Contacts of the strand formed by residues 217 - 223 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A LYS* 3.4 40.2 - - + +
156A ILE 3.7 3.8 - - - -
157A ILE* 3.5 28.7 - - + -
189A LEU* 3.6 28.0 - - + -
209A LYS* 3.7 33.9 - - + -
210A PHE* 3.3 36.1 - + + -
213A GLU 4.9 0.8 + - - -
215A GLY* 4.3 7.9 + - - +
216A ILE* 1.3 100.7 - - + +
218A LYS* 1.3 67.0 + - - +
219A LEU 5.0 0.4 - - - +
260A TYR 5.0 1.4 - - - +
261A ASN 4.9 1.4 - - - +
262A VAL* 3.9 14.0 - - - +
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Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 3.4 40.6 - - + -
101A ILE* 4.1 2.4 - - + +
143A ALA* 4.8 1.1 - - + +
151A TYR* 3.3 30.1 - - + +
152A PRO* 4.5 17.4 - - - +
153A GLY 4.2 13.2 - - - -
154A GLY* 3.6 19.7 - - - +
155A LYS 2.8 9.3 + - - +
215A GLY* 2.8 39.2 + - - -
217A PHE* 1.3 75.8 + - - +
219A LEU* 1.3 60.4 + - + +
261A ASN* 5.2 3.2 + - - +
262A VAL* 3.5 5.1 - - - -
263A ALA* 2.9 25.7 + - - +
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Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ILE* 3.9 13.2 - - + -
116A ILE* 4.6 4.5 - - + -
139A LEU* 3.7 32.1 - - + +
143A ALA* 3.9 6.7 - - + -
155A LYS 3.6 1.9 + - - +
156A ILE* 3.5 19.0 - - + -
157A ILE* 3.0 24.1 + - - +
210A PHE* 4.6 6.8 - - - -
217A PHE* 3.9 1.1 - - - +
218A LYS* 1.3 78.2 + - - +
220A LEU* 1.3 76.5 + - - +
221A ILE* 3.4 34.8 - - + -
262A VAL* 4.5 0.6 - - - +
263A ALA* 3.3 22.0 - - + +
265A PHE* 4.0 15.3 - - + -
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Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ILE* 3.4 25.6 - - + +
159A ILE* 4.4 7.6 - - + -
203A LEU* 4.7 6.1 - - + -
206A VAL* 4.4 22.4 - - + -
210A PHE* 4.5 9.0 - - + -
219A LEU* 1.3 75.4 - - - +
221A ILE* 1.3 76.3 + - - +
222A ILE* 4.1 15.0 - - + -
253A LEU* 3.6 31.0 - - + -
256A ILE* 4.7 6.1 - - + -
262A VAL* 4.6 3.1 - - + -
263A ALA 3.0 10.0 + - - +
264A VAL* 3.3 13.9 - - + +
265A PHE 2.8 27.9 + - - +
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A SER* 3.6 32.8 - - - +
139A LEU* 4.3 4.0 - - + -
140A CYS* 4.0 16.6 - - - -
156A ILE* 4.0 5.2 - - + -
157A ILE 2.8 9.0 + - - +
158A PHE* 3.5 24.9 - - + -
159A ILE 2.9 24.6 + - - -
219A LEU* 3.4 37.0 - - + -
220A LEU* 1.3 81.7 - - - +
222A ILE* 1.3 71.7 + - - +
223A ASP* 4.3 1.1 - - + +
265A PHE* 3.2 24.0 - - + +
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.5 24.0 - - + +
161A THR* 4.9 1.1 - - + -
199A GLN* 4.1 14.1 - - + +
203A LEU* 4.6 12.8 - - + -
220A LEU* 4.1 14.8 - - + -
221A ILE* 1.3 77.9 - - - +
223A ASP* 1.3 61.0 + - - +
224A SER* 3.6 21.8 - - - +
225A ILE* 3.9 13.9 - - + -
253A LEU* 3.7 41.3 - - + -
264A VAL* 4.8 0.2 - - + -
265A PHE 3.1 7.1 + - - -
266A VAL* 3.2 16.8 - - + +
267A THR 3.2 22.5 + - - -
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Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LYS* 5.2 0.7 - - - +
133A THR* 3.2 28.2 + - - +
136A SER* 4.2 9.5 + - - +
137A HIS* 5.8 0.2 - - - -
158A PHE* 3.9 29.4 - - + -
159A ILE 2.9 7.5 + - - -
160A ASP* 3.4 5.2 - - - +
161A THR* 2.7 28.7 + - - -
162A GLU* 3.5 14.0 + - - +
164A THR* 3.7 12.6 + - - -
221A ILE* 4.5 2.0 - - + -
222A ILE* 1.3 73.1 - - - +
224A SER* 1.3 52.9 + - - +
267A THR* 2.5 34.3 + - + +
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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