Contacts of the strand formed by residues 217 - 223 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46J ILE* 3.9 29.8 - - + -
141J VAL* 3.5 15.7 - - + +
143J ALA* 3.6 26.2 - - + -
170J VAL* 6.0 0.2 - - + -
211J LEU* 3.5 35.7 - - + +
214J ASP 3.2 4.8 + - - +
215J ASP 3.1 3.8 - - - +
216J ARG* 1.3 75.1 - - - +
218J LYS* 1.3 60.4 + - - +
219J ALA 3.7 11.0 - - - +
220J VAL* 4.1 9.6 - - + -
241J LYS* 3.1 26.3 + - + +
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Residues in contact with LYS 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J GLN* 5.6 1.6 - - - +
139J MET* 3.7 46.4 - - + +
140J GLY* 5.1 1.1 - - - -
141J VAL 2.9 13.9 + - - +
215J ASP 2.9 26.5 - - - -
216J ARG* 3.1 25.8 - - - +
217J VAL* 1.3 73.8 - - - +
219J ALA* 1.3 61.1 + - - +
241J LYS* 3.6 15.7 - - - +
242J ARG* 3.5 12.8 + - - +
473J LYS* 5.9 1.8 - - - +
453K LYS* 5.8 5.5 - - - +
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Residues in contact with ALA 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J MET* 4.7 5.6 - - + -
141J VAL 4.0 2.0 + - - -
142J VAL* 3.7 19.7 - - + -
143J ALA 2.9 25.9 + - - +
217J VAL* 3.6 3.3 + - - +
218J LYS* 1.3 80.4 - - - +
220J VAL* 1.3 67.4 + - - +
241J LYS* 4.5 0.4 - - - +
242J ARG* 3.4 29.6 - - + -
470J PHE* 4.0 15.9 - - + +
471J TYR* 5.3 0.2 - - + -
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Residues in contact with VAL 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J ALA* 3.5 9.9 - - + +
145J ILE* 4.1 15.5 - - + -
212J LEU* 3.8 34.1 - - + -
217J VAL* 4.1 9.0 - - + -
219J ALA* 1.3 81.2 - - - +
221J SER* 1.3 65.5 + - - +
232J ILE* 3.9 17.7 - - + -
236J ALA* 4.4 1.8 - - + -
241J LYS* 3.9 25.8 - - + -
242J ARG 3.0 6.2 + - - +
243J CYS* 3.3 12.5 - - - -
244J GLN 3.0 26.0 + - - +
470J PHE* 3.5 2.6 - - - -
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Residues in contact with SER 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J VAL* 5.6 0.2 - - - -
143J ALA 3.0 10.7 + - - -
144J GLY* 3.5 2.0 - - - -
145J ILE* 3.0 25.8 + - - +
158J MET* 3.6 20.5 - - - +
169J PHE* 5.8 0.2 - - - -
220J VAL* 1.3 73.1 - - - +
222J PHE* 1.3 60.1 + - - +
244J GLN* 2.6 33.3 + - - -
470J PHE* 3.2 12.6 - - - -
471J TYR* 2.9 21.5 + - - -
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Residues in contact with PHE 222 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J ILE* 3.4 33.4 - - + -
146J THR 6.1 0.7 - - - -
158J MET* 4.3 0.2 - - - +
220J VAL* 5.0 0.2 - - + -
221J SER* 1.3 74.6 - - - +
223J VAL* 1.3 72.4 + - - +
224J GLY* 3.2 33.2 - - - -
225J SER 3.9 1.1 - - - -
228J ILE* 3.6 32.5 - - + -
229J ALA* 3.6 31.6 - - + -
232J ILE* 3.8 29.6 - - + -
244J GLN* 2.9 14.1 + - - +
245J ALA* 3.4 4.7 - - + -
246J LEU* 2.9 32.4 + - - +
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Residues in contact with VAL 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J ILE 3.0 10.6 + - - +
146J THR 3.8 0.3 - - - -
147J PRO* 3.1 36.0 - - + +
154J VAL* 3.7 23.1 - - + -
157J TRP* 4.0 27.8 - - + -
158J MET* 3.7 18.2 - - + -
222J PHE* 1.3 86.8 - - - +
224J GLY* 1.3 62.3 + - - +
246J LEU* 3.6 23.8 - - + +
247J GLY 5.9 0.4 - - - +
280J CYS* 5.4 10.3 - - + -
449J PHE* 6.3 0.2 - - + -
462J ALA* 5.5 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