Contacts of the strand formed by residues 217 - 223 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C LYS* 3.4 40.2 - - + -
156C ILE* 3.7 9.4 - - - -
157C ILE* 3.7 26.5 - - + -
187C ASN 5.0 0.7 - - - -
189C LEU* 3.6 26.2 - - + -
209C LYS* 3.4 24.9 - - + -
210C PHE* 3.4 35.9 - + + -
213C GLU 5.1 0.2 + - - -
215C GLY* 4.4 4.9 + - - +
216C ILE* 1.3 104.2 + - + +
218C LYS* 1.3 68.5 + - - +
219C LEU 4.9 0.9 - - - +
260C TYR 5.0 0.5 - - - +
261C ASN 4.7 0.7 - - - +
262C VAL* 3.3 15.9 - - - +
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Residues in contact with LYS 218 (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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99C PHE* 3.4 40.0 - - + -
101C ILE* 4.0 2.9 - - + +
143C ALA* 5.0 1.1 - - + +
151C TYR* 3.3 30.7 - - + +
152C PRO* 4.6 17.4 - - - +
153C GLY 4.5 10.5 - - - -
154C GLY* 3.7 21.3 - - - +
155C LYS 2.7 13.7 + - - +
215C GLY* 3.4 36.6 + - - -
216C ILE 4.8 0.4 - - - -
217C PHE* 1.3 81.3 - - - +
219C LEU* 1.3 56.4 + - + +
261C ASN* 5.1 5.4 + - - +
262C VAL* 3.5 5.8 - - - +
263C ALA* 2.9 26.5 + - - +
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ILE* 3.8 18.2 - - + -
116C ILE* 5.0 3.1 - - + -
139C LEU* 3.6 43.7 - - + +
143C ALA* 3.8 9.4 - - + -
155C LYS 3.4 1.8 + - - +
156C ILE* 3.2 16.2 - - + -
157C ILE* 2.9 27.9 + - - +
210C PHE* 5.0 2.8 - - - -
217C PHE* 3.8 1.6 - - - -
218C LYS* 1.3 79.8 + - - +
220C LEU* 1.3 85.2 + - - +
221C ILE* 3.7 18.2 - - + -
262C VAL* 4.3 2.9 - - - +
263C ALA* 3.3 14.1 - - + +
265C PHE* 4.0 15.7 - - + +
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Residues in contact with LEU 220 (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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157C ILE* 3.4 20.4 - - + +
159C ILE* 4.5 11.2 - - + -
203C LEU* 4.0 15.0 - - + -
206C VAL* 4.0 18.4 - - + -
210C PHE* 4.5 4.7 - - + -
219C LEU* 1.3 76.2 - - - +
221C ILE* 1.3 75.0 + - - +
222C ILE* 4.2 9.9 - - + -
253C LEU* 3.7 29.8 - - + -
256C ILE* 4.6 8.3 - - + -
262C VAL* 4.7 7.0 - - + -
263C ALA 2.8 13.8 + - - +
264C VAL* 3.3 11.7 - - + +
265C PHE 3.0 25.1 + - - +
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Residues in contact with ILE 221 (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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136C SER* 3.7 39.0 - - - +
139C LEU* 4.3 2.7 - - + -
140C CYS* 3.9 4.5 - - - -
156C ILE* 3.8 17.7 - - + -
157C ILE 2.7 12.7 + - - +
158C PHE* 3.5 37.4 - - + -
159C ILE 2.9 23.7 + - - -
219C LEU* 3.7 29.6 - - + -
220C LEU* 1.3 75.6 - - - +
222C ILE* 1.3 76.2 + - - +
223C ASP* 4.0 0.4 - - + -
265C PHE* 3.5 19.1 - - + +
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Residues in contact with ILE 222 (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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159C ILE* 3.5 24.9 - - + +
161C THR* 4.8 1.1 - - + -
199C GLN* 4.2 10.5 - - + +
203C LEU* 4.7 14.4 - - + -
220C LEU* 4.2 14.8 - - + +
221C ILE* 1.3 81.9 - - - +
223C ASP* 1.3 57.9 - - - +
224C SER* 3.5 23.3 - - - +
225C ILE* 3.8 14.8 - - + -
249C MET* 5.8 0.2 - - - -
253C LEU* 3.7 39.3 - - + -
264C VAL* 5.2 0.9 - - + -
265C PHE 3.1 5.5 + - - -
266C VAL* 3.3 31.6 - - + +
267C THR 3.3 4.9 + - - -
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Residues in contact with ASP 223 (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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132C LYS* 5.4 1.0 - - - +
133C THR* 3.1 29.2 + - - +
136C SER* 3.9 19.3 + - - +
137C HIS* 5.6 0.5 - - - -
158C PHE* 3.9 24.3 - - + -
159C ILE 3.0 7.0 + - - -
160C ASP* 3.4 5.6 - - - +
161C THR* 2.8 26.7 + - - -
162C GLU* 3.2 18.8 - - - +
164C THR* 3.8 8.8 + - - -
165C PHE 5.9 0.2 + - - -
221C ILE* 4.0 0.6 - - + +
222C ILE* 1.3 69.1 - - - +
224C SER* 1.3 54.5 + - - +
267C THR* 2.5 28.5 + - - +
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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