Contacts of the strand formed by residues 217 - 223 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46H ILE* 4.0 31.6 - - + -
141H VAL* 3.7 12.1 - - + +
143H ALA* 3.6 29.4 - - + +
170H VAL* 6.1 0.2 - - + -
211H LEU* 3.6 32.1 - - + +
214H ASP 3.1 6.3 + - - +
215H ASP 3.8 4.9 - - - +
216H ARG* 1.3 77.6 - - - +
218H LYS* 1.3 61.9 + - - +
219H ALA 3.7 11.4 - - - +
220H VAL* 4.1 9.2 - - + -
241H LYS* 3.3 26.9 + - + +
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Residues in contact with LYS 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453G LYS* 5.9 5.1 - - - +
50H GLN* 5.6 1.8 - - - +
139H MET* 3.7 46.9 + - + +
140H GLY* 5.0 1.3 - - - -
141H VAL 3.0 16.8 + - - +
215H ASP 3.2 26.2 - - - -
216H ARG* 3.3 21.3 - - - +
217H VAL* 1.3 73.4 - - - +
219H ALA* 1.3 60.4 + - - +
241H LYS* 3.7 8.1 - - - +
242H ARG* 3.5 20.8 + - - +
473H LYS* 5.6 5.3 - - - +
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Residues in contact with ALA 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H MET* 4.6 5.4 - - + -
141H VAL 4.0 2.0 + - - -
142H VAL* 3.7 18.7 - - + -
143H ALA 2.8 27.5 + - - +
217H VAL* 3.6 3.3 - - - +
218H LYS* 1.3 81.4 - - - +
220H VAL* 1.3 66.8 + - - +
221H SER 4.3 0.2 - - - -
241H LYS* 4.9 0.2 - - - -
242H ARG* 3.4 27.6 - - + -
470H PHE* 3.8 17.9 - - + +
471H TYR* 5.1 0.4 - - + -
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Residues in contact with VAL 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H ALA* 3.4 10.1 - - + +
145H ILE* 4.1 15.7 - - + -
211H LEU 5.2 1.1 - - - +
212H LEU* 3.9 23.6 - - + -
217H VAL* 4.1 9.0 - - + -
219H ALA* 1.3 78.7 - - - +
221H SER* 1.3 65.4 + - - +
232H ILE* 3.8 28.0 - - + -
236H ALA* 4.5 1.3 - - + -
241H LYS* 4.0 23.8 - - + -
242H ARG 3.0 7.7 + - - +
243H CYS* 3.3 14.6 - - + -
244H GLN 3.1 23.9 + - - -
470H PHE* 3.5 3.5 - - - -
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Residues in contact with SER 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H VAL* 5.3 0.4 - - - +
143H ALA 2.9 10.9 + - - -
144H GLY* 3.4 1.1 - - - -
145H ILE* 2.9 28.6 + - - +
158H MET* 3.6 19.3 - - - +
219H ALA 4.3 0.2 - - - -
220H VAL* 1.3 73.6 - - - +
222H PHE* 1.3 59.5 + - - +
223H VAL* 6.0 0.2 - - - -
244H GLN* 2.6 34.4 + - - +
470H PHE* 3.6 1.6 - - - -
471H TYR* 2.8 31.3 + - - -
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Residues in contact with PHE 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H ILE* 3.4 33.0 - - + -
146H THR 6.0 0.4 - - - -
220H VAL 4.0 0.2 + - - -
221H SER* 1.3 73.8 - - - +
223H VAL* 1.3 68.3 + - - +
224H GLY* 3.3 31.2 - - - -
225H SER 3.7 1.3 - - - -
228H ILE* 3.5 33.4 - - + -
229H ALA* 3.6 29.2 - - + -
232H ILE* 3.8 31.0 - - + -
244H GLN 2.7 15.0 + - - +
245H ALA* 3.2 6.5 - - + -
246H LEU* 2.7 41.5 + - - +
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Residues in contact with VAL 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H ILE 3.1 10.2 + - - +
146H THR 3.9 0.9 - - - -
147H PRO* 3.2 31.0 - - + +
154H VAL* 3.8 19.7 - - + -
157H TRP* 4.0 33.9 - - + -
158H MET* 3.6 18.6 - - + -
221H SER* 6.0 0.2 - - - -
222H PHE* 1.3 88.3 - - - +
224H GLY* 1.3 59.8 + - - +
246H LEU* 3.6 25.8 - - + -
247H GLY 5.9 0.9 - - - +
280H CYS* 5.4 10.3 - - + -
449H PHE* 6.2 0.4 - - + -
462H ALA* 5.4 1.1 - - + -
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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