Contacts of the strand formed by residues 217 - 223 (chain D) in PDB entry 4HYY
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 PHE 217 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D LYS* 3.4 42.6 - - + -
156D ILE 3.6 10.3 - - - -
157D ILE* 3.6 28.3 - - + -
187D ASN 5.0 0.7 - - - -
189D LEU* 3.6 27.4 - - + -
209D LYS* 3.9 25.4 - - + -
210D PHE* 3.3 35.7 - + + -
213D GLU 4.9 0.6 + - - -
215D GLY* 4.6 5.2 + - - +
216D ILE* 1.3 101.9 + - + +
218D LYS* 1.3 64.7 + - - +
219D LEU 4.9 1.1 - - - +
260D TYR 4.8 1.4 - - - +
261D ASN 4.7 1.0 - - - +
262D VAL* 3.3 17.0 - - - +
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Residues in contact with LYS 218 (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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99D PHE* 3.6 40.1 - - + -
101D ILE* 3.9 3.0 - - + +
143D ALA* 4.9 1.3 - - + +
151D TYR* 3.4 30.3 - - + +
152D PRO* 4.6 15.2 - - - +
153D GLY 4.0 13.2 - - - -
154D GLY* 3.6 18.8 - - - +
155D LYS 2.9 8.2 + - - +
215D GLY* 3.1 41.5 + - - -
217D PHE* 1.3 74.4 + - - +
219D LEU* 1.3 58.9 + - + +
261D ASN* 5.3 3.2 + - - +
262D VAL* 4.1 4.3 - - - -
263D ALA* 2.9 27.2 + - - +
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Residues in contact with LEU 219 (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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101D ILE* 3.9 15.5 - - + -
116D ILE* 5.2 2.5 - - + -
139D LEU* 3.6 37.0 - - + +
143D ALA* 4.0 6.3 - - + -
155D LYS 3.4 2.9 + - - +
156D ILE* 3.4 18.4 - - + -
157D ILE* 2.9 26.7 + - - +
210D PHE* 4.8 3.5 - - - -
217D PHE* 3.9 0.9 - - - -
218D LYS* 1.3 78.4 + - - +
220D LEU* 1.3 81.6 + - - +
221D ILE* 3.5 33.0 - - + -
262D VAL* 5.1 2.0 - - - -
263D ALA* 3.3 16.2 - - + +
265D PHE* 4.1 14.1 - - + +
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Residues in contact with LEU 220 (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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157D ILE* 3.5 17.7 - - + +
159D ILE* 4.6 6.7 - - + -
203D LEU* 4.3 7.2 - - + -
206D VAL* 4.2 25.4 - - + -
210D PHE* 4.6 10.1 - - + -
219D LEU* 1.3 77.2 - - - +
221D ILE* 1.3 77.8 + - - +
222D ILE* 3.6 15.3 - - + -
253D LEU* 3.7 28.7 - - + -
256D ILE* 4.3 13.9 - - + -
262D VAL* 4.8 2.2 - - + -
263D ALA 2.8 13.2 + - - +
264D VAL* 3.1 12.1 - - + +
265D PHE 2.8 25.8 + - - +
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Residues in contact with ILE 221 (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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136D SER* 3.7 31.2 - - - +
139D LEU* 4.4 2.5 - - + -
140D CYS* 4.0 2.9 - - - -
156D ILE* 4.0 10.1 - - + -
157D ILE 2.7 12.2 + - - +
158D PHE* 3.9 33.9 - - + -
159D ILE 2.9 24.9 + - - -
219D LEU* 3.5 37.2 - - + -
220D LEU* 1.3 79.7 - - - +
222D ILE* 1.3 73.3 + - - +
223D ASP* 4.0 3.8 - - + +
265D PHE* 3.3 26.0 - - + +
267D THR* 5.9 0.2 - - + -
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Residues in contact with ILE 222 (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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159D ILE* 3.4 22.4 - - + +
161D THR* 4.8 0.7 - - + -
199D GLN* 4.0 15.3 - - + +
203D LEU* 4.3 13.0 - - + -
220D LEU* 3.6 13.9 + - + -
221D ILE* 1.3 79.0 - - - +
223D ASP* 1.3 60.3 + - - +
224D SER* 3.6 24.5 - - - +
225D ILE* 3.8 13.5 - - + -
253D LEU* 3.7 42.0 - - + -
264D VAL* 5.0 0.7 - - + -
265D PHE 3.0 6.1 + - - -
266D VAL* 3.3 15.6 - - + +
267D THR 3.3 21.5 + - - -
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Residues in contact with ASP 223 (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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128D PHE* 5.6 1.7 - - - -
132D LYS* 5.6 0.3 - - - +
133D THR* 3.4 25.2 + - - +
136D SER* 4.2 12.1 + - - +
137D HIS* 6.0 0.3 - - - -
158D PHE* 4.1 25.3 - - + -
159D ILE 2.9 8.0 + - - -
160D ASP* 3.3 9.9 - - - +
161D THR* 2.7 26.7 + - - -
162D GLU* 3.7 9.9 - - - +
164D THR* 3.7 13.5 + - - -
165D PHE 5.8 0.2 + - - -
221D ILE* 4.0 2.8 - - + -
222D ILE* 1.3 73.1 - - - +
224D SER* 1.3 52.9 + - - +
267D THR* 2.4 35.9 + - + +
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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