Contacts of the strand formed by residues 211 - 215 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C ALA* 4.1 8.1 - - + -
204C PHE 3.6 14.8 - - - +
205C VAL* 4.2 6.3 - - + +
209C GLY 4.1 1.2 + - - -
210C GLU* 1.3 73.5 - - - +
212C TYR* 1.3 61.8 + - - +
213C VAL* 3.9 11.0 - - + -
237C LEU* 3.5 8.4 - - - +
238C VAL* 2.8 55.8 + - + +
241C ILE* 4.0 12.3 - - + -
245C VAL* 3.9 18.0 - - + +
248C VAL* 3.8 33.0 - - + -
257C VAL* 3.7 26.5 - - + -
266C PHE* 4.3 3.8 - - + -
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Residues in contact with TYR 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ILE* 4.9 10.7 - - + +
188C ILE* 3.6 36.5 - - + +
190C LYS* 5.1 2.1 + - - +
203C ALA* 3.1 6.4 - - - +
204C PHE* 2.9 68.2 + + + -
206C THR* 3.9 5.4 - - + -
210C GLU* 2.9 45.2 + - + -
211C LEU* 1.3 74.4 - - - +
213C VAL* 1.3 62.8 + - - +
214C PHE* 4.0 2.1 - - - -
235C PRO* 4.0 10.1 - - + -
236C GLN* 3.2 27.8 - - - +
237C LEU* 3.7 25.4 - - + +
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Residues in contact with VAL 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C HIS* 4.3 6.3 - - + -
202C SER 3.4 13.9 - - - +
203C ALA* 3.8 12.8 - - + -
211C LEU* 3.9 11.9 - - + -
212C TYR* 1.3 79.9 - - - +
214C PHE* 1.3 66.0 + - - +
221C LYS 4.3 4.9 - - - +
222C LEU* 3.5 43.3 - - + +
224C LEU* 4.3 7.2 - - + +
232C HIS* 5.9 0.5 - - - -
234C THR 4.1 1.2 - - - +
236C GLN* 3.0 31.2 + - - +
238C VAL* 3.6 23.8 - - + -
250C CYS* 5.6 0.2 - - - -
255C THR* 5.3 2.2 - - + +
266C PHE* 4.8 5.8 - - + -
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Residues in contact with PHE 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C MET* 3.8 18.4 - - + -
170C GLY 3.5 8.1 - - - +
171C GLN* 3.3 21.0 - - - -
172C ILE 3.7 4.9 - - - -
173C GLY* 3.4 28.5 - - - -
186C VAL* 4.7 1.3 - - + -
195C ILE* 4.9 0.2 - - + -
201C HIS* 3.5 2.6 - - - +
202C SER* 2.9 48.9 + - - +
203C ALA* 4.1 3.6 - - - -
204C PHE* 3.5 34.5 - + - -
212C TYR 4.0 5.8 - - - -
213C VAL* 1.3 83.3 - - - +
215C GLY* 1.3 59.9 + - - +
222C LEU* 3.8 9.2 - - - -
232C HIS* 3.5 14.1 - - - +
234C THR 3.7 13.7 - - - +
235C PRO* 3.7 17.9 - - + -
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Residues in contact with GLY 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C GLU 3.0 16.2 - - - -
170C GLY 3.5 12.5 + - - -
171C GLN* 3.8 2.0 - - - -
200C TYR 3.7 8.5 - - - -
201C HIS* 4.1 1.1 - - - -
214C PHE* 1.3 74.3 - - - +
216C GLU* 1.3 65.5 + - - -
217C PRO 3.2 0.9 - - - -
222C LEU* 3.6 3.9 - - - +
232C HIS* 2.8 35.7 + - - +
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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