Contacts of the strand formed by residues 217 - 223 (chain G) in PDB entry 4ZZ7
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 217 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46G ILE* 3.7 33.4 - - + -
141G VAL* 3.7 12.3 - - + +
143G ALA* 3.7 17.0 - - + +
211G LEU* 3.4 35.2 - - + +
214G ASP 3.2 6.5 + - - +
215G ASP 3.9 3.6 - - - +
216G ARG* 1.3 74.5 - - - +
218G LYS* 1.3 61.9 + - - +
219G ALA 3.6 19.5 - - - +
220G VAL* 4.0 10.5 - - + -
241G LYS* 2.9 27.2 + - - +
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Residues in contact with LYS 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G GLN* 5.6 1.3 - - - +
139G MET* 3.6 44.3 - - + +
140G GLY* 5.2 1.1 - - - -
141G VAL 3.0 15.1 + - - +
215G ASP 3.0 26.2 - - - -
216G ARG* 3.1 24.4 + - - +
217G VAL* 1.3 73.4 - - - +
219G ALA* 1.3 61.4 + - - +
241G LYS* 3.7 9.5 - - - +
242G ARG* 3.6 20.4 + - - +
473G LYS* 5.7 4.3 - - - +
453H LYS* 5.8 5.9 - - - +
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Residues in contact with ALA 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G MET* 4.7 4.9 - - + -
141G VAL 3.8 3.2 + - - -
142G VAL* 3.6 19.5 - - + -
143G ALA 2.8 27.3 + - - -
217G VAL* 3.6 2.6 - - - +
218G LYS* 1.3 80.8 - - - +
220G VAL* 1.3 66.2 + - - +
221G SER 4.3 0.2 - - - -
241G LYS* 4.9 0.2 - - - -
242G ARG* 3.6 26.9 - - + -
470G PHE* 3.9 19.1 - - + +
471G TYR* 5.1 0.2 - - + -
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Residues in contact with VAL 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G ALA* 3.5 9.6 - - + +
145G ILE* 4.3 15.7 - - + -
211G LEU 5.2 0.4 - - - +
212G LEU* 3.8 33.0 - - + -
217G VAL* 4.0 9.9 - - + -
219G ALA* 1.3 81.9 - - - +
221G SER* 1.3 66.0 + - - +
232G ILE* 3.9 17.9 - - + -
236G ALA* 4.6 0.4 - - + -
241G LYS* 3.9 23.8 - - + -
242G ARG 3.2 9.4 + - - +
243G CYS* 3.3 9.1 - - + -
244G GLN 3.1 26.5 + - - +
470G PHE* 3.4 3.0 - - - -
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Residues in contact with SER 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G VAL* 5.2 0.2 - - - +
143G ALA 2.9 12.7 + - - -
144G GLY* 3.4 0.3 - - - -
145G ILE* 2.9 26.9 + - - +
158G MET* 3.2 22.9 - - - +
169G PHE* 5.7 0.2 - - - -
219G ALA 4.3 0.2 - - - -
220G VAL* 1.3 73.0 - - - +
222G PHE* 1.3 60.0 + - - +
244G GLN* 2.6 32.2 + - - -
470G PHE* 3.4 9.7 - - - -
471G TYR* 2.6 25.0 + - - -
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Residues in contact with PHE 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G ILE* 3.3 36.8 - - + -
146G THR 6.0 0.4 - - - -
220G VAL* 4.0 0.8 - - + -
221G SER* 1.3 73.9 - - - +
223G VAL* 1.3 80.4 + - - +
224G GLY* 3.3 27.8 - - - -
225G SER 4.2 0.2 - - - -
228G ILE* 3.5 32.1 - - + -
229G ALA* 3.7 26.5 - - + -
232G ILE* 3.9 31.2 - - + -
244G GLN 2.9 15.9 + - - +
245G ALA* 3.4 5.0 - - + -
246G LEU* 2.9 35.8 + - - +
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Residues in contact with VAL 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G ILE 3.1 10.9 + - - +
146G THR 3.8 1.4 - - - -
147G PRO* 3.2 34.2 - - + +
154G VAL* 3.7 24.2 - - + -
157G TRP* 4.2 24.2 - - + -
158G MET* 3.8 16.8 - - + -
222G PHE* 1.3 91.5 - - - +
224G GLY* 1.3 62.4 + - - +
246G LEU* 3.7 24.9 - - + -
247G GLY 6.0 0.2 - - - +
280G CYS* 5.3 11.7 - - + -
449G PHE* 6.1 0.2 - - + -
462G ALA* 5.4 0.9 - - + -
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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