215 (chain D) in PDB entry 4JHN
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 LEU 211 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D ALA* 4.3 7.4 - - + -
204D PHE 3.6 5.2 - - - +
205D VAL* 4.7 1.8 - - + +
209D GLY 3.9 1.4 + - - -
210D GLU* 1.3 71.4 - - - +
212D TYR* 1.3 67.1 + - - +
213D VAL* 3.1 34.5 - - + -
237D LEU* 3.4 7.8 - - - +
238D VAL* 2.9 46.8 + - + +
241D ILE* 3.8 19.5 - - + -
245D VAL* 4.0 19.7 - - + +
248D VAL* 4.9 7.4 - - + -
257D VAL* 3.5 37.5 - - + -
266D PHE* 4.5 3.4 - - + -
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Residues in contact with TYR 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B LYS* 4.8 4.0 + - - -
188D ILE* 3.6 35.5 - - + +
190D LYS* 4.7 1.2 + - - -
203D ALA* 3.1 7.1 - - - +
204D PHE* 2.9 68.0 + + + -
206D THR* 3.8 7.2 - - + -
210D GLU* 2.7 42.9 + - + -
211D LEU* 1.3 75.2 - - - +
213D VAL* 1.3 62.5 + - - +
214D PHE* 4.0 2.4 - - - -
235D PRO* 4.0 11.0 - - + -
236D GLN* 3.2 25.1 - - - +
237D LEU* 3.4 24.6 - - + +
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Residues in contact with VAL 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D HIS* 5.8 2.7 - - + -
202D SER 3.6 5.4 - - - +
203D ALA* 3.9 10.3 - - + -
211D LEU* 3.1 27.8 - - + -
212D TYR* 1.3 72.7 - - - +
214D PHE* 1.3 65.1 + - - +
221D LYS 5.3 1.1 - - - +
222D LEU* 2.9 40.6 - - + +
224D LEU* 3.7 20.9 - - + +
232D HIS* 5.9 0.3 - - - -
234D THR 3.9 1.4 - - - +
236D GLN* 2.9 28.1 + - - +
238D VAL* 3.5 13.7 - - + -
255D THR* 5.4 2.5 - - + -
266D PHE* 4.9 7.6 - - + -
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Residues in contact with PHE 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D MET* 3.9 14.8 - - - -
170D GLY 3.5 8.3 - - - +
171D GLN 3.4 21.3 - - - -
172D ILE* 3.6 6.3 - - - -
173D GLY* 3.3 27.4 - - - -
186D VAL* 4.7 0.7 - - + -
195D ILE* 4.7 0.7 - - + -
201D HIS* 3.5 4.2 - - - +
202D SER* 2.9 48.8 + - - +
203D ALA* 4.2 3.1 - - - -
204D PHE* 3.5 37.5 - + - -
212D TYR 4.0 6.3 - - - -
213D VAL* 1.3 82.3 - - - +
215D GLY* 1.3 59.4 + - - +
222D LEU* 3.8 10.4 - - - +
232D HIS* 3.6 13.7 - - - +
234D THR 3.8 13.2 - - - +
235D PRO* 3.6 16.8 - - + -
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Residues in contact with GLY 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D GLU 3.0 15.0 - - - -
170D GLY 3.4 12.4 + - - -
171D GLN* 3.6 7.6 - - - -
200D TYR 3.7 3.4 - - - -
201D HIS* 4.0 0.9 - - - -
214D PHE* 1.3 74.7 - - - +
216D GLU* 1.3 66.2 + - - -
217D PRO 3.2 1.6 - - - -
222D LEU* 3.7 3.8 - - - +
232D HIS* 2.8 35.2 + - - +
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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