Contacts of the strand formed by residues 223 - 229 (chain D) in PDB entry 3F7F
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 VAL 223 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164D HIS* 2.9 28.3 + - - -
165D PHE* 3.9 17.1 - - + -
177D PHE* 3.7 33.3 - - + +
178D LEU 5.1 0.4 + - - -
181D GLY* 5.6 0.8 + - - -
183D LEU* 4.9 5.6 - - + -
221D ASP 4.0 0.2 + - - -
222D SER* 1.3 73.8 - - - +
224D ILE* 1.3 63.2 + - - +
225D SER 3.0 28.7 - - - +
226D CYS* 4.3 0.4 - - + -
236D VAL* 3.5 31.6 - - + -
237D LEU 3.2 8.3 - - - +
238D THR* 4.6 6.3 - - + -
276D VAL* 4.3 2.6 - - - +
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Residues in contact with ILE 224 (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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164D HIS* 5.6 0.7 - - - +
165D PHE* 4.8 0.2 - - - -
222D SER* 3.9 0.4 - - - +
223D VAL* 1.3 75.5 - - - +
225D SER* 1.3 62.1 + - - +
237D LEU* 2.6 42.2 + - + +
238D THR 3.6 8.7 - - - +
239D GLN* 3.6 32.5 - - + +
241D CYS* 5.4 0.2 - - - -
273D VAL* 3.4 46.4 - - + +
275D ALA 4.0 11.4 - - - +
276D VAL* 3.2 22.7 - - + +
277D GLY 2.9 21.8 + - - +
279D TYR* 3.5 14.6 - - + -
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Residues in contact with SER 225 (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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165D PHE* 4.1 6.1 - - - -
223D VAL* 3.0 11.5 - - - +
224D ILE* 1.3 78.9 + - - +
226D CYS* 1.3 61.6 + - - +
236D VAL* 3.5 0.6 - - - -
237D LEU* 3.0 36.1 + - - -
277D GLY 2.7 25.2 + - - -
278D GLU* 4.3 0.3 - - - -
279D TYR* 3.1 18.3 + - - +
280D LEU* 3.9 26.0 - - - -
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Residues in contact with CYS 226 (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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165D PHE* 3.6 23.8 - - + -
167D PHE* 3.1 28.3 - - + -
177D PHE* 3.7 20.6 - - + -
223D VAL* 4.3 0.2 - - + -
225D SER* 1.3 78.5 - - - +
227D LYS* 1.3 75.2 + - - +
234D LEU* 3.3 39.7 - - - -
235D ILE 3.3 9.4 - - - +
236D VAL* 4.1 1.3 - - + -
280D LEU* 4.5 2.1 - - - +
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Residues in contact with LYS 227 (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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167D PHE* 4.0 6.1 - - + -
226D CYS* 1.3 80.2 + - - +
228D LEU* 1.3 60.7 + - - +
234D LEU* 4.3 1.6 - - - -
235D ILE* 2.9 47.5 + - + +
278D GLU* 5.6 5.4 + - - -
280D LEU* 3.5 39.9 - - + +
281D SER* 4.3 10.9 - - - +
282D LEU* 3.4 33.0 - - + +
287D LEU* 5.1 0.9 - - + -
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Residues in contact with LEU 228 (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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167D PHE* 3.4 21.7 - - + -
168D TYR 4.9 0.4 - - - +
169D VAL* 3.2 43.3 - - + +
227D LYS* 1.3 74.6 - - - +
229D PHE* 1.3 58.7 + - - +
230D HIS 4.3 0.2 + - - -
231D GLU* 3.2 48.6 + - - +
232D ARG 4.1 3.8 - - - +
233D TYR 3.3 22.2 - - - +
234D LEU* 4.1 10.8 - - + -
248D LEU* 4.5 2.2 - - + -
282D LEU* 4.8 8.9 - - - +
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Residues in contact with PHE 229 (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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227D LYS 3.5 1.0 + - - -
228D LEU* 1.3 73.0 - - - +
230D HIS* 1.3 109.7 + + + +
231D GLU* 2.7 5.1 + - - -
232D ARG 2.8 11.1 + - - -
233D TYR* 2.7 41.5 + + + +
235D ILE* 3.1 23.3 - - + -
282D LEU* 3.5 20.6 - - + -
284D ASN 3.6 19.7 - - - -
285D ASN* 4.3 9.4 - - + -
303D LEU* 3.6 33.7 - - + -
304D LEU* 5.6 0.4 - - - -
311D LEU* 4.1 15.9 - - + -
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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